Datasets:
Add files using upload-large-folder tool
Browse filesThis view is limited to 50 files because it contains too many changes.
See raw diff
- data/files/A001Z/records.jsonl +3 -0
- data/files/A0020/project.json +191 -0
- data/files/A0021/records.jsonl +3 -0
- data/files/A0022/project.json +194 -0
- data/files/A0022/records.jsonl +3 -0
- data/files/A0023/project.json +263 -0
- data/files/A0023/records.jsonl +3 -0
- data/files/A0024/project.json +197 -0
- data/files/A0024/records.jsonl +3 -0
- data/files/A0025/project.json +196 -0
- data/files/A0025/records.jsonl +3 -0
- data/files/A0026/project.json +265 -0
- data/files/A0026/records.jsonl +3 -0
- data/files/A0027/project.json +193 -0
- data/files/A0027/records.jsonl +3 -0
- data/files/A0028/project.json +193 -0
- data/files/A0028/records.jsonl +3 -0
- data/files/A0029/project.json +196 -0
- data/files/A0029/records.jsonl +3 -0
- data/files/A002A/project.json +191 -0
- data/files/A002A/records.jsonl +3 -0
- data/files/A002B/project.json +255 -0
- data/files/A002B/records.jsonl +3 -0
- data/files/A002C/project.json +340 -0
- data/files/A002C/records.jsonl +0 -0
- data/files/A002D/project.json +201 -0
- data/files/A002D/records.jsonl +3 -0
- data/files/A002E/project.json +178 -0
- data/files/A002E/records.jsonl +3 -0
- data/files/A002F/project.json +192 -0
- data/files/A002F/records.jsonl +3 -0
- data/files/A002G/project.json +256 -0
- data/files/A002G/records.jsonl +3 -0
- data/files/A002H/project.json +206 -0
- data/files/A002H/records.jsonl +3 -0
- data/files/A002I/project.json +189 -0
- data/files/A002I/records.jsonl +3 -0
- data/files/A002J/project.json +265 -0
- data/files/A002J/records.jsonl +3 -0
- data/files/A002K/project.json +191 -0
- data/files/A002K/records.jsonl +3 -0
- data/files/A002M/project.json +199 -0
- data/files/A002M/records.jsonl +3 -0
- data/files/A002N/project.json +270 -0
- data/files/A002N/records.jsonl +3 -0
- data/files/A002O/project.json +279 -0
- data/files/A002O/records.jsonl +3 -0
- data/files/A002P/project.json +329 -0
- data/files/A002P/records.jsonl +0 -0
- data/files/A002Q/project.json +190 -0
data/files/A001Z/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A001Z", "accession": "A001Z", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1TA3", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1TA3"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8L5C6", "Q00177"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA", "ASLNDLFVAAGKSYFGTCSDQALLQNSQNEAIVASQFGVITPENSMKWDALEPSQGNFGWSGADYLVDYATQHNKKVRGHTLVWHSQLPSWVSSIGDANTLRSVMTNHINEVVGRYKGKIMHWDVVNEIFNEDGTFRNSVFYNLLGEDFVRIAFETARAADPDAKLYINDYNLDSASYAKTQAMASYVKKWLAEGVPIDGIGSQAHYSSSHWSSTEAAGALSSLANTGVSEVAITELDIAGAASSDYLNLLNACLNEQKCVGITVWGVSDKDSWRASDSPLLFDGNYQPKDAYNAIVNALS"], "NUCLSEQ": [], "DOMAINS": ["Xylanase inhibitor protein 1", "GH18", "Interaction with fungal GH11 xylanase", "Interaction with fungal GH10 xylanase", "Endo-1,4-beta-xylanase C", "GH10"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8695, "SYSTRES": 575, "PROTATS": 8695, "PROTRES": 575, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.976, "BOXSIZEY": 10.976, "BOXSIZEZ": 7.7895, "mdName": "replica 1", "mdAtoms": 8695, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001Z/files/topology.tpr", "length": 2653360, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001Z/files/screenshot.jpg", "length": 25434, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001Z/files/trajectory.bin", "length": 521804340, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 5001, "atoms": 8695}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_01.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_02.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_03.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_04.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_05.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_06.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_07.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_08.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_09.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_10.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_11.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_12.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001Z/files/structure.pdb", "length": 704330, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001Z/files/trajectory.xtc", "length": 165128560, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_00.jpg", "length": 25453, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_01.jpg", "length": 26104, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_02.jpg", "length": 25379, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_03.jpg", "length": 25092, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_04.jpg", "length": 25366, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_05.jpg", "length": 25697, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_06.jpg", "length": 25482, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_07.jpg", "length": 25514, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_08.jpg", "length": 25937, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_09.jpg", "length": 25852, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_10.jpg", "length": 25925, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_11.jpg", "length": 25762, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_12.jpg", "length": 25687, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_13.jpg", "length": 25629, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_14.jpg", "length": 25764, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_15.jpg", "length": 25450, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_16.jpg", "length": 25838, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_17.jpg", "length": 26073, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_18.jpg", "length": 26190, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_19.jpg", "length": 26125, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_20.jpg", "length": 26363, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_00.jpg", "length": 23917, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_01.jpg", "length": 23736, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_02.jpg", "length": 24067, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_03.jpg", "length": 24608, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_04.jpg", "length": 23988, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_05.jpg", "length": 24226, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_06.jpg", "length": 23933, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_07.jpg", "length": 24194, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_08.jpg", "length": 24564, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_09.jpg", "length": 24357, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_10.jpg", "length": 23846, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_11.jpg", "length": 24124, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_12.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_13.jpg", "length": 24464, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_14.jpg", "length": 24311, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_15.jpg", "length": 24719, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_16.jpg", "length": 24055, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_17.jpg", "length": 24881, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_18.jpg", "length": 24725, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_19.jpg", "length": 24500, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001Z/files/pocket_01.pdb", "length": 29413, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001Z/files/pocket_02.pdb", "length": 11658, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001Z/files/pocket_03.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001Z/files/pocket_04.pdb", "length": 7705, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A001Z/files/pocket_05.pdb", "length": 5293, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A001Z/files/pocket_06.pdb", "length": 4690, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A001Z/files/pocket_07.pdb", "length": 4154, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A001Z/files/pocket_08.pdb", "length": 3886, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A001Z/files/pocket_09.pdb", "length": 3819, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A001Z/files/pocket_10.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A001Z", "accession": "A001Z", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1TA3", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1TA3"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8L5C6", "Q00177"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA", "ASLNDLFVAAGKSYFGTCSDQALLQNSQNEAIVASQFGVITPENSMKWDALEPSQGNFGWSGADYLVDYATQHNKKVRGHTLVWHSQLPSWVSSIGDANTLRSVMTNHINEVVGRYKGKIMHWDVVNEIFNEDGTFRNSVFYNLLGEDFVRIAFETARAADPDAKLYINDYNLDSASYAKTQAMASYVKKWLAEGVPIDGIGSQAHYSSSHWSSTEAAGALSSLANTGVSEVAITELDIAGAASSDYLNLLNACLNEQKCVGITVWGVSDKDSWRASDSPLLFDGNYQPKDAYNAIVNALS"], "NUCLSEQ": [], "DOMAINS": ["Xylanase inhibitor protein 1", "GH18", "Interaction with fungal GH11 xylanase", "Interaction with fungal GH10 xylanase", "Endo-1,4-beta-xylanase C", "GH10"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8695, "SYSTRES": 575, "PROTATS": 8695, "PROTRES": 575, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.976, "BOXSIZEY": 10.976, "BOXSIZEZ": 7.7895, "mdName": "replica 1", "mdAtoms": 8695, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001Z/files/topology.tpr", "length": 2653360, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001Z/files/screenshot.jpg", "length": 25434, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001Z/files/trajectory.bin", "length": 521804340, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 5001, "atoms": 8695}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_01.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_02.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_03.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_04.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_05.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_06.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_07.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_08.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_09.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_10.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_11.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_12.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001Z/files/structure.pdb", "length": 704330, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001Z/files/trajectory.xtc", "length": 165128560, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_00.jpg", "length": 25453, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_01.jpg", "length": 26104, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_02.jpg", "length": 25379, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_03.jpg", "length": 25092, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_04.jpg", "length": 25366, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_05.jpg", "length": 25697, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_06.jpg", "length": 25482, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_07.jpg", "length": 25514, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_08.jpg", "length": 25937, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_09.jpg", "length": 25852, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_10.jpg", "length": 25925, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_11.jpg", "length": 25762, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_12.jpg", "length": 25687, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_13.jpg", "length": 25629, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_14.jpg", "length": 25764, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_15.jpg", "length": 25450, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_16.jpg", "length": 25838, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_17.jpg", "length": 26073, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_18.jpg", "length": 26190, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_19.jpg", "length": 26125, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_20.jpg", "length": 26363, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_00.jpg", "length": 23917, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_01.jpg", "length": 23736, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_02.jpg", "length": 24067, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_03.jpg", "length": 24608, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_04.jpg", "length": 23988, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_05.jpg", "length": 24226, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_06.jpg", "length": 23933, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_07.jpg", "length": 24194, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_08.jpg", "length": 24564, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_09.jpg", "length": 24357, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_10.jpg", "length": 23846, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_11.jpg", "length": 24124, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_12.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_13.jpg", "length": 24464, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_14.jpg", "length": 24311, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_15.jpg", "length": 24719, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_16.jpg", "length": 24055, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_17.jpg", "length": 24881, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_18.jpg", "length": 24725, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_19.jpg", "length": 24500, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001Z/files/pocket_01.pdb", "length": 29413, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001Z/files/pocket_02.pdb", "length": 11658, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001Z/files/pocket_03.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001Z/files/pocket_04.pdb", "length": 7705, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A001Z/files/pocket_05.pdb", "length": 5293, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A001Z/files/pocket_06.pdb", "length": 4690, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A001Z/files/pocket_07.pdb", "length": 4154, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A001Z/files/pocket_08.pdb", "length": 3886, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A001Z/files/pocket_09.pdb", "length": 3819, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A001Z/files/pocket_10.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A001Z", "accession": "A001Z", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1TA3", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1TA3"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8L5C6", "Q00177"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA", "ASLNDLFVAAGKSYFGTCSDQALLQNSQNEAIVASQFGVITPENSMKWDALEPSQGNFGWSGADYLVDYATQHNKKVRGHTLVWHSQLPSWVSSIGDANTLRSVMTNHINEVVGRYKGKIMHWDVVNEIFNEDGTFRNSVFYNLLGEDFVRIAFETARAADPDAKLYINDYNLDSASYAKTQAMASYVKKWLAEGVPIDGIGSQAHYSSSHWSSTEAAGALSSLANTGVSEVAITELDIAGAASSDYLNLLNACLNEQKCVGITVWGVSDKDSWRASDSPLLFDGNYQPKDAYNAIVNALS"], "NUCLSEQ": [], "DOMAINS": ["Xylanase inhibitor protein 1", "GH18", "Interaction with fungal GH11 xylanase", "Interaction with fungal GH10 xylanase", "Endo-1,4-beta-xylanase C", "GH10"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8695, "SYSTRES": 575, "PROTATS": 8695, "PROTRES": 575, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.976, "BOXSIZEY": 10.976, "BOXSIZEZ": 7.7895, "mdName": "replica 1", "mdAtoms": 8695, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001Z/files/topology.tpr", "length": 2653360, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001Z/files/screenshot.jpg", "length": 25434, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001Z/files/trajectory.bin", "length": 521804340, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 5001, "atoms": 8695}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_01.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_02.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_03.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_04.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_05.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_06.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_07.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_08.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_09.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_10.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_11.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001Z/files/pca_trajectory_12.bin", "length": 414000, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0, "frames": 20, "atoms": 1725}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001Z/files/structure.pdb", "length": 704330, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001Z/files/trajectory.xtc", "length": 165128560, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_00.jpg", "length": 25453, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_01.jpg", "length": 26104, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_02.jpg", "length": 25379, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_03.jpg", "length": 25092, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_04.jpg", "length": 25366, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_05.jpg", "length": 25697, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_06.jpg", "length": 25482, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_07.jpg", "length": 25514, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_08.jpg", "length": 25937, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_09.jpg", "length": 25852, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_10.jpg", "length": 25925, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_11.jpg", "length": 25762, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_12.jpg", "length": 25687, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_13.jpg", "length": 25629, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_14.jpg", "length": 25764, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_15.jpg", "length": 25450, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_16.jpg", "length": 25838, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_17.jpg", "length": 26073, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_18.jpg", "length": 26190, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_19.jpg", "length": 26125, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001Z/files/clusters_00_screenshot_20.jpg", "length": 26363, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_00.jpg", "length": 23917, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_01.jpg", "length": 23736, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_02.jpg", "length": 24067, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_03.jpg", "length": 24608, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_04.jpg", "length": 23988, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_05.jpg", "length": 24226, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_06.jpg", "length": 23933, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_07.jpg", "length": 24194, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_08.jpg", "length": 24564, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_09.jpg", "length": 24357, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_10.jpg", "length": 23846, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_11.jpg", "length": 24124, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_12.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_13.jpg", "length": 24464, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_14.jpg", "length": 24311, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_15.jpg", "length": 24719, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_16.jpg", "length": 24055, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_17.jpg", "length": 24881, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_18.jpg", "length": 24725, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001Z/files/clusters_01_screenshot_19.jpg", "length": 24500, "contentType": "application/octet-stream", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001Z/files/pocket_01.pdb", "length": 29413, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001Z/files/pocket_02.pdb", "length": 11658, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001Z/files/pocket_03.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001Z/files/pocket_04.pdb", "length": 7705, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A001Z/files/pocket_05.pdb", "length": 5293, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A001Z/files/pocket_06.pdb", "length": 4690, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A001Z/files/pocket_07.pdb", "length": 4154, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A001Z/files/pocket_08.pdb", "length": 3886, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A001Z/files/pocket_09.pdb", "length": 3819, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A001Z/files/pocket_10.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6eb54cb64c83f073c54d", "md": 0}}]}
|
data/files/A0020/project.json
ADDED
|
@@ -0,0 +1,191 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0020",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1TDQ",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1TDQ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q05546",
|
| 31 |
+
"P07897"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"IPVIDGPTQILVRDVSDTVAFVEWTPPRAKVDFILLKYGLVGGEGGKTTFRLQPPLSQYSVQALRPGSRYEVSISAVRGTNESDASSTQFTTEIDAPKNLRVGSRTATSLDLEWDNSEAEAQEYKVVYSTLAGEQYHEVLVPKGIGPTTKTTLTDLVPGTEYGVGISAVMNSKQSIPATMNARTELDSPRDLMVTASSETSISLIWTKASGPIDHYRITFTPSSGISSEVTVPRDRTSYTLTDLEPGAEYIISITAERGRQQSLESTVDAF",
|
| 38 |
+
"EQCEEGWTKFQGHCYRHFPDRETWVDAERRCREQQSHLSSIVTPEEQEFVNKNAQDYQWIGLNDRTIEGDFRWSDGHSLQFEKWRPNQPDNFFATGEDCVVMIWHERGEWNDVPCNYQLPFTCKKG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tenascin-R",
|
| 43 |
+
"Fibronectin type-III 2",
|
| 44 |
+
"Fibronectin type-III 3",
|
| 45 |
+
"Fibronectin type-III 4",
|
| 46 |
+
"Fibronectin type-III 5",
|
| 47 |
+
"Aggrecan core protein",
|
| 48 |
+
"C-type lectin",
|
| 49 |
+
"Disordered",
|
| 50 |
+
"G3"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 6150,
|
| 62 |
+
"SYSTRES": 397,
|
| 63 |
+
"PROTATS": 6150,
|
| 64 |
+
"PROTRES": 397,
|
| 65 |
+
"NUCLATS": 0,
|
| 66 |
+
"NUCLRES": 0,
|
| 67 |
+
"LIPIATS": 0,
|
| 68 |
+
"LIPIRES": 0,
|
| 69 |
+
"CARBATS": 0,
|
| 70 |
+
"CARBRES": 0,
|
| 71 |
+
"SOLVATS": 0,
|
| 72 |
+
"SOLVRES": 0,
|
| 73 |
+
"COUNCAT": 0,
|
| 74 |
+
"COUNANI": 0,
|
| 75 |
+
"COUNION": 0,
|
| 76 |
+
"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
}
|
| 85 |
+
],
|
| 86 |
+
"PBC_SELECTION": null,
|
| 87 |
+
"CHAINNAMES": null,
|
| 88 |
+
"MEMBRANES": null,
|
| 89 |
+
"CUSTOMS": null,
|
| 90 |
+
"ORIENTATION": null,
|
| 91 |
+
"PTM": [],
|
| 92 |
+
"MULTIMERIC": null,
|
| 93 |
+
"COLLECTIONS": "dynarepo",
|
| 94 |
+
"WARNINGS": [],
|
| 95 |
+
"BOXSIZEX": 14.1353,
|
| 96 |
+
"BOXSIZEY": 14.1353,
|
| 97 |
+
"BOXSIZEZ": 9.97361,
|
| 98 |
+
"mdName": "replica 1",
|
| 99 |
+
"mdAtoms": 6150,
|
| 100 |
+
"mdFrames": 5001
|
| 101 |
+
},
|
| 102 |
+
"mds": [
|
| 103 |
+
"replica 1",
|
| 104 |
+
"replica 2",
|
| 105 |
+
"replica 3"
|
| 106 |
+
],
|
| 107 |
+
"mdref": 0,
|
| 108 |
+
"files": [
|
| 109 |
+
"topology.tpr",
|
| 110 |
+
"screenshot.jpg",
|
| 111 |
+
"trajectory.bin",
|
| 112 |
+
"pca_trajectory_01.bin",
|
| 113 |
+
"pca_trajectory_02.bin",
|
| 114 |
+
"pca_trajectory_03.bin",
|
| 115 |
+
"pca_trajectory_04.bin",
|
| 116 |
+
"pca_trajectory_05.bin",
|
| 117 |
+
"pca_trajectory_06.bin",
|
| 118 |
+
"pca_trajectory_07.bin",
|
| 119 |
+
"pca_trajectory_08.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
+
"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.jpg",
|
| 162 |
+
"clusters_01_screenshot_20.jpg",
|
| 163 |
+
"pocket_01.pdb",
|
| 164 |
+
"pocket_02.pdb",
|
| 165 |
+
"pocket_03.pdb"
|
| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
+
"clusters",
|
| 169 |
+
"clusters-00",
|
| 170 |
+
"clusters-01",
|
| 171 |
+
"dist-perres",
|
| 172 |
+
"energies",
|
| 173 |
+
"fluctuation",
|
| 174 |
+
"hbonds",
|
| 175 |
+
"interactions",
|
| 176 |
+
"pca",
|
| 177 |
+
"pockets",
|
| 178 |
+
"rgyr",
|
| 179 |
+
"rmsd-pairwise",
|
| 180 |
+
"rmsd-perres",
|
| 181 |
+
"rmsds",
|
| 182 |
+
"sasa",
|
| 183 |
+
"tmscores"
|
| 184 |
+
],
|
| 185 |
+
"mdIndex": 0,
|
| 186 |
+
"mdNumber": 1,
|
| 187 |
+
"refframe": 0,
|
| 188 |
+
"internalId": "683f70861c4421a26ebfbf8d",
|
| 189 |
+
"creationDate": "2025-06-03T22:00:38.000Z",
|
| 190 |
+
"identifier": "A0020"
|
| 191 |
+
}
|
data/files/A0021/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0021", "accession": "A0021", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1TE1", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1TE1"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8L5C6", "Q9HFH0"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA", "QSITTSQTGTNNGYYYSFWTNGGGEVTYTNGDNGEYSVTWVDCGDFTSGKGWNPANAQTVTYSGEFNPSGNAYLAVYGWTTDPLVEYYILESYGTYNPSSGLTSLGQVTSDGGTYDIYSTQRVNQPSIEGTSTFNQYWSVRTEKRVGGTVTTANHFAAWKALGLEMGTYNYMIVSTEGYESSGSSTITVS"], "NUCLSEQ": [], "DOMAINS": ["Xylanase inhibitor protein 1", "GH18", "Interaction with fungal GH11 xylanase", "Interaction with fungal GH10 xylanase", "Endo-1,4-beta-xylanase C", "GH11", "Interaction with protein inhibitor XIP-I"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6959, "SYSTRES": 464, "PROTATS": 6959, "PROTRES": 464, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.0241, "BOXSIZEY": 10.0241, "BOXSIZEZ": 7.09512, "mdName": "replica 1", "mdAtoms": 6959, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0021/files/topology.tpr", "length": 2167456, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0021/files/screenshot.jpg", "length": 26944, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0021/files/trajectory.bin", "length": 417623508, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 5001, "atoms": 6959}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_01.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_02.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_03.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_04.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_05.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_06.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_07.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_08.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0021/files/structure.pdb", "length": 563714, "contentType": "chemical/x-pdb", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0021/files/trajectory.xtc", "length": 131722800, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_00.jpg", "length": 26850, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_01.jpg", "length": 27303, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_02.jpg", "length": 26481, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_03.jpg", "length": 27270, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_04.jpg", "length": 27206, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_05.jpg", "length": 26572, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_06.jpg", "length": 27434, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_07.jpg", "length": 26965, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_08.jpg", "length": 28052, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_09.jpg", "length": 26943, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_10.jpg", "length": 26978, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_11.jpg", "length": 27812, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_12.jpg", "length": 27814, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_13.jpg", "length": 27772, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_14.jpg", "length": 27052, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_15.jpg", "length": 26872, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_16.jpg", "length": 27114, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_17.jpg", "length": 27601, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_18.jpg", "length": 27673, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_19.jpg", "length": 26964, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_00.jpg", "length": 26799, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_01.jpg", "length": 26937, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_02.jpg", "length": 26901, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_03.jpg", "length": 26479, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_04.jpg", "length": 27031, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_05.jpg", "length": 26348, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_06.jpg", "length": 26817, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_07.jpg", "length": 26585, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_08.jpg", "length": 26997, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_09.jpg", "length": 27044, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_10.jpg", "length": 27695, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_11.jpg", "length": 27123, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_12.jpg", "length": 27656, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_13.jpg", "length": 27131, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_14.jpg", "length": 27649, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_15.jpg", "length": 27673, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_16.jpg", "length": 27632, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_17.jpg", "length": 27680, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_18.jpg", "length": 27868, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_19.jpg", "length": 26999, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_20.jpg", "length": 26665, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0021/files/pocket_01.pdb", "length": 26398, "contentType": "chemical/x-pdb", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0021", "accession": "A0021", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1TE1", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1TE1"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8L5C6", "Q9HFH0"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA", "QSITTSQTGTNNGYYYSFWTNGGGEVTYTNGDNGEYSVTWVDCGDFTSGKGWNPANAQTVTYSGEFNPSGNAYLAVYGWTTDPLVEYYILESYGTYNPSSGLTSLGQVTSDGGTYDIYSTQRVNQPSIEGTSTFNQYWSVRTEKRVGGTVTTANHFAAWKALGLEMGTYNYMIVSTEGYESSGSSTITVS"], "NUCLSEQ": [], "DOMAINS": ["Xylanase inhibitor protein 1", "GH18", "Interaction with fungal GH11 xylanase", "Interaction with fungal GH10 xylanase", "Endo-1,4-beta-xylanase C", "GH11", "Interaction with protein inhibitor XIP-I"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6959, "SYSTRES": 464, "PROTATS": 6959, "PROTRES": 464, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.0241, "BOXSIZEY": 10.0241, "BOXSIZEZ": 7.09512, "mdName": "replica 1", "mdAtoms": 6959, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0021/files/topology.tpr", "length": 2167456, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0021/files/screenshot.jpg", "length": 26944, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0021/files/trajectory.bin", "length": 417623508, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 5001, "atoms": 6959}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_01.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_02.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_03.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_04.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_05.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_06.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_07.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_08.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0021/files/structure.pdb", "length": 563714, "contentType": "chemical/x-pdb", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0021/files/trajectory.xtc", "length": 131722800, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_00.jpg", "length": 26850, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_01.jpg", "length": 27303, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_02.jpg", "length": 26481, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_03.jpg", "length": 27270, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_04.jpg", "length": 27206, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_05.jpg", "length": 26572, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_06.jpg", "length": 27434, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_07.jpg", "length": 26965, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_08.jpg", "length": 28052, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_09.jpg", "length": 26943, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_10.jpg", "length": 26978, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_11.jpg", "length": 27812, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_12.jpg", "length": 27814, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_13.jpg", "length": 27772, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_14.jpg", "length": 27052, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_15.jpg", "length": 26872, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_16.jpg", "length": 27114, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_17.jpg", "length": 27601, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_18.jpg", "length": 27673, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_19.jpg", "length": 26964, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_00.jpg", "length": 26799, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_01.jpg", "length": 26937, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_02.jpg", "length": 26901, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_03.jpg", "length": 26479, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_04.jpg", "length": 27031, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_05.jpg", "length": 26348, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_06.jpg", "length": 26817, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_07.jpg", "length": 26585, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_08.jpg", "length": 26997, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_09.jpg", "length": 27044, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_10.jpg", "length": 27695, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_11.jpg", "length": 27123, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_12.jpg", "length": 27656, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_13.jpg", "length": 27131, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_14.jpg", "length": 27649, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_15.jpg", "length": 27673, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_16.jpg", "length": 27632, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_17.jpg", "length": 27680, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_18.jpg", "length": 27868, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_19.jpg", "length": 26999, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_20.jpg", "length": 26665, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0021/files/pocket_01.pdb", "length": 26398, "contentType": "chemical/x-pdb", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0021", "accession": "A0021", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1TE1", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1TE1"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8L5C6", "Q9HFH0"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA", "QSITTSQTGTNNGYYYSFWTNGGGEVTYTNGDNGEYSVTWVDCGDFTSGKGWNPANAQTVTYSGEFNPSGNAYLAVYGWTTDPLVEYYILESYGTYNPSSGLTSLGQVTSDGGTYDIYSTQRVNQPSIEGTSTFNQYWSVRTEKRVGGTVTTANHFAAWKALGLEMGTYNYMIVSTEGYESSGSSTITVS"], "NUCLSEQ": [], "DOMAINS": ["Xylanase inhibitor protein 1", "GH18", "Interaction with fungal GH11 xylanase", "Interaction with fungal GH10 xylanase", "Endo-1,4-beta-xylanase C", "GH11", "Interaction with protein inhibitor XIP-I"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6959, "SYSTRES": 464, "PROTATS": 6959, "PROTRES": 464, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.0241, "BOXSIZEY": 10.0241, "BOXSIZEZ": 7.09512, "mdName": "replica 1", "mdAtoms": 6959, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0021/files/topology.tpr", "length": 2167456, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0021/files/screenshot.jpg", "length": 26944, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0021/files/trajectory.bin", "length": 417623508, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 5001, "atoms": 6959}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_01.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_02.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_03.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_04.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_05.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_06.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_07.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0021/files/pca_trajectory_08.bin", "length": 334080, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0, "frames": 20, "atoms": 1392}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0021/files/structure.pdb", "length": 563714, "contentType": "chemical/x-pdb", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0021/files/trajectory.xtc", "length": 131722800, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_00.jpg", "length": 26850, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_01.jpg", "length": 27303, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_02.jpg", "length": 26481, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_03.jpg", "length": 27270, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_04.jpg", "length": 27206, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_05.jpg", "length": 26572, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_06.jpg", "length": 27434, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_07.jpg", "length": 26965, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_08.jpg", "length": 28052, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_09.jpg", "length": 26943, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_10.jpg", "length": 26978, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_11.jpg", "length": 27812, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_12.jpg", "length": 27814, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_13.jpg", "length": 27772, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_14.jpg", "length": 27052, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_15.jpg", "length": 26872, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_16.jpg", "length": 27114, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_17.jpg", "length": 27601, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_18.jpg", "length": 27673, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0021/files/clusters_00_screenshot_19.jpg", "length": 26964, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_00.jpg", "length": 26799, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_01.jpg", "length": 26937, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_02.jpg", "length": 26901, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_03.jpg", "length": 26479, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_04.jpg", "length": 27031, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_05.jpg", "length": 26348, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_06.jpg", "length": 26817, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_07.jpg", "length": 26585, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_08.jpg", "length": 26997, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_09.jpg", "length": 27044, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_10.jpg", "length": 27695, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_11.jpg", "length": 27123, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_12.jpg", "length": 27656, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_13.jpg", "length": 27131, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_14.jpg", "length": 27649, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_15.jpg", "length": 27673, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_16.jpg", "length": 27632, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_17.jpg", "length": 27680, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_18.jpg", "length": 27868, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_19.jpg", "length": 26999, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A0021/files/clusters_01_screenshot_20.jpg", "length": 26665, "contentType": "application/octet-stream", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0021/files/pocket_01.pdb", "length": 26398, "contentType": "chemical/x-pdb", "metadata": {"project": "683f723409fd1861bf285540", "md": 0}}]}
|
data/files/A0022/project.json
ADDED
|
@@ -0,0 +1,194 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0022",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1U0S",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1U0S"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q56312",
|
| 31 |
+
"Q56310"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS",
|
| 38 |
+
"GFKTFYIKVILKEGTQLKSARIYLVFHKLEELKCEVVRTIPSVEEIEEEKFENEVELFVISPVDLEKLSEALSSIADIERVIIKEV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Chemotaxis protein CheY",
|
| 43 |
+
"Response regulatory",
|
| 44 |
+
"Chemotaxis protein CheA"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 3294,
|
| 56 |
+
"SYSTRES": 204,
|
| 57 |
+
"PROTATS": 3294,
|
| 58 |
+
"PROTRES": 204,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 8.14965,
|
| 90 |
+
"BOXSIZEY": 8.14965,
|
| 91 |
+
"BOXSIZEZ": 5.76276,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 3294,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"structure.pdb",
|
| 119 |
+
"trajectory.xtc",
|
| 120 |
+
"clusters_00_screenshot_00.jpg",
|
| 121 |
+
"clusters_00_screenshot_01.jpg",
|
| 122 |
+
"clusters_00_screenshot_02.jpg",
|
| 123 |
+
"clusters_00_screenshot_03.jpg",
|
| 124 |
+
"clusters_00_screenshot_04.jpg",
|
| 125 |
+
"clusters_00_screenshot_05.jpg",
|
| 126 |
+
"clusters_00_screenshot_06.jpg",
|
| 127 |
+
"clusters_00_screenshot_07.jpg",
|
| 128 |
+
"clusters_00_screenshot_08.jpg",
|
| 129 |
+
"clusters_00_screenshot_09.jpg",
|
| 130 |
+
"clusters_00_screenshot_10.jpg",
|
| 131 |
+
"clusters_00_screenshot_11.jpg",
|
| 132 |
+
"clusters_00_screenshot_12.jpg",
|
| 133 |
+
"clusters_00_screenshot_13.jpg",
|
| 134 |
+
"clusters_00_screenshot_14.jpg",
|
| 135 |
+
"clusters_00_screenshot_15.jpg",
|
| 136 |
+
"clusters_00_screenshot_16.jpg",
|
| 137 |
+
"clusters_00_screenshot_17.jpg",
|
| 138 |
+
"clusters_00_screenshot_18.jpg",
|
| 139 |
+
"clusters_00_screenshot_19.jpg",
|
| 140 |
+
"clusters_00_screenshot_20.jpg",
|
| 141 |
+
"clusters_00_screenshot_21.jpg",
|
| 142 |
+
"clusters_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.jpg",
|
| 162 |
+
"pocket_01.pdb",
|
| 163 |
+
"pocket_02.pdb",
|
| 164 |
+
"pocket_03.pdb",
|
| 165 |
+
"pocket_04.pdb",
|
| 166 |
+
"pocket_05.pdb",
|
| 167 |
+
"pocket_06.pdb",
|
| 168 |
+
"pocket_07.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
+
"clusters",
|
| 172 |
+
"clusters-00",
|
| 173 |
+
"clusters-01",
|
| 174 |
+
"dist-perres",
|
| 175 |
+
"energies",
|
| 176 |
+
"fluctuation",
|
| 177 |
+
"hbonds",
|
| 178 |
+
"interactions",
|
| 179 |
+
"pca",
|
| 180 |
+
"pockets",
|
| 181 |
+
"rgyr",
|
| 182 |
+
"rmsd-pairwise",
|
| 183 |
+
"rmsd-perres",
|
| 184 |
+
"rmsds",
|
| 185 |
+
"sasa",
|
| 186 |
+
"tmscores"
|
| 187 |
+
],
|
| 188 |
+
"mdIndex": 0,
|
| 189 |
+
"mdNumber": 1,
|
| 190 |
+
"refframe": 1,
|
| 191 |
+
"internalId": "683f739aa4cb36641d896080",
|
| 192 |
+
"creationDate": "2025-06-03T22:13:46.000Z",
|
| 193 |
+
"identifier": "A0022"
|
| 194 |
+
}
|
data/files/A0022/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0022", "accession": "A0022", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1U0S", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1U0S"], "FORCED_REFERENCES": null, "REFERENCES": ["Q56312", "Q56310"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS", "GFKTFYIKVILKEGTQLKSARIYLVFHKLEELKCEVVRTIPSVEEIEEEKFENEVELFVISPVDLEKLSEALSSIADIERVIIKEV"], "NUCLSEQ": [], "DOMAINS": ["Chemotaxis protein CheY", "Response regulatory", "Chemotaxis protein CheA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3294, "SYSTRES": 204, "PROTATS": 3294, "PROTRES": 204, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.14965, "BOXSIZEY": 8.14965, "BOXSIZEZ": 5.76276, "mdName": "replica 1", "mdAtoms": 3294, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0022/files/topology.tpr", "length": 1172324, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0022/files/screenshot.jpg", "length": 19591, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0022/files/trajectory.bin", "length": 197679528, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 5001, "atoms": 3294}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_01.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_02.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_03.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_04.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_05.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_06.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_07.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_08.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_09.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_10.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_11.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_12.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0022/files/structure.pdb", "length": 266849, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0022/files/trajectory.xtc", "length": 62717644, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_00.jpg", "length": 19091, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_01.jpg", "length": 19344, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_02.jpg", "length": 19524, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_03.jpg", "length": 19784, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_04.jpg", "length": 19433, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_05.jpg", "length": 18727, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_06.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_07.jpg", "length": 19443, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_08.jpg", "length": 19587, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_09.jpg", "length": 20196, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_10.jpg", "length": 19870, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_11.jpg", "length": 19429, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_12.jpg", "length": 19282, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_13.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_14.jpg", "length": 19837, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_15.jpg", "length": 19476, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_16.jpg", "length": 19190, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_17.jpg", "length": 20118, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_18.jpg", "length": 19962, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_19.jpg", "length": 19551, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_20.jpg", "length": 19075, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_21.jpg", "length": 19371, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_00.jpg", "length": 20317, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_01.jpg", "length": 19960, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_02.jpg", "length": 20439, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_03.jpg", "length": 20108, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_04.jpg", "length": 20851, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_05.jpg", "length": 20657, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_06.jpg", "length": 21205, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_07.jpg", "length": 20733, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_08.jpg", "length": 21023, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_09.jpg", "length": 20561, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_10.jpg", "length": 20875, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_11.jpg", "length": 20970, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_12.jpg", "length": 20125, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_13.jpg", "length": 20429, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_14.jpg", "length": 20562, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_15.jpg", "length": 20876, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_16.jpg", "length": 20598, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_17.jpg", "length": 20890, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_18.jpg", "length": 20235, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_19.jpg", "length": 19691, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0022/files/pocket_01.pdb", "length": 9581, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0022/files/pocket_02.pdb", "length": 8308, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0022/files/pocket_03.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0022/files/pocket_04.pdb", "length": 4623, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0022/files/pocket_05.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0022/files/pocket_06.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0022/files/pocket_07.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0022", "accession": "A0022", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1U0S", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1U0S"], "FORCED_REFERENCES": null, "REFERENCES": ["Q56312", "Q56310"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS", "GFKTFYIKVILKEGTQLKSARIYLVFHKLEELKCEVVRTIPSVEEIEEEKFENEVELFVISPVDLEKLSEALSSIADIERVIIKEV"], "NUCLSEQ": [], "DOMAINS": ["Chemotaxis protein CheY", "Response regulatory", "Chemotaxis protein CheA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3294, "SYSTRES": 204, "PROTATS": 3294, "PROTRES": 204, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.14965, "BOXSIZEY": 8.14965, "BOXSIZEZ": 5.76276, "mdName": "replica 1", "mdAtoms": 3294, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0022/files/topology.tpr", "length": 1172324, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0022/files/screenshot.jpg", "length": 19591, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0022/files/trajectory.bin", "length": 197679528, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 5001, "atoms": 3294}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_01.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_02.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_03.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_04.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_05.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_06.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_07.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_08.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_09.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_10.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_11.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_12.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0022/files/structure.pdb", "length": 266849, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0022/files/trajectory.xtc", "length": 62717644, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_00.jpg", "length": 19091, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_01.jpg", "length": 19344, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_02.jpg", "length": 19524, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_03.jpg", "length": 19784, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_04.jpg", "length": 19433, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_05.jpg", "length": 18727, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_06.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_07.jpg", "length": 19443, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_08.jpg", "length": 19587, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_09.jpg", "length": 20196, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_10.jpg", "length": 19870, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_11.jpg", "length": 19429, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_12.jpg", "length": 19282, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_13.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_14.jpg", "length": 19837, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_15.jpg", "length": 19476, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_16.jpg", "length": 19190, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_17.jpg", "length": 20118, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_18.jpg", "length": 19962, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_19.jpg", "length": 19551, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_20.jpg", "length": 19075, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_21.jpg", "length": 19371, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_00.jpg", "length": 20317, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_01.jpg", "length": 19960, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_02.jpg", "length": 20439, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_03.jpg", "length": 20108, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_04.jpg", "length": 20851, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_05.jpg", "length": 20657, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_06.jpg", "length": 21205, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_07.jpg", "length": 20733, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_08.jpg", "length": 21023, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_09.jpg", "length": 20561, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_10.jpg", "length": 20875, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_11.jpg", "length": 20970, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_12.jpg", "length": 20125, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_13.jpg", "length": 20429, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_14.jpg", "length": 20562, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_15.jpg", "length": 20876, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_16.jpg", "length": 20598, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_17.jpg", "length": 20890, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_18.jpg", "length": 20235, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_19.jpg", "length": 19691, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0022/files/pocket_01.pdb", "length": 9581, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0022/files/pocket_02.pdb", "length": 8308, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0022/files/pocket_03.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0022/files/pocket_04.pdb", "length": 4623, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0022/files/pocket_05.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0022/files/pocket_06.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0022/files/pocket_07.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0022", "accession": "A0022", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1U0S", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1U0S"], "FORCED_REFERENCES": null, "REFERENCES": ["Q56312", "Q56310"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS", "GFKTFYIKVILKEGTQLKSARIYLVFHKLEELKCEVVRTIPSVEEIEEEKFENEVELFVISPVDLEKLSEALSSIADIERVIIKEV"], "NUCLSEQ": [], "DOMAINS": ["Chemotaxis protein CheY", "Response regulatory", "Chemotaxis protein CheA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3294, "SYSTRES": 204, "PROTATS": 3294, "PROTRES": 204, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.14965, "BOXSIZEY": 8.14965, "BOXSIZEZ": 5.76276, "mdName": "replica 1", "mdAtoms": 3294, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0022/files/topology.tpr", "length": 1172324, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0022/files/screenshot.jpg", "length": 19591, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0022/files/trajectory.bin", "length": 197679528, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 5001, "atoms": 3294}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_01.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_02.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_03.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_04.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_05.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_06.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_07.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_08.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_09.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_10.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_11.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0022/files/pca_trajectory_12.bin", "length": 146880, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0, "frames": 20, "atoms": 612}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0022/files/structure.pdb", "length": 266849, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0022/files/trajectory.xtc", "length": 62717644, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_00.jpg", "length": 19091, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_01.jpg", "length": 19344, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_02.jpg", "length": 19524, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_03.jpg", "length": 19784, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_04.jpg", "length": 19433, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_05.jpg", "length": 18727, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_06.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_07.jpg", "length": 19443, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_08.jpg", "length": 19587, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_09.jpg", "length": 20196, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_10.jpg", "length": 19870, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_11.jpg", "length": 19429, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_12.jpg", "length": 19282, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_13.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_14.jpg", "length": 19837, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_15.jpg", "length": 19476, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_16.jpg", "length": 19190, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_17.jpg", "length": 20118, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_18.jpg", "length": 19962, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_19.jpg", "length": 19551, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_20.jpg", "length": 19075, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0022/files/clusters_00_screenshot_21.jpg", "length": 19371, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_00.jpg", "length": 20317, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_01.jpg", "length": 19960, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_02.jpg", "length": 20439, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_03.jpg", "length": 20108, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_04.jpg", "length": 20851, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_05.jpg", "length": 20657, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_06.jpg", "length": 21205, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_07.jpg", "length": 20733, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_08.jpg", "length": 21023, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_09.jpg", "length": 20561, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_10.jpg", "length": 20875, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_11.jpg", "length": 20970, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_12.jpg", "length": 20125, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_13.jpg", "length": 20429, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_14.jpg", "length": 20562, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_15.jpg", "length": 20876, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_16.jpg", "length": 20598, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_17.jpg", "length": 20890, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_18.jpg", "length": 20235, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0022/files/clusters_01_screenshot_19.jpg", "length": 19691, "contentType": "application/octet-stream", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0022/files/pocket_01.pdb", "length": 9581, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0022/files/pocket_02.pdb", "length": 8308, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0022/files/pocket_03.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0022/files/pocket_04.pdb", "length": 4623, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0022/files/pocket_05.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0022/files/pocket_06.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0022/files/pocket_07.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f739aa4cb36641d896080", "md": 0}}]}
|
data/files/A0023/project.json
ADDED
|
@@ -0,0 +1,263 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0023",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1UEX",
|
| 6 |
+
"DESCRIPTION": "Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Author Omid Mokhtari",
|
| 9 |
+
"Author Hamed Khakzad",
|
| 10 |
+
"Author Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": [
|
| 25 |
+
{
|
| 26 |
+
"name": "Link_name",
|
| 27 |
+
"url": "www.link-name.org"
|
| 28 |
+
}
|
| 29 |
+
],
|
| 30 |
+
"PDBIDS": [
|
| 31 |
+
"1UEX"
|
| 32 |
+
],
|
| 33 |
+
"FORCED_REFERENCES": null,
|
| 34 |
+
"REFERENCES": [
|
| 35 |
+
"Q7LZK5",
|
| 36 |
+
"Q7LZK8",
|
| 37 |
+
"P04275"
|
| 38 |
+
],
|
| 39 |
+
"INPUT_LIGANDS": null,
|
| 40 |
+
"LIGANDS": [],
|
| 41 |
+
"LIGANDNAMES": null,
|
| 42 |
+
"PROTSEQ": [
|
| 43 |
+
"EPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVEYHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQRDEIVSYLCDLAPEAP",
|
| 44 |
+
"GCLPDWSSYKGHCYKVFKVEKTWADAEKFCKELVNGGHLMSVNSREEGEFISKLALEKMRIVLVWIGLSHFWRICPLRWTDGARLDYRALSDEPICFVAESFHNKWIQWTCNRKKSFVCKYRV",
|
| 45 |
+
"GCLPDWSSYKGHCYKVFKKVGTWEDAEKFCVENSGHLASIDSKEEADFVTKLASQTLTKFVYDAWIGLRDESKTQQCSPQWTDGSSVVYENVDEPTKCFGLDVHTEYRTWTDLPCGEKNPFICKS"
|
| 46 |
+
],
|
| 47 |
+
"NUCLSEQ": [],
|
| 48 |
+
"DOMAINS": [
|
| 49 |
+
"Snaclec bitiscetin subunit alpha",
|
| 50 |
+
"C-type lectin",
|
| 51 |
+
"Snaclec bitiscetin subunit beta",
|
| 52 |
+
"C-type lectin",
|
| 53 |
+
"von Willebrand factor",
|
| 54 |
+
"VWFA 1; binding site for platelet glycoprotein Ib"
|
| 55 |
+
],
|
| 56 |
+
"FRAMESTEP": 0.02,
|
| 57 |
+
"TIMESTEP": 5000,
|
| 58 |
+
"TEMP": 310,
|
| 59 |
+
"ENSEMBLE": "NPT",
|
| 60 |
+
"FF": [
|
| 61 |
+
"CHARMM36m"
|
| 62 |
+
],
|
| 63 |
+
"WAT": "TIP3P",
|
| 64 |
+
"BOXTYPE": "Dodecahedron",
|
| 65 |
+
"SYSTATS": 7270,
|
| 66 |
+
"SYSTRES": 450,
|
| 67 |
+
"PROTATS": 7270,
|
| 68 |
+
"PROTRES": 450,
|
| 69 |
+
"NUCLATS": 0,
|
| 70 |
+
"NUCLRES": 0,
|
| 71 |
+
"LIPIATS": 0,
|
| 72 |
+
"LIPIRES": 0,
|
| 73 |
+
"CARBATS": 0,
|
| 74 |
+
"CARBRES": 0,
|
| 75 |
+
"SOLVATS": 0,
|
| 76 |
+
"SOLVRES": 0,
|
| 77 |
+
"COUNCAT": 0,
|
| 78 |
+
"COUNANI": 0,
|
| 79 |
+
"COUNION": 0,
|
| 80 |
+
"INTERACTIONS": [
|
| 81 |
+
{
|
| 82 |
+
"name": "chain A-chain B interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain B",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain B",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain A-chain C interaction",
|
| 91 |
+
"agent_1": "chain A",
|
| 92 |
+
"agent_2": "chain C",
|
| 93 |
+
"selection_1": "chain A",
|
| 94 |
+
"selection_2": "chain C",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
},
|
| 97 |
+
{
|
| 98 |
+
"name": "chain B-chain C interaction",
|
| 99 |
+
"agent_1": "chain B",
|
| 100 |
+
"agent_2": "chain C",
|
| 101 |
+
"selection_1": "chain B",
|
| 102 |
+
"selection_2": "chain C",
|
| 103 |
+
"type": "protein-protein"
|
| 104 |
+
}
|
| 105 |
+
],
|
| 106 |
+
"PBC_SELECTION": null,
|
| 107 |
+
"CHAINNAMES": null,
|
| 108 |
+
"MEMBRANES": null,
|
| 109 |
+
"CUSTOMS": null,
|
| 110 |
+
"ORIENTATION": null,
|
| 111 |
+
"PTM": [],
|
| 112 |
+
"MULTIMERIC": null,
|
| 113 |
+
"COLLECTIONS": "dynarepo",
|
| 114 |
+
"WARNINGS": [],
|
| 115 |
+
"BOXSIZEX": 10.3738,
|
| 116 |
+
"BOXSIZEY": 10.3738,
|
| 117 |
+
"BOXSIZEZ": 7.38044,
|
| 118 |
+
"mdName": "replica 1",
|
| 119 |
+
"mdAtoms": 7270,
|
| 120 |
+
"mdFrames": 5001
|
| 121 |
+
},
|
| 122 |
+
"mds": [
|
| 123 |
+
"replica 1",
|
| 124 |
+
"replica 2",
|
| 125 |
+
"replica 3"
|
| 126 |
+
],
|
| 127 |
+
"mdref": 0,
|
| 128 |
+
"files": [
|
| 129 |
+
"topology.tpr",
|
| 130 |
+
"screenshot.jpg",
|
| 131 |
+
"trajectory.bin",
|
| 132 |
+
"pca_trajectory_01.bin",
|
| 133 |
+
"pca_trajectory_02.bin",
|
| 134 |
+
"pca_trajectory_03.bin",
|
| 135 |
+
"pca_trajectory_04.bin",
|
| 136 |
+
"pca_trajectory_05.bin",
|
| 137 |
+
"pca_trajectory_06.bin",
|
| 138 |
+
"pca_trajectory_07.bin",
|
| 139 |
+
"pca_trajectory_08.bin",
|
| 140 |
+
"pca_trajectory_09.bin",
|
| 141 |
+
"pca_trajectory_10.bin",
|
| 142 |
+
"pca_trajectory_11.bin",
|
| 143 |
+
"structure.pdb",
|
| 144 |
+
"trajectory.xtc",
|
| 145 |
+
"clusters_00_screenshot_00.jpg",
|
| 146 |
+
"clusters_00_screenshot_01.jpg",
|
| 147 |
+
"clusters_00_screenshot_02.jpg",
|
| 148 |
+
"clusters_00_screenshot_03.jpg",
|
| 149 |
+
"clusters_00_screenshot_04.jpg",
|
| 150 |
+
"clusters_00_screenshot_05.jpg",
|
| 151 |
+
"clusters_00_screenshot_06.jpg",
|
| 152 |
+
"clusters_00_screenshot_07.jpg",
|
| 153 |
+
"clusters_00_screenshot_08.jpg",
|
| 154 |
+
"clusters_00_screenshot_09.jpg",
|
| 155 |
+
"clusters_00_screenshot_10.jpg",
|
| 156 |
+
"clusters_00_screenshot_11.jpg",
|
| 157 |
+
"clusters_00_screenshot_12.jpg",
|
| 158 |
+
"clusters_00_screenshot_13.jpg",
|
| 159 |
+
"clusters_00_screenshot_14.jpg",
|
| 160 |
+
"clusters_00_screenshot_15.jpg",
|
| 161 |
+
"clusters_00_screenshot_16.jpg",
|
| 162 |
+
"clusters_00_screenshot_17.jpg",
|
| 163 |
+
"clusters_00_screenshot_18.jpg",
|
| 164 |
+
"clusters_00_screenshot_19.jpg",
|
| 165 |
+
"clusters_00_screenshot_20.jpg",
|
| 166 |
+
"clusters_00_screenshot_21.jpg",
|
| 167 |
+
"clusters_01_screenshot_00.jpg",
|
| 168 |
+
"clusters_01_screenshot_01.jpg",
|
| 169 |
+
"clusters_01_screenshot_02.jpg",
|
| 170 |
+
"clusters_01_screenshot_03.jpg",
|
| 171 |
+
"clusters_01_screenshot_04.jpg",
|
| 172 |
+
"clusters_01_screenshot_05.jpg",
|
| 173 |
+
"clusters_01_screenshot_06.jpg",
|
| 174 |
+
"clusters_01_screenshot_07.jpg",
|
| 175 |
+
"clusters_01_screenshot_08.jpg",
|
| 176 |
+
"clusters_01_screenshot_09.jpg",
|
| 177 |
+
"clusters_01_screenshot_10.jpg",
|
| 178 |
+
"clusters_01_screenshot_11.jpg",
|
| 179 |
+
"clusters_01_screenshot_12.jpg",
|
| 180 |
+
"clusters_01_screenshot_13.jpg",
|
| 181 |
+
"clusters_01_screenshot_14.jpg",
|
| 182 |
+
"clusters_01_screenshot_15.jpg",
|
| 183 |
+
"clusters_01_screenshot_16.jpg",
|
| 184 |
+
"clusters_01_screenshot_17.jpg",
|
| 185 |
+
"clusters_01_screenshot_18.jpg",
|
| 186 |
+
"clusters_02_screenshot_00.jpg",
|
| 187 |
+
"clusters_02_screenshot_01.jpg",
|
| 188 |
+
"clusters_02_screenshot_02.jpg",
|
| 189 |
+
"clusters_02_screenshot_03.jpg",
|
| 190 |
+
"clusters_02_screenshot_04.jpg",
|
| 191 |
+
"clusters_02_screenshot_05.jpg",
|
| 192 |
+
"clusters_02_screenshot_06.jpg",
|
| 193 |
+
"clusters_02_screenshot_07.jpg",
|
| 194 |
+
"clusters_02_screenshot_08.jpg",
|
| 195 |
+
"clusters_02_screenshot_09.jpg",
|
| 196 |
+
"clusters_02_screenshot_10.jpg",
|
| 197 |
+
"clusters_02_screenshot_11.jpg",
|
| 198 |
+
"clusters_02_screenshot_12.jpg",
|
| 199 |
+
"clusters_02_screenshot_13.jpg",
|
| 200 |
+
"clusters_02_screenshot_14.jpg",
|
| 201 |
+
"clusters_02_screenshot_15.jpg",
|
| 202 |
+
"clusters_02_screenshot_16.jpg",
|
| 203 |
+
"clusters_02_screenshot_17.jpg",
|
| 204 |
+
"clusters_02_screenshot_18.jpg",
|
| 205 |
+
"clusters_02_screenshot_19.jpg",
|
| 206 |
+
"clusters_03_screenshot_00.jpg",
|
| 207 |
+
"clusters_03_screenshot_01.jpg",
|
| 208 |
+
"clusters_03_screenshot_02.jpg",
|
| 209 |
+
"clusters_03_screenshot_03.jpg",
|
| 210 |
+
"clusters_03_screenshot_04.jpg",
|
| 211 |
+
"clusters_03_screenshot_05.jpg",
|
| 212 |
+
"clusters_03_screenshot_06.jpg",
|
| 213 |
+
"clusters_03_screenshot_07.jpg",
|
| 214 |
+
"clusters_03_screenshot_08.jpg",
|
| 215 |
+
"clusters_03_screenshot_09.jpg",
|
| 216 |
+
"clusters_03_screenshot_10.jpg",
|
| 217 |
+
"clusters_03_screenshot_11.jpg",
|
| 218 |
+
"clusters_03_screenshot_12.jpg",
|
| 219 |
+
"clusters_03_screenshot_13.jpg",
|
| 220 |
+
"clusters_03_screenshot_14.jpg",
|
| 221 |
+
"clusters_03_screenshot_15.jpg",
|
| 222 |
+
"clusters_03_screenshot_16.jpg",
|
| 223 |
+
"clusters_03_screenshot_17.jpg",
|
| 224 |
+
"clusters_03_screenshot_18.jpg",
|
| 225 |
+
"clusters_03_screenshot_19.jpg",
|
| 226 |
+
"pocket_01.pdb",
|
| 227 |
+
"pocket_02.pdb",
|
| 228 |
+
"pocket_03.pdb",
|
| 229 |
+
"pocket_04.pdb",
|
| 230 |
+
"pocket_05.pdb",
|
| 231 |
+
"pocket_06.pdb",
|
| 232 |
+
"pocket_07.pdb",
|
| 233 |
+
"pocket_08.pdb",
|
| 234 |
+
"pocket_09.pdb",
|
| 235 |
+
"pocket_10.pdb"
|
| 236 |
+
],
|
| 237 |
+
"analyses": [
|
| 238 |
+
"clusters",
|
| 239 |
+
"clusters-00",
|
| 240 |
+
"clusters-01",
|
| 241 |
+
"clusters-02",
|
| 242 |
+
"clusters-03",
|
| 243 |
+
"dist-perres",
|
| 244 |
+
"energies",
|
| 245 |
+
"fluctuation",
|
| 246 |
+
"hbonds",
|
| 247 |
+
"interactions",
|
| 248 |
+
"pca",
|
| 249 |
+
"pockets",
|
| 250 |
+
"rgyr",
|
| 251 |
+
"rmsd-pairwise",
|
| 252 |
+
"rmsd-perres",
|
| 253 |
+
"rmsds",
|
| 254 |
+
"sasa",
|
| 255 |
+
"tmscores"
|
| 256 |
+
],
|
| 257 |
+
"mdIndex": 0,
|
| 258 |
+
"mdNumber": 1,
|
| 259 |
+
"refframe": 1,
|
| 260 |
+
"internalId": "683f74fa35f780aa264ecffc",
|
| 261 |
+
"creationDate": "2025-06-03T22:19:38.000Z",
|
| 262 |
+
"identifier": "A0023"
|
| 263 |
+
}
|
data/files/A0023/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0023", "accession": "A0023", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UEX", "DESCRIPTION": "Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Author Omid Mokhtari", "Author Hamed Khakzad", "Author Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": [{"name": "Link_name", "url": "www.link-name.org"}], "PDBIDS": ["1UEX"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7LZK5", "Q7LZK8", "P04275"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVEYHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQRDEIVSYLCDLAPEAP", "GCLPDWSSYKGHCYKVFKVEKTWADAEKFCKELVNGGHLMSVNSREEGEFISKLALEKMRIVLVWIGLSHFWRICPLRWTDGARLDYRALSDEPICFVAESFHNKWIQWTCNRKKSFVCKYRV", "GCLPDWSSYKGHCYKVFKKVGTWEDAEKFCVENSGHLASIDSKEEADFVTKLASQTLTKFVYDAWIGLRDESKTQQCSPQWTDGSSVVYENVDEPTKCFGLDVHTEYRTWTDLPCGEKNPFICKS"], "NUCLSEQ": [], "DOMAINS": ["Snaclec bitiscetin subunit alpha", "C-type lectin", "Snaclec bitiscetin subunit beta", "C-type lectin", "von Willebrand factor", "VWFA 1; binding site for platelet glycoprotein Ib"], "FRAMESTEP": 0.02, "TIMESTEP": 5000, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7270, "SYSTRES": 450, "PROTATS": 7270, "PROTRES": 450, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.3738, "BOXSIZEY": 10.3738, "BOXSIZEZ": 7.38044, "mdName": "replica 1", "mdAtoms": 7270, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0023/files/topology.tpr", "length": 2284868, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0023/files/screenshot.jpg", "length": 22395, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0023/files/trajectory.bin", "length": 436287240, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 5001, "atoms": 7270}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_01.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_02.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_03.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_04.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_05.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_06.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_07.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_08.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_09.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_10.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_11.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0023/files/structure.pdb", "length": 588905, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0023/files/trajectory.xtc", "length": 138330860, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_00.jpg", "length": 21198, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_01.jpg", "length": 21054, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_02.jpg", "length": 20949, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_03.jpg", "length": 20764, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_04.jpg", "length": 20909, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_05.jpg", "length": 20783, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_06.jpg", "length": 20754, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_07.jpg", "length": 20565, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_08.jpg", "length": 20631, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_09.jpg", "length": 20794, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_10.jpg", "length": 20802, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_11.jpg", "length": 21040, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_12.jpg", "length": 20938, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_13.jpg", "length": 21082, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_14.jpg", "length": 21064, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_15.jpg", "length": 21091, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_16.jpg", "length": 21383, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_17.jpg", "length": 20883, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_18.jpg", "length": 20852, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_19.jpg", "length": 20660, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_20.jpg", "length": 21066, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_21.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_00.jpg", "length": 23144, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_01.jpg", "length": 23450, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_02.jpg", "length": 23185, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_03.jpg", "length": 23561, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_04.jpg", "length": 23859, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_05.jpg", "length": 23520, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_06.jpg", "length": 23408, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_07.jpg", "length": 23311, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_08.jpg", "length": 23328, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_09.jpg", "length": 23940, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_10.jpg", "length": 22563, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_11.jpg", "length": 23377, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_12.jpg", "length": 23196, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_13.jpg", "length": 23020, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_14.jpg", "length": 22882, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_15.jpg", "length": 22836, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_16.jpg", "length": 22768, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_17.jpg", "length": 22668, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_18.jpg", "length": 23129, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_00.jpg", "length": 21557, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_01.jpg", "length": 21633, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_02.jpg", "length": 21322, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_03.jpg", "length": 21427, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_04.jpg", "length": 21590, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_05.jpg", "length": 21443, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_06.jpg", "length": 21248, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_07.jpg", "length": 21651, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_08.jpg", "length": 21500, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_09.jpg", "length": 21569, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_10.jpg", "length": 21453, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_11.jpg", "length": 21333, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_12.jpg", "length": 21612, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_13.jpg", "length": 21300, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_14.jpg", "length": 21446, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_15.jpg", "length": 21701, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_16.jpg", "length": 21086, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_17.jpg", "length": 21173, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_18.jpg", "length": 21787, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_19.jpg", "length": 21181, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_00.jpg", "length": 20878, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_01.jpg", "length": 21756, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_02.jpg", "length": 21489, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_03.jpg", "length": 21741, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_04.jpg", "length": 21343, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_05.jpg", "length": 21515, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_06.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_07.jpg", "length": 21099, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_08.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_09.jpg", "length": 21365, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_10.jpg", "length": 20947, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_11.jpg", "length": 21145, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_12.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_13.jpg", "length": 21390, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_14.jpg", "length": 21025, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_15.jpg", "length": 21165, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_16.jpg", "length": 21124, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_17.jpg", "length": 20770, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_18.jpg", "length": 20898, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_19.jpg", "length": 20988, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0023/files/pocket_01.pdb", "length": 68206, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0023/files/pocket_02.pdb", "length": 21574, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0023/files/pocket_03.pdb", "length": 19028, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0023/files/pocket_04.pdb", "length": 9045, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0023/files/pocket_05.pdb", "length": 7638, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0023/files/pocket_06.pdb", "length": 6365, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0023/files/pocket_07.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0023/files/pocket_08.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0023/files/pocket_09.pdb", "length": 5159, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0023/files/pocket_10.pdb", "length": 4824, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0023", "accession": "A0023", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UEX", "DESCRIPTION": "Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Author Omid Mokhtari", "Author Hamed Khakzad", "Author Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": [{"name": "Link_name", "url": "www.link-name.org"}], "PDBIDS": ["1UEX"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7LZK5", "Q7LZK8", "P04275"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVEYHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQRDEIVSYLCDLAPEAP", "GCLPDWSSYKGHCYKVFKVEKTWADAEKFCKELVNGGHLMSVNSREEGEFISKLALEKMRIVLVWIGLSHFWRICPLRWTDGARLDYRALSDEPICFVAESFHNKWIQWTCNRKKSFVCKYRV", "GCLPDWSSYKGHCYKVFKKVGTWEDAEKFCVENSGHLASIDSKEEADFVTKLASQTLTKFVYDAWIGLRDESKTQQCSPQWTDGSSVVYENVDEPTKCFGLDVHTEYRTWTDLPCGEKNPFICKS"], "NUCLSEQ": [], "DOMAINS": ["Snaclec bitiscetin subunit alpha", "C-type lectin", "Snaclec bitiscetin subunit beta", "C-type lectin", "von Willebrand factor", "VWFA 1; binding site for platelet glycoprotein Ib"], "FRAMESTEP": 0.02, "TIMESTEP": 5000, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7270, "SYSTRES": 450, "PROTATS": 7270, "PROTRES": 450, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.3738, "BOXSIZEY": 10.3738, "BOXSIZEZ": 7.38044, "mdName": "replica 1", "mdAtoms": 7270, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0023/files/topology.tpr", "length": 2284868, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0023/files/screenshot.jpg", "length": 22395, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0023/files/trajectory.bin", "length": 436287240, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 5001, "atoms": 7270}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_01.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_02.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_03.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_04.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_05.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_06.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_07.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_08.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_09.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_10.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_11.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0023/files/structure.pdb", "length": 588905, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0023/files/trajectory.xtc", "length": 138330860, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_00.jpg", "length": 21198, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_01.jpg", "length": 21054, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_02.jpg", "length": 20949, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_03.jpg", "length": 20764, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_04.jpg", "length": 20909, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_05.jpg", "length": 20783, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_06.jpg", "length": 20754, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_07.jpg", "length": 20565, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_08.jpg", "length": 20631, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_09.jpg", "length": 20794, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_10.jpg", "length": 20802, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_11.jpg", "length": 21040, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_12.jpg", "length": 20938, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_13.jpg", "length": 21082, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_14.jpg", "length": 21064, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_15.jpg", "length": 21091, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_16.jpg", "length": 21383, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_17.jpg", "length": 20883, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_18.jpg", "length": 20852, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_19.jpg", "length": 20660, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_20.jpg", "length": 21066, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_21.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_00.jpg", "length": 23144, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_01.jpg", "length": 23450, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_02.jpg", "length": 23185, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_03.jpg", "length": 23561, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_04.jpg", "length": 23859, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_05.jpg", "length": 23520, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_06.jpg", "length": 23408, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_07.jpg", "length": 23311, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_08.jpg", "length": 23328, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_09.jpg", "length": 23940, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_10.jpg", "length": 22563, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_11.jpg", "length": 23377, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_12.jpg", "length": 23196, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_13.jpg", "length": 23020, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_14.jpg", "length": 22882, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_15.jpg", "length": 22836, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_16.jpg", "length": 22768, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_17.jpg", "length": 22668, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_18.jpg", "length": 23129, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_00.jpg", "length": 21557, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_01.jpg", "length": 21633, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_02.jpg", "length": 21322, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_03.jpg", "length": 21427, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_04.jpg", "length": 21590, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_05.jpg", "length": 21443, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_06.jpg", "length": 21248, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_07.jpg", "length": 21651, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_08.jpg", "length": 21500, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_09.jpg", "length": 21569, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_10.jpg", "length": 21453, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_11.jpg", "length": 21333, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_12.jpg", "length": 21612, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_13.jpg", "length": 21300, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_14.jpg", "length": 21446, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_15.jpg", "length": 21701, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_16.jpg", "length": 21086, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_17.jpg", "length": 21173, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_18.jpg", "length": 21787, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_19.jpg", "length": 21181, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_00.jpg", "length": 20878, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_01.jpg", "length": 21756, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_02.jpg", "length": 21489, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_03.jpg", "length": 21741, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_04.jpg", "length": 21343, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_05.jpg", "length": 21515, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_06.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_07.jpg", "length": 21099, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_08.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_09.jpg", "length": 21365, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_10.jpg", "length": 20947, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_11.jpg", "length": 21145, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_12.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_13.jpg", "length": 21390, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_14.jpg", "length": 21025, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_15.jpg", "length": 21165, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_16.jpg", "length": 21124, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_17.jpg", "length": 20770, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_18.jpg", "length": 20898, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_19.jpg", "length": 20988, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0023/files/pocket_01.pdb", "length": 68206, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0023/files/pocket_02.pdb", "length": 21574, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0023/files/pocket_03.pdb", "length": 19028, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0023/files/pocket_04.pdb", "length": 9045, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0023/files/pocket_05.pdb", "length": 7638, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0023/files/pocket_06.pdb", "length": 6365, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0023/files/pocket_07.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0023/files/pocket_08.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0023/files/pocket_09.pdb", "length": 5159, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0023/files/pocket_10.pdb", "length": 4824, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0023", "accession": "A0023", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UEX", "DESCRIPTION": "Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Author Omid Mokhtari", "Author Hamed Khakzad", "Author Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": [{"name": "Link_name", "url": "www.link-name.org"}], "PDBIDS": ["1UEX"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7LZK5", "Q7LZK8", "P04275"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EPPLHDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMERLRISQKWVRVAVVEYHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQRDEIVSYLCDLAPEAP", "GCLPDWSSYKGHCYKVFKVEKTWADAEKFCKELVNGGHLMSVNSREEGEFISKLALEKMRIVLVWIGLSHFWRICPLRWTDGARLDYRALSDEPICFVAESFHNKWIQWTCNRKKSFVCKYRV", "GCLPDWSSYKGHCYKVFKKVGTWEDAEKFCVENSGHLASIDSKEEADFVTKLASQTLTKFVYDAWIGLRDESKTQQCSPQWTDGSSVVYENVDEPTKCFGLDVHTEYRTWTDLPCGEKNPFICKS"], "NUCLSEQ": [], "DOMAINS": ["Snaclec bitiscetin subunit alpha", "C-type lectin", "Snaclec bitiscetin subunit beta", "C-type lectin", "von Willebrand factor", "VWFA 1; binding site for platelet glycoprotein Ib"], "FRAMESTEP": 0.02, "TIMESTEP": 5000, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7270, "SYSTRES": 450, "PROTATS": 7270, "PROTRES": 450, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.3738, "BOXSIZEY": 10.3738, "BOXSIZEZ": 7.38044, "mdName": "replica 1", "mdAtoms": 7270, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0023/files/topology.tpr", "length": 2284868, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0023/files/screenshot.jpg", "length": 22395, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0023/files/trajectory.bin", "length": 436287240, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 5001, "atoms": 7270}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_01.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_02.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_03.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_04.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_05.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_06.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_07.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_08.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_09.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_10.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0023/files/pca_trajectory_11.bin", "length": 324000, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0, "frames": 20, "atoms": 1350}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0023/files/structure.pdb", "length": 588905, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0023/files/trajectory.xtc", "length": 138330860, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_00.jpg", "length": 21198, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_01.jpg", "length": 21054, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_02.jpg", "length": 20949, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_03.jpg", "length": 20764, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_04.jpg", "length": 20909, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_05.jpg", "length": 20783, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_06.jpg", "length": 20754, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_07.jpg", "length": 20565, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_08.jpg", "length": 20631, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_09.jpg", "length": 20794, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_10.jpg", "length": 20802, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_11.jpg", "length": 21040, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_12.jpg", "length": 20938, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_13.jpg", "length": 21082, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_14.jpg", "length": 21064, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_15.jpg", "length": 21091, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_16.jpg", "length": 21383, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_17.jpg", "length": 20883, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_18.jpg", "length": 20852, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_19.jpg", "length": 20660, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_20.jpg", "length": 21066, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0023/files/clusters_00_screenshot_21.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_00.jpg", "length": 23144, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_01.jpg", "length": 23450, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_02.jpg", "length": 23185, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_03.jpg", "length": 23561, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_04.jpg", "length": 23859, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_05.jpg", "length": 23520, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_06.jpg", "length": 23408, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_07.jpg", "length": 23311, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_08.jpg", "length": 23328, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_09.jpg", "length": 23940, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_10.jpg", "length": 22563, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_11.jpg", "length": 23377, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_12.jpg", "length": 23196, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_13.jpg", "length": 23020, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_14.jpg", "length": 22882, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_15.jpg", "length": 22836, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_16.jpg", "length": 22768, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_17.jpg", "length": 22668, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_01_screenshot_18.jpg", "length": 23129, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_00.jpg", "length": 21557, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_01.jpg", "length": 21633, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_02.jpg", "length": 21322, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_03.jpg", "length": 21427, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_04.jpg", "length": 21590, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_05.jpg", "length": 21443, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_06.jpg", "length": 21248, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_07.jpg", "length": 21651, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_08.jpg", "length": 21500, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_09.jpg", "length": 21569, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_10.jpg", "length": 21453, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_11.jpg", "length": 21333, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_12.jpg", "length": 21612, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_13.jpg", "length": 21300, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_14.jpg", "length": 21446, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_15.jpg", "length": 21701, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_16.jpg", "length": 21086, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_17.jpg", "length": 21173, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_18.jpg", "length": 21787, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_02_screenshot_19.jpg", "length": 21181, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_00.jpg", "length": 20878, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_01.jpg", "length": 21756, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_02.jpg", "length": 21489, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_03.jpg", "length": 21741, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_04.jpg", "length": 21343, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_05.jpg", "length": 21515, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_06.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_07.jpg", "length": 21099, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_08.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_09.jpg", "length": 21365, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_10.jpg", "length": 20947, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_11.jpg", "length": 21145, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_12.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_13.jpg", "length": 21390, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_14.jpg", "length": 21025, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_15.jpg", "length": 21165, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_16.jpg", "length": 21124, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_17.jpg", "length": 20770, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_18.jpg", "length": 20898, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A0023/files/clusters_03_screenshot_19.jpg", "length": 20988, "contentType": "application/octet-stream", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0023/files/pocket_01.pdb", "length": 68206, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0023/files/pocket_02.pdb", "length": 21574, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0023/files/pocket_03.pdb", "length": 19028, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0023/files/pocket_04.pdb", "length": 9045, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0023/files/pocket_05.pdb", "length": 7638, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0023/files/pocket_06.pdb", "length": 6365, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0023/files/pocket_07.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0023/files/pocket_08.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0023/files/pocket_09.pdb", "length": 5159, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0023/files/pocket_10.pdb", "length": 4824, "contentType": "chemical/x-pdb", "metadata": {"project": "683f74fa35f780aa264ecffc", "md": 0}}]}
|
data/files/A0024/project.json
ADDED
|
@@ -0,0 +1,197 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0024",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1UGH",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1UGH"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P13051",
|
| 31 |
+
"P14739"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL",
|
| 38 |
+
"NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Uracil-DNA glycosylase",
|
| 43 |
+
"Uracil-DNA glycosylase inhibitor"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
"SYSTATS": 4863,
|
| 55 |
+
"SYSTRES": 305,
|
| 56 |
+
"PROTATS": 4863,
|
| 57 |
+
"PROTRES": 305,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
+
"SOLVRES": 0,
|
| 66 |
+
"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
+
"MEMBRANES": null,
|
| 82 |
+
"CUSTOMS": null,
|
| 83 |
+
"ORIENTATION": null,
|
| 84 |
+
"PTM": [],
|
| 85 |
+
"MULTIMERIC": null,
|
| 86 |
+
"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
+
"BOXSIZEX": 8.47508,
|
| 89 |
+
"BOXSIZEY": 8.47508,
|
| 90 |
+
"BOXSIZEZ": 6.00649,
|
| 91 |
+
"mdName": "replica 1",
|
| 92 |
+
"mdAtoms": 4863,
|
| 93 |
+
"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
+
"mdref": 0,
|
| 101 |
+
"files": [
|
| 102 |
+
"topology.tpr",
|
| 103 |
+
"screenshot.jpg",
|
| 104 |
+
"trajectory.bin",
|
| 105 |
+
"pca_trajectory_01.bin",
|
| 106 |
+
"pca_trajectory_02.bin",
|
| 107 |
+
"pca_trajectory_03.bin",
|
| 108 |
+
"pca_trajectory_04.bin",
|
| 109 |
+
"pca_trajectory_05.bin",
|
| 110 |
+
"pca_trajectory_06.bin",
|
| 111 |
+
"pca_trajectory_07.bin",
|
| 112 |
+
"pca_trajectory_08.bin",
|
| 113 |
+
"pca_trajectory_09.bin",
|
| 114 |
+
"pca_trajectory_10.bin",
|
| 115 |
+
"pca_trajectory_11.bin",
|
| 116 |
+
"pca_trajectory_12.bin",
|
| 117 |
+
"pca_trajectory_13.bin",
|
| 118 |
+
"pca_trajectory_14.bin",
|
| 119 |
+
"pca_trajectory_15.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
+
"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_01_screenshot_00.jpg",
|
| 142 |
+
"clusters_01_screenshot_01.jpg",
|
| 143 |
+
"clusters_01_screenshot_02.jpg",
|
| 144 |
+
"clusters_01_screenshot_03.jpg",
|
| 145 |
+
"clusters_01_screenshot_04.jpg",
|
| 146 |
+
"clusters_01_screenshot_05.jpg",
|
| 147 |
+
"clusters_01_screenshot_06.jpg",
|
| 148 |
+
"clusters_01_screenshot_07.jpg",
|
| 149 |
+
"clusters_01_screenshot_08.jpg",
|
| 150 |
+
"clusters_01_screenshot_09.jpg",
|
| 151 |
+
"clusters_01_screenshot_10.jpg",
|
| 152 |
+
"clusters_01_screenshot_11.jpg",
|
| 153 |
+
"clusters_01_screenshot_12.jpg",
|
| 154 |
+
"clusters_01_screenshot_13.jpg",
|
| 155 |
+
"clusters_01_screenshot_14.jpg",
|
| 156 |
+
"clusters_01_screenshot_15.jpg",
|
| 157 |
+
"clusters_01_screenshot_16.jpg",
|
| 158 |
+
"clusters_01_screenshot_17.jpg",
|
| 159 |
+
"clusters_01_screenshot_18.jpg",
|
| 160 |
+
"clusters_01_screenshot_19.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb",
|
| 165 |
+
"pocket_05.pdb",
|
| 166 |
+
"pocket_06.pdb",
|
| 167 |
+
"pocket_07.pdb",
|
| 168 |
+
"pocket_08.pdb",
|
| 169 |
+
"pocket_09.pdb",
|
| 170 |
+
"pocket_10.pdb"
|
| 171 |
+
],
|
| 172 |
+
"analyses": [
|
| 173 |
+
"mem-map",
|
| 174 |
+
"clusters",
|
| 175 |
+
"clusters-00",
|
| 176 |
+
"clusters-01",
|
| 177 |
+
"dist-perres",
|
| 178 |
+
"energies",
|
| 179 |
+
"fluctuation",
|
| 180 |
+
"hbonds",
|
| 181 |
+
"interactions",
|
| 182 |
+
"pca",
|
| 183 |
+
"pockets",
|
| 184 |
+
"rgyr",
|
| 185 |
+
"rmsd-pairwise",
|
| 186 |
+
"rmsd-perres",
|
| 187 |
+
"rmsds",
|
| 188 |
+
"sasa",
|
| 189 |
+
"tmscores"
|
| 190 |
+
],
|
| 191 |
+
"mdIndex": 0,
|
| 192 |
+
"mdNumber": 1,
|
| 193 |
+
"refframe": 1,
|
| 194 |
+
"internalId": "683f76bea396e03843709f82",
|
| 195 |
+
"creationDate": "2025-06-03T22:27:10.000Z",
|
| 196 |
+
"identifier": "A0024"
|
| 197 |
+
}
|
data/files/A0024/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0024", "accession": "A0024", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UGH", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1UGH"], "FORCED_REFERENCES": null, "REFERENCES": ["P13051", "P14739"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL", "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"], "NUCLSEQ": [], "DOMAINS": ["Uracil-DNA glycosylase", "Uracil-DNA glycosylase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4863, "SYSTRES": 305, "PROTATS": 4863, "PROTRES": 305, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.47508, "BOXSIZEY": 8.47508, "BOXSIZEZ": 6.00649, "mdName": "replica 1", "mdAtoms": 4863, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0024/files/topology.tpr", "length": 1592244, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0024/files/screenshot.jpg", "length": 24851, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0024/files/trajectory.bin", "length": 291838356, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 5001, "atoms": 4863}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_01.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_02.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_03.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_04.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_05.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_06.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_07.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_08.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_09.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_10.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_11.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_12.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_13.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_14.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_15.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0024/files/structure.pdb", "length": 393938, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0024/files/trajectory.xtc", "length": 92564956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_00.jpg", "length": 25369, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_01.jpg", "length": 25994, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_02.jpg", "length": 25049, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_03.jpg", "length": 25589, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_04.jpg", "length": 25246, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_05.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_06.jpg", "length": 25258, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_07.jpg", "length": 25523, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_08.jpg", "length": 25475, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_09.jpg", "length": 25529, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_10.jpg", "length": 25187, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_11.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_12.jpg", "length": 25178, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_13.jpg", "length": 25329, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_14.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_15.jpg", "length": 25140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_16.jpg", "length": 25850, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_17.jpg", "length": 25854, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_18.jpg", "length": 25028, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_00.jpg", "length": 23093, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_01.jpg", "length": 23318, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_02.jpg", "length": 22575, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_03.jpg", "length": 22433, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_04.jpg", "length": 22957, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_05.jpg", "length": 22640, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_06.jpg", "length": 22337, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_07.jpg", "length": 22797, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_08.jpg", "length": 22783, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_09.jpg", "length": 22490, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_10.jpg", "length": 22710, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_11.jpg", "length": 23255, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_12.jpg", "length": 22654, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_13.jpg", "length": 22417, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_14.jpg", "length": 22794, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_15.jpg", "length": 22619, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_16.jpg", "length": 23140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_17.jpg", "length": 22549, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_18.jpg", "length": 23263, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_19.jpg", "length": 22721, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0024/files/pocket_01.pdb", "length": 22043, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0024/files/pocket_02.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0024/files/pocket_03.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0024/files/pocket_04.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0024/files/pocket_05.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0024/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0024/files/pocket_07.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0024/files/pocket_08.pdb", "length": 5226, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0024/files/pocket_09.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0024/files/pocket_10.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0024", "accession": "A0024", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UGH", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1UGH"], "FORCED_REFERENCES": null, "REFERENCES": ["P13051", "P14739"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL", "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"], "NUCLSEQ": [], "DOMAINS": ["Uracil-DNA glycosylase", "Uracil-DNA glycosylase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4863, "SYSTRES": 305, "PROTATS": 4863, "PROTRES": 305, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.47508, "BOXSIZEY": 8.47508, "BOXSIZEZ": 6.00649, "mdName": "replica 1", "mdAtoms": 4863, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0024/files/topology.tpr", "length": 1592244, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0024/files/screenshot.jpg", "length": 24851, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0024/files/trajectory.bin", "length": 291838356, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 5001, "atoms": 4863}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_01.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_02.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_03.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_04.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_05.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_06.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_07.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_08.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_09.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_10.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_11.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_12.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_13.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_14.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_15.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0024/files/structure.pdb", "length": 393938, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0024/files/trajectory.xtc", "length": 92564956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_00.jpg", "length": 25369, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_01.jpg", "length": 25994, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_02.jpg", "length": 25049, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_03.jpg", "length": 25589, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_04.jpg", "length": 25246, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_05.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_06.jpg", "length": 25258, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_07.jpg", "length": 25523, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_08.jpg", "length": 25475, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_09.jpg", "length": 25529, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_10.jpg", "length": 25187, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_11.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_12.jpg", "length": 25178, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_13.jpg", "length": 25329, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_14.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_15.jpg", "length": 25140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_16.jpg", "length": 25850, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_17.jpg", "length": 25854, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_18.jpg", "length": 25028, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_00.jpg", "length": 23093, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_01.jpg", "length": 23318, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_02.jpg", "length": 22575, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_03.jpg", "length": 22433, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_04.jpg", "length": 22957, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_05.jpg", "length": 22640, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_06.jpg", "length": 22337, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_07.jpg", "length": 22797, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_08.jpg", "length": 22783, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_09.jpg", "length": 22490, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_10.jpg", "length": 22710, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_11.jpg", "length": 23255, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_12.jpg", "length": 22654, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_13.jpg", "length": 22417, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_14.jpg", "length": 22794, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_15.jpg", "length": 22619, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_16.jpg", "length": 23140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_17.jpg", "length": 22549, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_18.jpg", "length": 23263, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_19.jpg", "length": 22721, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0024/files/pocket_01.pdb", "length": 22043, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0024/files/pocket_02.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0024/files/pocket_03.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0024/files/pocket_04.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0024/files/pocket_05.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0024/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0024/files/pocket_07.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0024/files/pocket_08.pdb", "length": 5226, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0024/files/pocket_09.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0024/files/pocket_10.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0024", "accession": "A0024", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UGH", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1UGH"], "FORCED_REFERENCES": null, "REFERENCES": ["P13051", "P14739"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL", "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"], "NUCLSEQ": [], "DOMAINS": ["Uracil-DNA glycosylase", "Uracil-DNA glycosylase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4863, "SYSTRES": 305, "PROTATS": 4863, "PROTRES": 305, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.47508, "BOXSIZEY": 8.47508, "BOXSIZEZ": 6.00649, "mdName": "replica 1", "mdAtoms": 4863, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0024/files/topology.tpr", "length": 1592244, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0024/files/screenshot.jpg", "length": 24851, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0024/files/trajectory.bin", "length": 291838356, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 5001, "atoms": 4863}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_01.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_02.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_03.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_04.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_05.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_06.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_07.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_08.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_09.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_10.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_11.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_12.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_13.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_14.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_15.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0024/files/structure.pdb", "length": 393938, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0024/files/trajectory.xtc", "length": 92564956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_00.jpg", "length": 25369, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_01.jpg", "length": 25994, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_02.jpg", "length": 25049, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_03.jpg", "length": 25589, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_04.jpg", "length": 25246, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_05.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_06.jpg", "length": 25258, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_07.jpg", "length": 25523, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_08.jpg", "length": 25475, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_09.jpg", "length": 25529, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_10.jpg", "length": 25187, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_11.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_12.jpg", "length": 25178, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_13.jpg", "length": 25329, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_14.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_15.jpg", "length": 25140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_16.jpg", "length": 25850, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_17.jpg", "length": 25854, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_18.jpg", "length": 25028, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_00.jpg", "length": 23093, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_01.jpg", "length": 23318, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_02.jpg", "length": 22575, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_03.jpg", "length": 22433, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_04.jpg", "length": 22957, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_05.jpg", "length": 22640, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_06.jpg", "length": 22337, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_07.jpg", "length": 22797, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_08.jpg", "length": 22783, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_09.jpg", "length": 22490, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_10.jpg", "length": 22710, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_11.jpg", "length": 23255, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_12.jpg", "length": 22654, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_13.jpg", "length": 22417, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_14.jpg", "length": 22794, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_15.jpg", "length": 22619, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_16.jpg", "length": 23140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_17.jpg", "length": 22549, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_18.jpg", "length": 23263, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_19.jpg", "length": 22721, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0024/files/pocket_01.pdb", "length": 22043, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0024/files/pocket_02.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0024/files/pocket_03.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0024/files/pocket_04.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0024/files/pocket_05.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0024/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0024/files/pocket_07.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0024/files/pocket_08.pdb", "length": 5226, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0024/files/pocket_09.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0024/files/pocket_10.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}]}
|
data/files/A0025/project.json
ADDED
|
@@ -0,0 +1,196 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0025",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1UUZ",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1UUZ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9HXB1",
|
| 31 |
+
"P00698"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL",
|
| 38 |
+
"EEQPRLFELLGQPGYKATWHAMFKGESDVPKWVSDASGPSSPSTSLSLEGQPYVLANSCKPHDCGNNRLLVAFRGDKSAAYGLQVSLPDEPAEVMQTPSKYATYRWYGEPSRQVRELLMKQLESDPNWKL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Inhibitor of vertebrate lysozyme",
|
| 43 |
+
"Important for lysozyme inhibition",
|
| 44 |
+
"Lysozyme C",
|
| 45 |
+
"C-type lysozyme"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 3976,
|
| 57 |
+
"SYSTRES": 259,
|
| 58 |
+
"PROTATS": 3976,
|
| 59 |
+
"PROTRES": 259,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
+
"CARBATS": 0,
|
| 65 |
+
"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
+
"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
+
"CHAINNAMES": null,
|
| 83 |
+
"MEMBRANES": null,
|
| 84 |
+
"CUSTOMS": null,
|
| 85 |
+
"ORIENTATION": null,
|
| 86 |
+
"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
+
"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
+
"BOXSIZEX": 8.2319,
|
| 91 |
+
"BOXSIZEY": 8.2319,
|
| 92 |
+
"BOXSIZEZ": 5.84874,
|
| 93 |
+
"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 3976,
|
| 95 |
+
"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
+
"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
+
"files": [
|
| 104 |
+
"topology.tpr",
|
| 105 |
+
"screenshot.jpg",
|
| 106 |
+
"trajectory.bin",
|
| 107 |
+
"pca_trajectory_01.bin",
|
| 108 |
+
"pca_trajectory_02.bin",
|
| 109 |
+
"pca_trajectory_03.bin",
|
| 110 |
+
"pca_trajectory_04.bin",
|
| 111 |
+
"pca_trajectory_05.bin",
|
| 112 |
+
"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
+
"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"pca_trajectory_13.bin",
|
| 120 |
+
"pca_trajectory_14.bin",
|
| 121 |
+
"pca_trajectory_15.bin",
|
| 122 |
+
"pca_trajectory_16.bin",
|
| 123 |
+
"pca_trajectory_17.bin",
|
| 124 |
+
"pca_trajectory_18.bin",
|
| 125 |
+
"structure.pdb",
|
| 126 |
+
"trajectory.xtc",
|
| 127 |
+
"clusters_00_screenshot_00.jpg",
|
| 128 |
+
"clusters_00_screenshot_01.jpg",
|
| 129 |
+
"clusters_00_screenshot_02.jpg",
|
| 130 |
+
"clusters_00_screenshot_03.jpg",
|
| 131 |
+
"clusters_00_screenshot_04.jpg",
|
| 132 |
+
"clusters_00_screenshot_05.jpg",
|
| 133 |
+
"clusters_00_screenshot_06.jpg",
|
| 134 |
+
"clusters_00_screenshot_07.jpg",
|
| 135 |
+
"clusters_00_screenshot_08.jpg",
|
| 136 |
+
"clusters_00_screenshot_09.jpg",
|
| 137 |
+
"clusters_00_screenshot_10.jpg",
|
| 138 |
+
"clusters_00_screenshot_11.jpg",
|
| 139 |
+
"clusters_00_screenshot_12.jpg",
|
| 140 |
+
"clusters_00_screenshot_13.jpg",
|
| 141 |
+
"clusters_00_screenshot_14.jpg",
|
| 142 |
+
"clusters_00_screenshot_15.jpg",
|
| 143 |
+
"clusters_00_screenshot_16.jpg",
|
| 144 |
+
"clusters_01_screenshot_00.jpg",
|
| 145 |
+
"clusters_01_screenshot_01.jpg",
|
| 146 |
+
"clusters_01_screenshot_02.jpg",
|
| 147 |
+
"clusters_01_screenshot_03.jpg",
|
| 148 |
+
"clusters_01_screenshot_04.jpg",
|
| 149 |
+
"clusters_01_screenshot_05.jpg",
|
| 150 |
+
"clusters_01_screenshot_06.jpg",
|
| 151 |
+
"clusters_01_screenshot_07.jpg",
|
| 152 |
+
"clusters_01_screenshot_08.jpg",
|
| 153 |
+
"clusters_01_screenshot_09.jpg",
|
| 154 |
+
"clusters_01_screenshot_10.jpg",
|
| 155 |
+
"clusters_01_screenshot_11.jpg",
|
| 156 |
+
"clusters_01_screenshot_12.jpg",
|
| 157 |
+
"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
+
"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"clusters_01_screenshot_17.jpg",
|
| 162 |
+
"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"clusters_01_screenshot_19.jpg",
|
| 164 |
+
"pocket_01.pdb",
|
| 165 |
+
"pocket_02.pdb",
|
| 166 |
+
"pocket_03.pdb",
|
| 167 |
+
"pocket_04.pdb",
|
| 168 |
+
"pocket_05.pdb",
|
| 169 |
+
"pocket_06.pdb",
|
| 170 |
+
"pocket_07.pdb"
|
| 171 |
+
],
|
| 172 |
+
"analyses": [
|
| 173 |
+
"clusters",
|
| 174 |
+
"clusters-00",
|
| 175 |
+
"clusters-01",
|
| 176 |
+
"dist-perres",
|
| 177 |
+
"energies",
|
| 178 |
+
"fluctuation",
|
| 179 |
+
"hbonds",
|
| 180 |
+
"interactions",
|
| 181 |
+
"pca",
|
| 182 |
+
"pockets",
|
| 183 |
+
"rgyr",
|
| 184 |
+
"rmsd-pairwise",
|
| 185 |
+
"rmsd-perres",
|
| 186 |
+
"rmsds",
|
| 187 |
+
"sasa",
|
| 188 |
+
"tmscores"
|
| 189 |
+
],
|
| 190 |
+
"mdIndex": 0,
|
| 191 |
+
"mdNumber": 1,
|
| 192 |
+
"refframe": 0,
|
| 193 |
+
"internalId": "683f780f7add6932f201d2e6",
|
| 194 |
+
"creationDate": "2025-06-03T22:32:47.000Z",
|
| 195 |
+
"identifier": "A0025"
|
| 196 |
+
}
|
data/files/A0025/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0025", "accession": "A0025", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UUZ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1UUZ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9HXB1", "P00698"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL", "EEQPRLFELLGQPGYKATWHAMFKGESDVPKWVSDASGPSSPSTSLSLEGQPYVLANSCKPHDCGNNRLLVAFRGDKSAAYGLQVSLPDEPAEVMQTPSKYATYRWYGEPSRQVRELLMKQLESDPNWKL"], "NUCLSEQ": [], "DOMAINS": ["Inhibitor of vertebrate lysozyme", "Important for lysozyme inhibition", "Lysozyme C", "C-type lysozyme"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3976, "SYSTRES": 259, "PROTATS": 3976, "PROTRES": 259, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.2319, "BOXSIZEY": 8.2319, "BOXSIZEZ": 5.84874, "mdName": "replica 1", "mdAtoms": 3976, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0025/files/topology.tpr", "length": 1349060, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0025/files/screenshot.jpg", "length": 23253, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0025/files/trajectory.bin", "length": 238607712, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 5001, "atoms": 3976}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_01.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_02.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_03.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_04.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_05.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_06.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_07.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_08.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_09.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_10.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_11.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_12.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_13.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_14.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_15.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_16.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_17.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_18.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0025/files/structure.pdb", "length": 322091, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0025/files/trajectory.xtc", "length": 75513212, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_00.jpg", "length": 23070, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_01.jpg", "length": 22815, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_02.jpg", "length": 22986, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_03.jpg", "length": 22665, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_04.jpg", "length": 22634, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_05.jpg", "length": 22828, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_06.jpg", "length": 22497, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_07.jpg", "length": 22372, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_08.jpg", "length": 22716, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_09.jpg", "length": 22225, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_10.jpg", "length": 22264, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_11.jpg", "length": 22269, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_12.jpg", "length": 22880, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_13.jpg", "length": 21959, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_14.jpg", "length": 21872, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_15.jpg", "length": 22359, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_16.jpg", "length": 22746, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_00.jpg", "length": 25015, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_01.jpg", "length": 24716, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_02.jpg", "length": 24641, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_03.jpg", "length": 24603, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_04.jpg", "length": 24304, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_05.jpg", "length": 24384, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_06.jpg", "length": 24495, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_07.jpg", "length": 24429, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_08.jpg", "length": 24234, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_09.jpg", "length": 24319, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_10.jpg", "length": 24457, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_11.jpg", "length": 24661, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_12.jpg", "length": 24072, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_13.jpg", "length": 24512, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_14.jpg", "length": 24869, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_15.jpg", "length": 25213, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_16.jpg", "length": 24976, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_17.jpg", "length": 24058, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_18.jpg", "length": 24663, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_19.jpg", "length": 24810, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0025/files/pocket_01.pdb", "length": 14003, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0025/files/pocket_02.pdb", "length": 13266, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0025/files/pocket_03.pdb", "length": 11457, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0025/files/pocket_04.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0025/files/pocket_05.pdb", "length": 9916, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0025/files/pocket_06.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0025/files/pocket_07.pdb", "length": 3953, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0025", "accession": "A0025", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UUZ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1UUZ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9HXB1", "P00698"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL", "EEQPRLFELLGQPGYKATWHAMFKGESDVPKWVSDASGPSSPSTSLSLEGQPYVLANSCKPHDCGNNRLLVAFRGDKSAAYGLQVSLPDEPAEVMQTPSKYATYRWYGEPSRQVRELLMKQLESDPNWKL"], "NUCLSEQ": [], "DOMAINS": ["Inhibitor of vertebrate lysozyme", "Important for lysozyme inhibition", "Lysozyme C", "C-type lysozyme"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3976, "SYSTRES": 259, "PROTATS": 3976, "PROTRES": 259, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.2319, "BOXSIZEY": 8.2319, "BOXSIZEZ": 5.84874, "mdName": "replica 1", "mdAtoms": 3976, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0025/files/topology.tpr", "length": 1349060, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0025/files/screenshot.jpg", "length": 23253, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0025/files/trajectory.bin", "length": 238607712, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 5001, "atoms": 3976}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_01.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_02.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_03.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_04.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_05.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_06.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_07.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_08.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_09.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_10.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_11.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_12.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_13.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_14.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_15.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_16.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_17.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_18.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0025/files/structure.pdb", "length": 322091, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0025/files/trajectory.xtc", "length": 75513212, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_00.jpg", "length": 23070, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_01.jpg", "length": 22815, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_02.jpg", "length": 22986, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_03.jpg", "length": 22665, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_04.jpg", "length": 22634, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_05.jpg", "length": 22828, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_06.jpg", "length": 22497, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_07.jpg", "length": 22372, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_08.jpg", "length": 22716, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_09.jpg", "length": 22225, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_10.jpg", "length": 22264, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_11.jpg", "length": 22269, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_12.jpg", "length": 22880, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_13.jpg", "length": 21959, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_14.jpg", "length": 21872, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_15.jpg", "length": 22359, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_16.jpg", "length": 22746, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_00.jpg", "length": 25015, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_01.jpg", "length": 24716, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_02.jpg", "length": 24641, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_03.jpg", "length": 24603, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_04.jpg", "length": 24304, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_05.jpg", "length": 24384, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_06.jpg", "length": 24495, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_07.jpg", "length": 24429, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_08.jpg", "length": 24234, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_09.jpg", "length": 24319, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_10.jpg", "length": 24457, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_11.jpg", "length": 24661, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_12.jpg", "length": 24072, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_13.jpg", "length": 24512, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_14.jpg", "length": 24869, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_15.jpg", "length": 25213, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_16.jpg", "length": 24976, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_17.jpg", "length": 24058, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_18.jpg", "length": 24663, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_19.jpg", "length": 24810, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0025/files/pocket_01.pdb", "length": 14003, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0025/files/pocket_02.pdb", "length": 13266, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0025/files/pocket_03.pdb", "length": 11457, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0025/files/pocket_04.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0025/files/pocket_05.pdb", "length": 9916, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0025/files/pocket_06.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0025/files/pocket_07.pdb", "length": 3953, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0025", "accession": "A0025", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1UUZ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1UUZ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9HXB1", "P00698"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL", "EEQPRLFELLGQPGYKATWHAMFKGESDVPKWVSDASGPSSPSTSLSLEGQPYVLANSCKPHDCGNNRLLVAFRGDKSAAYGLQVSLPDEPAEVMQTPSKYATYRWYGEPSRQVRELLMKQLESDPNWKL"], "NUCLSEQ": [], "DOMAINS": ["Inhibitor of vertebrate lysozyme", "Important for lysozyme inhibition", "Lysozyme C", "C-type lysozyme"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3976, "SYSTRES": 259, "PROTATS": 3976, "PROTRES": 259, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.2319, "BOXSIZEY": 8.2319, "BOXSIZEZ": 5.84874, "mdName": "replica 1", "mdAtoms": 3976, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0025/files/topology.tpr", "length": 1349060, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0025/files/screenshot.jpg", "length": 23253, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0025/files/trajectory.bin", "length": 238607712, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 5001, "atoms": 3976}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_01.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_02.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_03.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_04.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_05.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_06.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_07.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_08.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_09.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_10.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_11.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_12.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_13.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_14.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_15.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_16.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_17.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A0025/files/pca_trajectory_18.bin", "length": 186480, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0, "frames": 20, "atoms": 777}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0025/files/structure.pdb", "length": 322091, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0025/files/trajectory.xtc", "length": 75513212, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_00.jpg", "length": 23070, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_01.jpg", "length": 22815, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_02.jpg", "length": 22986, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_03.jpg", "length": 22665, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_04.jpg", "length": 22634, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_05.jpg", "length": 22828, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_06.jpg", "length": 22497, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_07.jpg", "length": 22372, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_08.jpg", "length": 22716, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_09.jpg", "length": 22225, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_10.jpg", "length": 22264, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_11.jpg", "length": 22269, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_12.jpg", "length": 22880, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_13.jpg", "length": 21959, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_14.jpg", "length": 21872, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_15.jpg", "length": 22359, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0025/files/clusters_00_screenshot_16.jpg", "length": 22746, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_00.jpg", "length": 25015, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_01.jpg", "length": 24716, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_02.jpg", "length": 24641, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_03.jpg", "length": 24603, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_04.jpg", "length": 24304, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_05.jpg", "length": 24384, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_06.jpg", "length": 24495, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_07.jpg", "length": 24429, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_08.jpg", "length": 24234, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_09.jpg", "length": 24319, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_10.jpg", "length": 24457, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_11.jpg", "length": 24661, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_12.jpg", "length": 24072, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_13.jpg", "length": 24512, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_14.jpg", "length": 24869, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_15.jpg", "length": 25213, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_16.jpg", "length": 24976, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_17.jpg", "length": 24058, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_18.jpg", "length": 24663, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0025/files/clusters_01_screenshot_19.jpg", "length": 24810, "contentType": "application/octet-stream", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0025/files/pocket_01.pdb", "length": 14003, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0025/files/pocket_02.pdb", "length": 13266, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0025/files/pocket_03.pdb", "length": 11457, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0025/files/pocket_04.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0025/files/pocket_05.pdb", "length": 9916, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0025/files/pocket_06.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0025/files/pocket_07.pdb", "length": 3953, "contentType": "chemical/x-pdb", "metadata": {"project": "683f780f7add6932f201d2e6", "md": 0}}]}
|
data/files/A0026/project.json
ADDED
|
@@ -0,0 +1,265 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0026",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1V7P",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1V7P"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q7T2Q1",
|
| 31 |
+
"Q7T2Q0",
|
| 32 |
+
"P17301"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"LIDVVVVCDESNSIYPWDAVKNFLEKFVQGLDIGPTKTQVGLIQYANNPRVVFNLNTYKTKEEMIVATSQTSQYGGDLTNTFGAIQYARKYAYSAASGGRRSATKVMVVVTDGESHDGSMLKAVIDQCNHDNILRFGIAVLGYLNRNALDTKNLIKEIKAIASIPTERYFFNVSDEAALLEKAGTLGEQIFSI",
|
| 39 |
+
"DFDCPSDWTAYDQHCYLAIGEPQNWYEAERFCTEQAKDGHLVSIQSREEGNFVAQLVSGFMHRSEIYVWIGLRDRREEQQCNPEWNDGSKIIYVNWKEGESKMCQGLTKWTNFHDWNNINCEDLYPFVCKFSAV",
|
| 40 |
+
"CPLGWSSFDQHCYKVFEPVKNWTEAEEICMQQHKGSRLASIHSSEEEAFVSKLASKALKFTSMWIGLNNPWKDCKWEWSDNARFDYKAWKRRPYCTVMVVKPDRIFWFTRGCEKSVSFVCKFLTDPA"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Snaclec EMS16 subunit alpha",
|
| 45 |
+
"C-type lectin",
|
| 46 |
+
"Key residue for binding with integrin",
|
| 47 |
+
"Snaclec EMS16 subunit beta",
|
| 48 |
+
"C-type lectin",
|
| 49 |
+
"Key residue for binding with integrin",
|
| 50 |
+
"Integrin alpha-2",
|
| 51 |
+
"VWFA"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
+
"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 7188,
|
| 63 |
+
"SYSTRES": 454,
|
| 64 |
+
"PROTATS": 7188,
|
| 65 |
+
"PROTRES": 454,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "chain A-chain B interaction",
|
| 80 |
+
"agent_1": "chain A",
|
| 81 |
+
"agent_2": "chain B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
+
"name": "chain A-chain C interaction",
|
| 88 |
+
"agent_1": "chain A",
|
| 89 |
+
"agent_2": "chain C",
|
| 90 |
+
"selection_1": "chain A",
|
| 91 |
+
"selection_2": "chain C",
|
| 92 |
+
"type": "protein-protein"
|
| 93 |
+
},
|
| 94 |
+
{
|
| 95 |
+
"name": "chain B-chain C interaction",
|
| 96 |
+
"agent_1": "chain B",
|
| 97 |
+
"agent_2": "chain C",
|
| 98 |
+
"selection_1": "chain B",
|
| 99 |
+
"selection_2": "chain C",
|
| 100 |
+
"type": "protein-protein"
|
| 101 |
+
}
|
| 102 |
+
],
|
| 103 |
+
"PBC_SELECTION": null,
|
| 104 |
+
"CHAINNAMES": null,
|
| 105 |
+
"MEMBRANES": null,
|
| 106 |
+
"CUSTOMS": null,
|
| 107 |
+
"ORIENTATION": null,
|
| 108 |
+
"PTM": [],
|
| 109 |
+
"MULTIMERIC": null,
|
| 110 |
+
"COLLECTIONS": "dynarepo",
|
| 111 |
+
"WARNINGS": [],
|
| 112 |
+
"BOXSIZEX": 11.0761,
|
| 113 |
+
"BOXSIZEY": 11.0761,
|
| 114 |
+
"BOXSIZEZ": 7.85687,
|
| 115 |
+
"mdName": "replica 1",
|
| 116 |
+
"mdAtoms": 7188,
|
| 117 |
+
"mdFrames": 5001
|
| 118 |
+
},
|
| 119 |
+
"mds": [
|
| 120 |
+
"replica 1",
|
| 121 |
+
"replica 2",
|
| 122 |
+
"replica 3"
|
| 123 |
+
],
|
| 124 |
+
"mdref": 0,
|
| 125 |
+
"files": [
|
| 126 |
+
"topology.tpr",
|
| 127 |
+
"screenshot.jpg",
|
| 128 |
+
"trajectory.bin",
|
| 129 |
+
"pca_trajectory_01.bin",
|
| 130 |
+
"pca_trajectory_02.bin",
|
| 131 |
+
"pca_trajectory_03.bin",
|
| 132 |
+
"pca_trajectory_04.bin",
|
| 133 |
+
"pca_trajectory_05.bin",
|
| 134 |
+
"pca_trajectory_06.bin",
|
| 135 |
+
"pca_trajectory_07.bin",
|
| 136 |
+
"pca_trajectory_08.bin",
|
| 137 |
+
"pca_trajectory_09.bin",
|
| 138 |
+
"pca_trajectory_10.bin",
|
| 139 |
+
"pca_trajectory_11.bin",
|
| 140 |
+
"pca_trajectory_12.bin",
|
| 141 |
+
"pca_trajectory_13.bin",
|
| 142 |
+
"pca_trajectory_14.bin",
|
| 143 |
+
"pca_trajectory_15.bin",
|
| 144 |
+
"structure.pdb",
|
| 145 |
+
"trajectory.xtc",
|
| 146 |
+
"clusters_00_screenshot_00.jpg",
|
| 147 |
+
"clusters_00_screenshot_01.jpg",
|
| 148 |
+
"clusters_00_screenshot_02.jpg",
|
| 149 |
+
"clusters_00_screenshot_03.jpg",
|
| 150 |
+
"clusters_00_screenshot_04.jpg",
|
| 151 |
+
"clusters_00_screenshot_05.jpg",
|
| 152 |
+
"clusters_00_screenshot_06.jpg",
|
| 153 |
+
"clusters_00_screenshot_07.jpg",
|
| 154 |
+
"clusters_00_screenshot_08.jpg",
|
| 155 |
+
"clusters_00_screenshot_09.jpg",
|
| 156 |
+
"clusters_00_screenshot_10.jpg",
|
| 157 |
+
"clusters_00_screenshot_11.jpg",
|
| 158 |
+
"clusters_00_screenshot_12.jpg",
|
| 159 |
+
"clusters_00_screenshot_13.jpg",
|
| 160 |
+
"clusters_00_screenshot_14.jpg",
|
| 161 |
+
"clusters_00_screenshot_15.jpg",
|
| 162 |
+
"clusters_00_screenshot_16.jpg",
|
| 163 |
+
"clusters_00_screenshot_17.jpg",
|
| 164 |
+
"clusters_00_screenshot_18.jpg",
|
| 165 |
+
"clusters_00_screenshot_19.jpg",
|
| 166 |
+
"clusters_00_screenshot_20.jpg",
|
| 167 |
+
"clusters_00_screenshot_21.jpg",
|
| 168 |
+
"clusters_00_screenshot_22.jpg",
|
| 169 |
+
"clusters_00_screenshot_23.jpg",
|
| 170 |
+
"clusters_01_screenshot_00.jpg",
|
| 171 |
+
"clusters_01_screenshot_01.jpg",
|
| 172 |
+
"clusters_01_screenshot_02.jpg",
|
| 173 |
+
"clusters_01_screenshot_03.jpg",
|
| 174 |
+
"clusters_01_screenshot_04.jpg",
|
| 175 |
+
"clusters_01_screenshot_05.jpg",
|
| 176 |
+
"clusters_01_screenshot_06.jpg",
|
| 177 |
+
"clusters_01_screenshot_07.jpg",
|
| 178 |
+
"clusters_01_screenshot_08.jpg",
|
| 179 |
+
"clusters_01_screenshot_09.jpg",
|
| 180 |
+
"clusters_01_screenshot_10.jpg",
|
| 181 |
+
"clusters_01_screenshot_11.jpg",
|
| 182 |
+
"clusters_01_screenshot_12.jpg",
|
| 183 |
+
"clusters_01_screenshot_13.jpg",
|
| 184 |
+
"clusters_01_screenshot_14.jpg",
|
| 185 |
+
"clusters_01_screenshot_15.jpg",
|
| 186 |
+
"clusters_01_screenshot_16.jpg",
|
| 187 |
+
"clusters_01_screenshot_17.jpg",
|
| 188 |
+
"clusters_01_screenshot_18.jpg",
|
| 189 |
+
"clusters_01_screenshot_19.jpg",
|
| 190 |
+
"clusters_02_screenshot_00.jpg",
|
| 191 |
+
"clusters_02_screenshot_01.jpg",
|
| 192 |
+
"clusters_02_screenshot_02.jpg",
|
| 193 |
+
"clusters_02_screenshot_03.jpg",
|
| 194 |
+
"clusters_02_screenshot_04.jpg",
|
| 195 |
+
"clusters_02_screenshot_05.jpg",
|
| 196 |
+
"clusters_02_screenshot_06.jpg",
|
| 197 |
+
"clusters_02_screenshot_07.jpg",
|
| 198 |
+
"clusters_02_screenshot_08.jpg",
|
| 199 |
+
"clusters_02_screenshot_09.jpg",
|
| 200 |
+
"clusters_02_screenshot_10.jpg",
|
| 201 |
+
"clusters_02_screenshot_11.jpg",
|
| 202 |
+
"clusters_02_screenshot_12.jpg",
|
| 203 |
+
"clusters_02_screenshot_13.jpg",
|
| 204 |
+
"clusters_02_screenshot_14.jpg",
|
| 205 |
+
"clusters_02_screenshot_15.jpg",
|
| 206 |
+
"clusters_02_screenshot_16.jpg",
|
| 207 |
+
"clusters_02_screenshot_17.jpg",
|
| 208 |
+
"clusters_02_screenshot_18.jpg",
|
| 209 |
+
"clusters_03_screenshot_00.jpg",
|
| 210 |
+
"clusters_03_screenshot_01.jpg",
|
| 211 |
+
"clusters_03_screenshot_02.jpg",
|
| 212 |
+
"clusters_03_screenshot_03.jpg",
|
| 213 |
+
"clusters_03_screenshot_04.jpg",
|
| 214 |
+
"clusters_03_screenshot_05.jpg",
|
| 215 |
+
"clusters_03_screenshot_06.jpg",
|
| 216 |
+
"clusters_03_screenshot_07.jpg",
|
| 217 |
+
"clusters_03_screenshot_08.jpg",
|
| 218 |
+
"clusters_03_screenshot_09.jpg",
|
| 219 |
+
"clusters_03_screenshot_10.jpg",
|
| 220 |
+
"clusters_03_screenshot_11.jpg",
|
| 221 |
+
"clusters_03_screenshot_12.jpg",
|
| 222 |
+
"clusters_03_screenshot_13.jpg",
|
| 223 |
+
"clusters_03_screenshot_14.jpg",
|
| 224 |
+
"clusters_03_screenshot_15.jpg",
|
| 225 |
+
"clusters_03_screenshot_16.jpg",
|
| 226 |
+
"clusters_03_screenshot_17.jpg",
|
| 227 |
+
"clusters_03_screenshot_18.jpg",
|
| 228 |
+
"pocket_01.pdb",
|
| 229 |
+
"pocket_02.pdb",
|
| 230 |
+
"pocket_03.pdb",
|
| 231 |
+
"pocket_04.pdb",
|
| 232 |
+
"pocket_05.pdb",
|
| 233 |
+
"pocket_06.pdb",
|
| 234 |
+
"pocket_07.pdb",
|
| 235 |
+
"pocket_08.pdb",
|
| 236 |
+
"pocket_09.pdb",
|
| 237 |
+
"pocket_10.pdb"
|
| 238 |
+
],
|
| 239 |
+
"analyses": [
|
| 240 |
+
"clusters",
|
| 241 |
+
"clusters-00",
|
| 242 |
+
"clusters-01",
|
| 243 |
+
"clusters-02",
|
| 244 |
+
"clusters-03",
|
| 245 |
+
"dist-perres",
|
| 246 |
+
"energies",
|
| 247 |
+
"fluctuation",
|
| 248 |
+
"hbonds",
|
| 249 |
+
"interactions",
|
| 250 |
+
"pca",
|
| 251 |
+
"pockets",
|
| 252 |
+
"rgyr",
|
| 253 |
+
"rmsd-pairwise",
|
| 254 |
+
"rmsd-perres",
|
| 255 |
+
"rmsds",
|
| 256 |
+
"sasa",
|
| 257 |
+
"tmscores"
|
| 258 |
+
],
|
| 259 |
+
"mdIndex": 0,
|
| 260 |
+
"mdNumber": 1,
|
| 261 |
+
"refframe": 1,
|
| 262 |
+
"internalId": "683f79d2f77378da06299cf3",
|
| 263 |
+
"creationDate": "2025-06-03T22:40:18.000Z",
|
| 264 |
+
"identifier": "A0026"
|
| 265 |
+
}
|
data/files/A0026/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0026", "accession": "A0026", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1V7P", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1V7P"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7T2Q1", "Q7T2Q0", "P17301"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["LIDVVVVCDESNSIYPWDAVKNFLEKFVQGLDIGPTKTQVGLIQYANNPRVVFNLNTYKTKEEMIVATSQTSQYGGDLTNTFGAIQYARKYAYSAASGGRRSATKVMVVVTDGESHDGSMLKAVIDQCNHDNILRFGIAVLGYLNRNALDTKNLIKEIKAIASIPTERYFFNVSDEAALLEKAGTLGEQIFSI", "DFDCPSDWTAYDQHCYLAIGEPQNWYEAERFCTEQAKDGHLVSIQSREEGNFVAQLVSGFMHRSEIYVWIGLRDRREEQQCNPEWNDGSKIIYVNWKEGESKMCQGLTKWTNFHDWNNINCEDLYPFVCKFSAV", "CPLGWSSFDQHCYKVFEPVKNWTEAEEICMQQHKGSRLASIHSSEEEAFVSKLASKALKFTSMWIGLNNPWKDCKWEWSDNARFDYKAWKRRPYCTVMVVKPDRIFWFTRGCEKSVSFVCKFLTDPA"], "NUCLSEQ": [], "DOMAINS": ["Snaclec EMS16 subunit alpha", "C-type lectin", "Key residue for binding with integrin", "Snaclec EMS16 subunit beta", "C-type lectin", "Key residue for binding with integrin", "Integrin alpha-2", "VWFA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7188, "SYSTRES": 454, "PROTATS": 7188, "PROTRES": 454, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0761, "BOXSIZEY": 11.0761, "BOXSIZEZ": 7.85687, "mdName": "replica 1", "mdAtoms": 7188, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0026/files/topology.tpr", "length": 2293804, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0026/files/screenshot.jpg", "length": 21422, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0026/files/trajectory.bin", "length": 431366256, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 5001, "atoms": 7188}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_01.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_02.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_03.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_04.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_05.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_06.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_07.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_08.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_09.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_10.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_11.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_12.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_13.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_14.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_15.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0026/files/structure.pdb", "length": 582263, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0026/files/trajectory.xtc", "length": 136961680, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_00.jpg", "length": 21707, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_01.jpg", "length": 21742, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_02.jpg", "length": 21566, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_03.jpg", "length": 21708, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_04.jpg", "length": 21539, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_05.jpg", "length": 22152, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_06.jpg", "length": 22060, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_07.jpg", "length": 21931, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_08.jpg", "length": 21947, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_09.jpg", "length": 21700, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_10.jpg", "length": 21574, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_11.jpg", "length": 21656, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_12.jpg", "length": 21631, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_13.jpg", "length": 21748, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_14.jpg", "length": 21702, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_15.jpg", "length": 21720, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_16.jpg", "length": 21932, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_17.jpg", "length": 21840, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_18.jpg", "length": 21756, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_19.jpg", "length": 21786, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_20.jpg", "length": 22157, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_21.jpg", "length": 21648, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_22.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_22.jpg", "length": 22204, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_23.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_23.jpg", "length": 21834, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_00.jpg", "length": 25596, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_01.jpg", "length": 25281, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_02.jpg", "length": 25098, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_03.jpg", "length": 24849, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_04.jpg", "length": 25218, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_05.jpg", "length": 25249, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_06.jpg", "length": 25437, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_07.jpg", "length": 25228, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_08.jpg", "length": 25189, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_09.jpg", "length": 25464, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_10.jpg", "length": 24912, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_11.jpg", "length": 25398, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_12.jpg", "length": 25072, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_13.jpg", "length": 24894, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_14.jpg", "length": 25003, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_15.jpg", "length": 25317, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_16.jpg", "length": 24871, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_17.jpg", "length": 25141, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_18.jpg", "length": 24752, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_19.jpg", "length": 25108, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_00.jpg", "length": 23025, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_01.jpg", "length": 23153, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_02.jpg", "length": 23304, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_03.jpg", "length": 23272, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_04.jpg", "length": 22925, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_05.jpg", "length": 22788, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_06.jpg", "length": 23173, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_07.jpg", "length": 22969, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_08.jpg", "length": 22732, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_09.jpg", "length": 22793, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_10.jpg", "length": 23664, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_11.jpg", "length": 23170, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_12.jpg", "length": 23378, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_13.jpg", "length": 22732, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_14.jpg", "length": 22976, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_15.jpg", "length": 23170, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_16.jpg", "length": 23029, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_17.jpg", "length": 23364, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_18.jpg", "length": 22656, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_00.jpg", "length": 21895, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_01.jpg", "length": 21838, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_02.jpg", "length": 22009, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_03.jpg", "length": 21782, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_04.jpg", "length": 21779, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_05.jpg", "length": 22307, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_06.jpg", "length": 21888, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_07.jpg", "length": 22084, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_08.jpg", "length": 22241, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_09.jpg", "length": 21866, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_10.jpg", "length": 22563, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_11.jpg", "length": 21821, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_12.jpg", "length": 21878, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_13.jpg", "length": 22300, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_14.jpg", "length": 22130, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_15.jpg", "length": 22006, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_16.jpg", "length": 21706, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_17.jpg", "length": 21701, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_18.jpg", "length": 21695, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0026/files/pocket_01.pdb", "length": 64521, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0026/files/pocket_02.pdb", "length": 15611, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0026/files/pocket_03.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0026/files/pocket_04.pdb", "length": 12462, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0026/files/pocket_05.pdb", "length": 12127, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0026/files/pocket_06.pdb", "length": 9715, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0026/files/pocket_07.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0026/files/pocket_08.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0026/files/pocket_09.pdb", "length": 5829, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0026/files/pocket_10.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0026", "accession": "A0026", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1V7P", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1V7P"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7T2Q1", "Q7T2Q0", "P17301"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["LIDVVVVCDESNSIYPWDAVKNFLEKFVQGLDIGPTKTQVGLIQYANNPRVVFNLNTYKTKEEMIVATSQTSQYGGDLTNTFGAIQYARKYAYSAASGGRRSATKVMVVVTDGESHDGSMLKAVIDQCNHDNILRFGIAVLGYLNRNALDTKNLIKEIKAIASIPTERYFFNVSDEAALLEKAGTLGEQIFSI", "DFDCPSDWTAYDQHCYLAIGEPQNWYEAERFCTEQAKDGHLVSIQSREEGNFVAQLVSGFMHRSEIYVWIGLRDRREEQQCNPEWNDGSKIIYVNWKEGESKMCQGLTKWTNFHDWNNINCEDLYPFVCKFSAV", "CPLGWSSFDQHCYKVFEPVKNWTEAEEICMQQHKGSRLASIHSSEEEAFVSKLASKALKFTSMWIGLNNPWKDCKWEWSDNARFDYKAWKRRPYCTVMVVKPDRIFWFTRGCEKSVSFVCKFLTDPA"], "NUCLSEQ": [], "DOMAINS": ["Snaclec EMS16 subunit alpha", "C-type lectin", "Key residue for binding with integrin", "Snaclec EMS16 subunit beta", "C-type lectin", "Key residue for binding with integrin", "Integrin alpha-2", "VWFA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7188, "SYSTRES": 454, "PROTATS": 7188, "PROTRES": 454, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0761, "BOXSIZEY": 11.0761, "BOXSIZEZ": 7.85687, "mdName": "replica 1", "mdAtoms": 7188, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0026/files/topology.tpr", "length": 2293804, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0026/files/screenshot.jpg", "length": 21422, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0026/files/trajectory.bin", "length": 431366256, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 5001, "atoms": 7188}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_01.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_02.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_03.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_04.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_05.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_06.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_07.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_08.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_09.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_10.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_11.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_12.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_13.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_14.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_15.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0026/files/structure.pdb", "length": 582263, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0026/files/trajectory.xtc", "length": 136961680, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_00.jpg", "length": 21707, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_01.jpg", "length": 21742, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_02.jpg", "length": 21566, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_03.jpg", "length": 21708, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_04.jpg", "length": 21539, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_05.jpg", "length": 22152, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_06.jpg", "length": 22060, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_07.jpg", "length": 21931, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_08.jpg", "length": 21947, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_09.jpg", "length": 21700, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_10.jpg", "length": 21574, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_11.jpg", "length": 21656, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_12.jpg", "length": 21631, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_13.jpg", "length": 21748, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_14.jpg", "length": 21702, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_15.jpg", "length": 21720, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_16.jpg", "length": 21932, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_17.jpg", "length": 21840, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_18.jpg", "length": 21756, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_19.jpg", "length": 21786, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_20.jpg", "length": 22157, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_21.jpg", "length": 21648, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_22.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_22.jpg", "length": 22204, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_23.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_23.jpg", "length": 21834, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_00.jpg", "length": 25596, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_01.jpg", "length": 25281, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_02.jpg", "length": 25098, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_03.jpg", "length": 24849, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_04.jpg", "length": 25218, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_05.jpg", "length": 25249, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_06.jpg", "length": 25437, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_07.jpg", "length": 25228, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_08.jpg", "length": 25189, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_09.jpg", "length": 25464, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_10.jpg", "length": 24912, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_11.jpg", "length": 25398, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_12.jpg", "length": 25072, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_13.jpg", "length": 24894, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_14.jpg", "length": 25003, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_15.jpg", "length": 25317, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_16.jpg", "length": 24871, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_17.jpg", "length": 25141, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_18.jpg", "length": 24752, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_19.jpg", "length": 25108, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_00.jpg", "length": 23025, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_01.jpg", "length": 23153, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_02.jpg", "length": 23304, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_03.jpg", "length": 23272, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_04.jpg", "length": 22925, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_05.jpg", "length": 22788, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_06.jpg", "length": 23173, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_07.jpg", "length": 22969, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_08.jpg", "length": 22732, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_09.jpg", "length": 22793, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_10.jpg", "length": 23664, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_11.jpg", "length": 23170, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_12.jpg", "length": 23378, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_13.jpg", "length": 22732, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_14.jpg", "length": 22976, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_15.jpg", "length": 23170, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_16.jpg", "length": 23029, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_17.jpg", "length": 23364, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_18.jpg", "length": 22656, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_00.jpg", "length": 21895, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_01.jpg", "length": 21838, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_02.jpg", "length": 22009, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_03.jpg", "length": 21782, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_04.jpg", "length": 21779, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_05.jpg", "length": 22307, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_06.jpg", "length": 21888, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_07.jpg", "length": 22084, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_08.jpg", "length": 22241, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_09.jpg", "length": 21866, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_10.jpg", "length": 22563, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_11.jpg", "length": 21821, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_12.jpg", "length": 21878, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_13.jpg", "length": 22300, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_14.jpg", "length": 22130, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_15.jpg", "length": 22006, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_16.jpg", "length": 21706, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_17.jpg", "length": 21701, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_18.jpg", "length": 21695, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0026/files/pocket_01.pdb", "length": 64521, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0026/files/pocket_02.pdb", "length": 15611, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0026/files/pocket_03.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0026/files/pocket_04.pdb", "length": 12462, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0026/files/pocket_05.pdb", "length": 12127, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0026/files/pocket_06.pdb", "length": 9715, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0026/files/pocket_07.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0026/files/pocket_08.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0026/files/pocket_09.pdb", "length": 5829, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0026/files/pocket_10.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0026", "accession": "A0026", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1V7P", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1V7P"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7T2Q1", "Q7T2Q0", "P17301"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["LIDVVVVCDESNSIYPWDAVKNFLEKFVQGLDIGPTKTQVGLIQYANNPRVVFNLNTYKTKEEMIVATSQTSQYGGDLTNTFGAIQYARKYAYSAASGGRRSATKVMVVVTDGESHDGSMLKAVIDQCNHDNILRFGIAVLGYLNRNALDTKNLIKEIKAIASIPTERYFFNVSDEAALLEKAGTLGEQIFSI", "DFDCPSDWTAYDQHCYLAIGEPQNWYEAERFCTEQAKDGHLVSIQSREEGNFVAQLVSGFMHRSEIYVWIGLRDRREEQQCNPEWNDGSKIIYVNWKEGESKMCQGLTKWTNFHDWNNINCEDLYPFVCKFSAV", "CPLGWSSFDQHCYKVFEPVKNWTEAEEICMQQHKGSRLASIHSSEEEAFVSKLASKALKFTSMWIGLNNPWKDCKWEWSDNARFDYKAWKRRPYCTVMVVKPDRIFWFTRGCEKSVSFVCKFLTDPA"], "NUCLSEQ": [], "DOMAINS": ["Snaclec EMS16 subunit alpha", "C-type lectin", "Key residue for binding with integrin", "Snaclec EMS16 subunit beta", "C-type lectin", "Key residue for binding with integrin", "Integrin alpha-2", "VWFA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7188, "SYSTRES": 454, "PROTATS": 7188, "PROTRES": 454, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0761, "BOXSIZEY": 11.0761, "BOXSIZEZ": 7.85687, "mdName": "replica 1", "mdAtoms": 7188, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0026/files/topology.tpr", "length": 2293804, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0026/files/screenshot.jpg", "length": 21422, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0026/files/trajectory.bin", "length": 431366256, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 5001, "atoms": 7188}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_01.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_02.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_03.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_04.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_05.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_06.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_07.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_08.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_09.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_10.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_11.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_12.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_13.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_14.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0026/files/pca_trajectory_15.bin", "length": 326880, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0, "frames": 20, "atoms": 1362}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0026/files/structure.pdb", "length": 582263, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0026/files/trajectory.xtc", "length": 136961680, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_00.jpg", "length": 21707, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_01.jpg", "length": 21742, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_02.jpg", "length": 21566, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_03.jpg", "length": 21708, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_04.jpg", "length": 21539, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_05.jpg", "length": 22152, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_06.jpg", "length": 22060, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_07.jpg", "length": 21931, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_08.jpg", "length": 21947, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_09.jpg", "length": 21700, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_10.jpg", "length": 21574, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_11.jpg", "length": 21656, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_12.jpg", "length": 21631, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_13.jpg", "length": 21748, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_14.jpg", "length": 21702, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_15.jpg", "length": 21720, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_16.jpg", "length": 21932, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_17.jpg", "length": 21840, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_18.jpg", "length": 21756, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_19.jpg", "length": 21786, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_20.jpg", "length": 22157, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_21.jpg", "length": 21648, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_22.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_22.jpg", "length": 22204, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_00_screenshot_23.jpg", "downloadUrl": "/projects/A0026/files/clusters_00_screenshot_23.jpg", "length": 21834, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_00.jpg", "length": 25596, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_01.jpg", "length": 25281, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_02.jpg", "length": 25098, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_03.jpg", "length": 24849, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_04.jpg", "length": 25218, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_05.jpg", "length": 25249, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_06.jpg", "length": 25437, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_07.jpg", "length": 25228, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_08.jpg", "length": 25189, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_09.jpg", "length": 25464, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_10.jpg", "length": 24912, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_11.jpg", "length": 25398, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_12.jpg", "length": 25072, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_13.jpg", "length": 24894, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_14.jpg", "length": 25003, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_15.jpg", "length": 25317, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_16.jpg", "length": 24871, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_17.jpg", "length": 25141, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_18.jpg", "length": 24752, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0026/files/clusters_01_screenshot_19.jpg", "length": 25108, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_00.jpg", "length": 23025, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_01.jpg", "length": 23153, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_02.jpg", "length": 23304, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_03.jpg", "length": 23272, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_04.jpg", "length": 22925, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_05.jpg", "length": 22788, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_06.jpg", "length": 23173, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_07.jpg", "length": 22969, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_08.jpg", "length": 22732, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_09.jpg", "length": 22793, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_10.jpg", "length": 23664, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_11.jpg", "length": 23170, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_12.jpg", "length": 23378, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_13.jpg", "length": 22732, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_14.jpg", "length": 22976, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_15.jpg", "length": 23170, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_16.jpg", "length": 23029, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_17.jpg", "length": 23364, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_02_screenshot_18.jpg", "length": 22656, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_00.jpg", "length": 21895, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_01.jpg", "length": 21838, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_02.jpg", "length": 22009, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_03.jpg", "length": 21782, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_04.jpg", "length": 21779, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_05.jpg", "length": 22307, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_06.jpg", "length": 21888, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_07.jpg", "length": 22084, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_08.jpg", "length": 22241, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_09.jpg", "length": 21866, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_10.jpg", "length": 22563, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_11.jpg", "length": 21821, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_12.jpg", "length": 21878, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_13.jpg", "length": 22300, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_14.jpg", "length": 22130, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_15.jpg", "length": 22006, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_16.jpg", "length": 21706, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_17.jpg", "length": 21701, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A0026/files/clusters_03_screenshot_18.jpg", "length": 21695, "contentType": "application/octet-stream", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0026/files/pocket_01.pdb", "length": 64521, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0026/files/pocket_02.pdb", "length": 15611, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0026/files/pocket_03.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0026/files/pocket_04.pdb", "length": 12462, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0026/files/pocket_05.pdb", "length": 12127, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0026/files/pocket_06.pdb", "length": 9715, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0026/files/pocket_07.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0026/files/pocket_08.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0026/files/pocket_09.pdb", "length": 5829, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0026/files/pocket_10.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "683f79d2f77378da06299cf3", "md": 0}}]}
|
data/files/A0027/project.json
ADDED
|
@@ -0,0 +1,193 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0027",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1VET",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1VET"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O88653",
|
| 31 |
+
"Q9JHS3"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDSAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELIKVVEV",
|
| 38 |
+
"MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ragulator complex protein LAMTOR3",
|
| 43 |
+
"Required for interaction with LAMTOR2",
|
| 44 |
+
"Ragulator complex protein LAMTOR2",
|
| 45 |
+
"Required for location at endosomes"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 3719,
|
| 57 |
+
"SYSTRES": 240,
|
| 58 |
+
"PROTATS": 3719,
|
| 59 |
+
"PROTRES": 240,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
+
"CARBATS": 0,
|
| 65 |
+
"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
+
"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
+
"CHAINNAMES": null,
|
| 83 |
+
"MEMBRANES": null,
|
| 84 |
+
"CUSTOMS": null,
|
| 85 |
+
"ORIENTATION": null,
|
| 86 |
+
"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
+
"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
+
"BOXSIZEX": 9.52256,
|
| 91 |
+
"BOXSIZEY": 9.52256,
|
| 92 |
+
"BOXSIZEZ": 6.72538,
|
| 93 |
+
"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 3719,
|
| 95 |
+
"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
+
"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
+
"files": [
|
| 104 |
+
"topology.tpr",
|
| 105 |
+
"screenshot.jpg",
|
| 106 |
+
"trajectory.bin",
|
| 107 |
+
"pca_trajectory_01.bin",
|
| 108 |
+
"pca_trajectory_02.bin",
|
| 109 |
+
"pca_trajectory_03.bin",
|
| 110 |
+
"pca_trajectory_04.bin",
|
| 111 |
+
"pca_trajectory_05.bin",
|
| 112 |
+
"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
+
"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"pca_trajectory_13.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
+
"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb",
|
| 165 |
+
"pocket_05.pdb",
|
| 166 |
+
"pocket_06.pdb",
|
| 167 |
+
"pocket_07.pdb"
|
| 168 |
+
],
|
| 169 |
+
"analyses": [
|
| 170 |
+
"clusters",
|
| 171 |
+
"clusters-00",
|
| 172 |
+
"clusters-01",
|
| 173 |
+
"dist-perres",
|
| 174 |
+
"energies",
|
| 175 |
+
"fluctuation",
|
| 176 |
+
"hbonds",
|
| 177 |
+
"interactions",
|
| 178 |
+
"pca",
|
| 179 |
+
"pockets",
|
| 180 |
+
"rgyr",
|
| 181 |
+
"rmsd-pairwise",
|
| 182 |
+
"rmsd-perres",
|
| 183 |
+
"rmsds",
|
| 184 |
+
"sasa",
|
| 185 |
+
"tmscores"
|
| 186 |
+
],
|
| 187 |
+
"mdIndex": 0,
|
| 188 |
+
"mdNumber": 1,
|
| 189 |
+
"refframe": 0,
|
| 190 |
+
"internalId": "683f7b6f2909088afce90800",
|
| 191 |
+
"creationDate": "2025-06-03T22:47:11.000Z",
|
| 192 |
+
"identifier": "A0027"
|
| 193 |
+
}
|
data/files/A0027/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0027", "accession": "A0027", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1VET", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1VET"], "FORCED_REFERENCES": null, "REFERENCES": ["O88653", "Q9JHS3"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDSAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELIKVVEV", "MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP"], "NUCLSEQ": [], "DOMAINS": ["Ragulator complex protein LAMTOR3", "Required for interaction with LAMTOR2", "Ragulator complex protein LAMTOR2", "Required for location at endosomes"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3719, "SYSTRES": 240, "PROTATS": 3719, "PROTRES": 240, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.52256, "BOXSIZEY": 9.52256, "BOXSIZEZ": 6.72538, "mdName": "replica 1", "mdAtoms": 3719, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0027/files/topology.tpr", "length": 1324120, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0027/files/screenshot.jpg", "length": 19517, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0027/files/trajectory.bin", "length": 223184628, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 5001, "atoms": 3719}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_01.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_02.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_03.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_04.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_05.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_06.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_07.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_08.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_09.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_10.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_11.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_12.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_13.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0027/files/structure.pdb", "length": 301274, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0027/files/trajectory.xtc", "length": 70864148, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_00.jpg", "length": 20128, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_01.jpg", "length": 19890, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_02.jpg", "length": 20595, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_03.jpg", "length": 19930, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_04.jpg", "length": 19222, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_05.jpg", "length": 20463, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_06.jpg", "length": 19439, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_07.jpg", "length": 20433, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_08.jpg", "length": 20403, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_09.jpg", "length": 20498, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_10.jpg", "length": 20884, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_11.jpg", "length": 20095, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_12.jpg", "length": 19831, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_13.jpg", "length": 20257, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_14.jpg", "length": 19929, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_15.jpg", "length": 19857, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_16.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_17.jpg", "length": 21032, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_18.jpg", "length": 20000, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_19.jpg", "length": 19950, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_00.jpg", "length": 20719, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_01.jpg", "length": 19902, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_02.jpg", "length": 20336, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_03.jpg", "length": 20289, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_04.jpg", "length": 19772, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_05.jpg", "length": 20279, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_06.jpg", "length": 20092, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_07.jpg", "length": 20231, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_08.jpg", "length": 20354, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_09.jpg", "length": 19781, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_10.jpg", "length": 20491, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_11.jpg", "length": 20087, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_12.jpg", "length": 19900, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_13.jpg", "length": 20101, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_14.jpg", "length": 20339, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_15.jpg", "length": 20186, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_16.jpg", "length": 19870, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_17.jpg", "length": 20067, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_18.jpg", "length": 19899, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0027/files/pocket_01.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0027/files/pocket_02.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0027/files/pocket_03.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0027/files/pocket_04.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0027/files/pocket_05.pdb", "length": 5159, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0027/files/pocket_06.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0027/files/pocket_07.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0027", "accession": "A0027", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1VET", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1VET"], "FORCED_REFERENCES": null, "REFERENCES": ["O88653", "Q9JHS3"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDSAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELIKVVEV", "MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP"], "NUCLSEQ": [], "DOMAINS": ["Ragulator complex protein LAMTOR3", "Required for interaction with LAMTOR2", "Ragulator complex protein LAMTOR2", "Required for location at endosomes"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3719, "SYSTRES": 240, "PROTATS": 3719, "PROTRES": 240, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.52256, "BOXSIZEY": 9.52256, "BOXSIZEZ": 6.72538, "mdName": "replica 1", "mdAtoms": 3719, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0027/files/topology.tpr", "length": 1324120, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0027/files/screenshot.jpg", "length": 19517, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0027/files/trajectory.bin", "length": 223184628, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 5001, "atoms": 3719}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_01.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_02.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_03.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_04.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_05.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_06.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_07.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_08.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_09.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_10.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_11.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_12.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_13.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0027/files/structure.pdb", "length": 301274, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0027/files/trajectory.xtc", "length": 70864148, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_00.jpg", "length": 20128, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_01.jpg", "length": 19890, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_02.jpg", "length": 20595, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_03.jpg", "length": 19930, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_04.jpg", "length": 19222, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_05.jpg", "length": 20463, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_06.jpg", "length": 19439, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_07.jpg", "length": 20433, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_08.jpg", "length": 20403, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_09.jpg", "length": 20498, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_10.jpg", "length": 20884, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_11.jpg", "length": 20095, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_12.jpg", "length": 19831, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_13.jpg", "length": 20257, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_14.jpg", "length": 19929, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_15.jpg", "length": 19857, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_16.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_17.jpg", "length": 21032, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_18.jpg", "length": 20000, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_19.jpg", "length": 19950, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_00.jpg", "length": 20719, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_01.jpg", "length": 19902, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_02.jpg", "length": 20336, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_03.jpg", "length": 20289, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_04.jpg", "length": 19772, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_05.jpg", "length": 20279, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_06.jpg", "length": 20092, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_07.jpg", "length": 20231, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_08.jpg", "length": 20354, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_09.jpg", "length": 19781, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_10.jpg", "length": 20491, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_11.jpg", "length": 20087, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_12.jpg", "length": 19900, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_13.jpg", "length": 20101, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_14.jpg", "length": 20339, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_15.jpg", "length": 20186, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_16.jpg", "length": 19870, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_17.jpg", "length": 20067, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_18.jpg", "length": 19899, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0027/files/pocket_01.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0027/files/pocket_02.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0027/files/pocket_03.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0027/files/pocket_04.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0027/files/pocket_05.pdb", "length": 5159, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0027/files/pocket_06.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0027/files/pocket_07.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0027", "accession": "A0027", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1VET", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1VET"], "FORCED_REFERENCES": null, "REFERENCES": ["O88653", "Q9JHS3"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDSAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELIKVVEV", "MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDSLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEP"], "NUCLSEQ": [], "DOMAINS": ["Ragulator complex protein LAMTOR3", "Required for interaction with LAMTOR2", "Ragulator complex protein LAMTOR2", "Required for location at endosomes"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3719, "SYSTRES": 240, "PROTATS": 3719, "PROTRES": 240, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.52256, "BOXSIZEY": 9.52256, "BOXSIZEZ": 6.72538, "mdName": "replica 1", "mdAtoms": 3719, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0027/files/topology.tpr", "length": 1324120, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0027/files/screenshot.jpg", "length": 19517, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0027/files/trajectory.bin", "length": 223184628, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 5001, "atoms": 3719}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_01.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_02.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_03.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_04.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_05.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_06.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_07.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_08.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_09.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_10.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_11.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_12.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0027/files/pca_trajectory_13.bin", "length": 172800, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0, "frames": 20, "atoms": 720}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0027/files/structure.pdb", "length": 301274, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0027/files/trajectory.xtc", "length": 70864148, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_00.jpg", "length": 20128, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_01.jpg", "length": 19890, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_02.jpg", "length": 20595, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_03.jpg", "length": 19930, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_04.jpg", "length": 19222, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_05.jpg", "length": 20463, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_06.jpg", "length": 19439, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_07.jpg", "length": 20433, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_08.jpg", "length": 20403, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_09.jpg", "length": 20498, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_10.jpg", "length": 20884, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_11.jpg", "length": 20095, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_12.jpg", "length": 19831, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_13.jpg", "length": 20257, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_14.jpg", "length": 19929, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_15.jpg", "length": 19857, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_16.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_17.jpg", "length": 21032, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_18.jpg", "length": 20000, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0027/files/clusters_00_screenshot_19.jpg", "length": 19950, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_00.jpg", "length": 20719, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_01.jpg", "length": 19902, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_02.jpg", "length": 20336, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_03.jpg", "length": 20289, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_04.jpg", "length": 19772, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_05.jpg", "length": 20279, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_06.jpg", "length": 20092, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_07.jpg", "length": 20231, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_08.jpg", "length": 20354, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_09.jpg", "length": 19781, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_10.jpg", "length": 20491, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_11.jpg", "length": 20087, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_12.jpg", "length": 19900, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_13.jpg", "length": 20101, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_14.jpg", "length": 20339, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_15.jpg", "length": 20186, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_16.jpg", "length": 19870, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_17.jpg", "length": 20067, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0027/files/clusters_01_screenshot_18.jpg", "length": 19899, "contentType": "application/octet-stream", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0027/files/pocket_01.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0027/files/pocket_02.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0027/files/pocket_03.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0027/files/pocket_04.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0027/files/pocket_05.pdb", "length": 5159, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0027/files/pocket_06.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0027/files/pocket_07.pdb", "length": 3283, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7b6f2909088afce90800", "md": 0}}]}
|
data/files/A0028/project.json
ADDED
|
@@ -0,0 +1,193 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0028",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1WQJ",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1WQJ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P22692",
|
| 31 |
+
"P05019"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"PETLCGAELVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCAP",
|
| 38 |
+
"AIHCPPCSEEKLARCRPPVGCEELVREPGCGCCATCALGLGMPCGVYTPRCGSGLRCYPPRGVEKPLHTLMHGQGVCMEL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Insulin-like growth factor-binding protein 4",
|
| 43 |
+
"IGFBP N-terminal",
|
| 44 |
+
"Insulin-like growth factor 1",
|
| 45 |
+
"B",
|
| 46 |
+
"C",
|
| 47 |
+
"A",
|
| 48 |
+
"D"
|
| 49 |
+
],
|
| 50 |
+
"FRAMESTEP": 0.1,
|
| 51 |
+
"TIMESTEP": 2,
|
| 52 |
+
"TEMP": 310,
|
| 53 |
+
"ENSEMBLE": "NPT",
|
| 54 |
+
"FF": [
|
| 55 |
+
"CHARMM36m"
|
| 56 |
+
],
|
| 57 |
+
"WAT": "TIP3P",
|
| 58 |
+
"BOXTYPE": "Dodecahedron",
|
| 59 |
+
"SYSTATS": 2080,
|
| 60 |
+
"SYSTRES": 142,
|
| 61 |
+
"PROTATS": 2080,
|
| 62 |
+
"PROTRES": 142,
|
| 63 |
+
"NUCLATS": 0,
|
| 64 |
+
"NUCLRES": 0,
|
| 65 |
+
"LIPIATS": 0,
|
| 66 |
+
"LIPIRES": 0,
|
| 67 |
+
"CARBATS": 0,
|
| 68 |
+
"CARBRES": 0,
|
| 69 |
+
"SOLVATS": 0,
|
| 70 |
+
"SOLVRES": 0,
|
| 71 |
+
"COUNCAT": 0,
|
| 72 |
+
"COUNANI": 0,
|
| 73 |
+
"COUNION": 0,
|
| 74 |
+
"INTERACTIONS": [
|
| 75 |
+
{
|
| 76 |
+
"name": "chain A-chain B interaction",
|
| 77 |
+
"agent_1": "chain A",
|
| 78 |
+
"agent_2": "chain B",
|
| 79 |
+
"selection_1": "chain A",
|
| 80 |
+
"selection_2": "chain B",
|
| 81 |
+
"type": "protein-protein"
|
| 82 |
+
}
|
| 83 |
+
],
|
| 84 |
+
"PBC_SELECTION": null,
|
| 85 |
+
"CHAINNAMES": null,
|
| 86 |
+
"MEMBRANES": null,
|
| 87 |
+
"CUSTOMS": null,
|
| 88 |
+
"ORIENTATION": null,
|
| 89 |
+
"PTM": [],
|
| 90 |
+
"MULTIMERIC": null,
|
| 91 |
+
"COLLECTIONS": "dynarepo",
|
| 92 |
+
"WARNINGS": [],
|
| 93 |
+
"BOXSIZEX": 8.60371,
|
| 94 |
+
"BOXSIZEY": 8.60371,
|
| 95 |
+
"BOXSIZEZ": 6.0882,
|
| 96 |
+
"mdName": "replica 1",
|
| 97 |
+
"mdAtoms": 2080,
|
| 98 |
+
"mdFrames": 5001
|
| 99 |
+
},
|
| 100 |
+
"mds": [
|
| 101 |
+
"replica 1",
|
| 102 |
+
"replica 2",
|
| 103 |
+
"replica 3"
|
| 104 |
+
],
|
| 105 |
+
"mdref": 0,
|
| 106 |
+
"files": [
|
| 107 |
+
"topology.tpr",
|
| 108 |
+
"screenshot.jpg",
|
| 109 |
+
"trajectory.bin",
|
| 110 |
+
"pca_trajectory_01.bin",
|
| 111 |
+
"pca_trajectory_02.bin",
|
| 112 |
+
"pca_trajectory_03.bin",
|
| 113 |
+
"pca_trajectory_04.bin",
|
| 114 |
+
"pca_trajectory_05.bin",
|
| 115 |
+
"pca_trajectory_06.bin",
|
| 116 |
+
"pca_trajectory_07.bin",
|
| 117 |
+
"pca_trajectory_08.bin",
|
| 118 |
+
"pca_trajectory_09.bin",
|
| 119 |
+
"pca_trajectory_10.bin",
|
| 120 |
+
"pca_trajectory_11.bin",
|
| 121 |
+
"structure.pdb",
|
| 122 |
+
"trajectory.xtc",
|
| 123 |
+
"clusters_00_screenshot_00.jpg",
|
| 124 |
+
"clusters_00_screenshot_01.jpg",
|
| 125 |
+
"clusters_00_screenshot_02.jpg",
|
| 126 |
+
"clusters_00_screenshot_03.jpg",
|
| 127 |
+
"clusters_00_screenshot_04.jpg",
|
| 128 |
+
"clusters_00_screenshot_05.jpg",
|
| 129 |
+
"clusters_00_screenshot_06.jpg",
|
| 130 |
+
"clusters_00_screenshot_07.jpg",
|
| 131 |
+
"clusters_00_screenshot_08.jpg",
|
| 132 |
+
"clusters_00_screenshot_09.jpg",
|
| 133 |
+
"clusters_00_screenshot_10.jpg",
|
| 134 |
+
"clusters_00_screenshot_11.jpg",
|
| 135 |
+
"clusters_00_screenshot_12.jpg",
|
| 136 |
+
"clusters_00_screenshot_13.jpg",
|
| 137 |
+
"clusters_00_screenshot_14.jpg",
|
| 138 |
+
"clusters_00_screenshot_15.jpg",
|
| 139 |
+
"clusters_00_screenshot_16.jpg",
|
| 140 |
+
"clusters_00_screenshot_17.jpg",
|
| 141 |
+
"clusters_00_screenshot_18.jpg",
|
| 142 |
+
"clusters_00_screenshot_19.jpg",
|
| 143 |
+
"clusters_00_screenshot_20.jpg",
|
| 144 |
+
"clusters_00_screenshot_21.jpg",
|
| 145 |
+
"clusters_01_screenshot_00.jpg",
|
| 146 |
+
"clusters_01_screenshot_01.jpg",
|
| 147 |
+
"clusters_01_screenshot_02.jpg",
|
| 148 |
+
"clusters_01_screenshot_03.jpg",
|
| 149 |
+
"clusters_01_screenshot_04.jpg",
|
| 150 |
+
"clusters_01_screenshot_05.jpg",
|
| 151 |
+
"clusters_01_screenshot_06.jpg",
|
| 152 |
+
"clusters_01_screenshot_07.jpg",
|
| 153 |
+
"clusters_01_screenshot_08.jpg",
|
| 154 |
+
"clusters_01_screenshot_09.jpg",
|
| 155 |
+
"clusters_01_screenshot_10.jpg",
|
| 156 |
+
"clusters_01_screenshot_11.jpg",
|
| 157 |
+
"clusters_01_screenshot_12.jpg",
|
| 158 |
+
"clusters_01_screenshot_13.jpg",
|
| 159 |
+
"clusters_01_screenshot_14.jpg",
|
| 160 |
+
"clusters_01_screenshot_15.jpg",
|
| 161 |
+
"clusters_01_screenshot_16.jpg",
|
| 162 |
+
"clusters_01_screenshot_17.jpg",
|
| 163 |
+
"clusters_01_screenshot_18.jpg",
|
| 164 |
+
"clusters_01_screenshot_19.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb"
|
| 168 |
+
],
|
| 169 |
+
"analyses": [
|
| 170 |
+
"clusters",
|
| 171 |
+
"clusters-00",
|
| 172 |
+
"clusters-01",
|
| 173 |
+
"dist-perres",
|
| 174 |
+
"energies",
|
| 175 |
+
"fluctuation",
|
| 176 |
+
"hbonds",
|
| 177 |
+
"interactions",
|
| 178 |
+
"pca",
|
| 179 |
+
"pockets",
|
| 180 |
+
"rgyr",
|
| 181 |
+
"rmsd-pairwise",
|
| 182 |
+
"rmsd-perres",
|
| 183 |
+
"rmsds",
|
| 184 |
+
"sasa",
|
| 185 |
+
"tmscores"
|
| 186 |
+
],
|
| 187 |
+
"mdIndex": 0,
|
| 188 |
+
"mdNumber": 1,
|
| 189 |
+
"refframe": 0,
|
| 190 |
+
"internalId": "683f7c7cdf7837a592e2fc5b",
|
| 191 |
+
"creationDate": "2025-06-03T22:51:40.000Z",
|
| 192 |
+
"identifier": "A0028"
|
| 193 |
+
}
|
data/files/A0028/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0028", "accession": "A0028", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WQJ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WQJ"], "FORCED_REFERENCES": null, "REFERENCES": ["P22692", "P05019"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PETLCGAELVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCAP", "AIHCPPCSEEKLARCRPPVGCEELVREPGCGCCATCALGLGMPCGVYTPRCGSGLRCYPPRGVEKPLHTLMHGQGVCMEL"], "NUCLSEQ": [], "DOMAINS": ["Insulin-like growth factor-binding protein 4", "IGFBP N-terminal", "Insulin-like growth factor 1", "B", "C", "A", "D"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2080, "SYSTRES": 142, "PROTATS": 2080, "PROTRES": 142, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.60371, "BOXSIZEY": 8.60371, "BOXSIZEZ": 6.0882, "mdName": "replica 1", "mdAtoms": 2080, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0028/files/topology.tpr", "length": 875412, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0028/files/screenshot.jpg", "length": 17233, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0028/files/trajectory.bin", "length": 124824960, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 5001, "atoms": 2080}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_01.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_02.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_03.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_04.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_05.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_06.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_07.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_08.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_09.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_10.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_11.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0028/files/structure.pdb", "length": 168515, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0028/files/trajectory.xtc", "length": 39945396, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_00.jpg", "length": 16404, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_01.jpg", "length": 15867, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_02.jpg", "length": 16198, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_03.jpg", "length": 15868, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_04.jpg", "length": 15832, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_05.jpg", "length": 15784, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_06.jpg", "length": 15168, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_07.jpg", "length": 15861, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_08.jpg", "length": 15831, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_09.jpg", "length": 15607, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_10.jpg", "length": 15658, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_11.jpg", "length": 16055, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_12.jpg", "length": 15258, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_13.jpg", "length": 15622, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_14.jpg", "length": 15839, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_15.jpg", "length": 16005, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_16.jpg", "length": 15586, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_17.jpg", "length": 16212, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_18.jpg", "length": 15855, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_19.jpg", "length": 15650, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_20.jpg", "length": 14839, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_21.jpg", "length": 15677, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_00.jpg", "length": 17778, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_01.jpg", "length": 17261, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_02.jpg", "length": 17112, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_03.jpg", "length": 17438, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_04.jpg", "length": 16879, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_05.jpg", "length": 17137, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_06.jpg", "length": 16774, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_07.jpg", "length": 17291, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_08.jpg", "length": 16541, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_09.jpg", "length": 16387, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_10.jpg", "length": 16329, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_11.jpg", "length": 16791, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_12.jpg", "length": 16772, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_13.jpg", "length": 17185, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_14.jpg", "length": 16633, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_15.jpg", "length": 17281, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_16.jpg", "length": 16872, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_17.jpg", "length": 16899, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_18.jpg", "length": 16980, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_19.jpg", "length": 17340, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0028/files/pocket_01.pdb", "length": 15276, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0028/files/pocket_02.pdb", "length": 14539, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0028/files/pocket_03.pdb", "length": 5293, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0028", "accession": "A0028", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WQJ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WQJ"], "FORCED_REFERENCES": null, "REFERENCES": ["P22692", "P05019"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PETLCGAELVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCAP", "AIHCPPCSEEKLARCRPPVGCEELVREPGCGCCATCALGLGMPCGVYTPRCGSGLRCYPPRGVEKPLHTLMHGQGVCMEL"], "NUCLSEQ": [], "DOMAINS": ["Insulin-like growth factor-binding protein 4", "IGFBP N-terminal", "Insulin-like growth factor 1", "B", "C", "A", "D"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2080, "SYSTRES": 142, "PROTATS": 2080, "PROTRES": 142, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.60371, "BOXSIZEY": 8.60371, "BOXSIZEZ": 6.0882, "mdName": "replica 1", "mdAtoms": 2080, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0028/files/topology.tpr", "length": 875412, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0028/files/screenshot.jpg", "length": 17233, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0028/files/trajectory.bin", "length": 124824960, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 5001, "atoms": 2080}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_01.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_02.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_03.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_04.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_05.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_06.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_07.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_08.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_09.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_10.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_11.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0028/files/structure.pdb", "length": 168515, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0028/files/trajectory.xtc", "length": 39945396, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_00.jpg", "length": 16404, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_01.jpg", "length": 15867, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_02.jpg", "length": 16198, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_03.jpg", "length": 15868, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_04.jpg", "length": 15832, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_05.jpg", "length": 15784, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_06.jpg", "length": 15168, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_07.jpg", "length": 15861, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_08.jpg", "length": 15831, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_09.jpg", "length": 15607, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_10.jpg", "length": 15658, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_11.jpg", "length": 16055, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_12.jpg", "length": 15258, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_13.jpg", "length": 15622, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_14.jpg", "length": 15839, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_15.jpg", "length": 16005, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_16.jpg", "length": 15586, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_17.jpg", "length": 16212, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_18.jpg", "length": 15855, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_19.jpg", "length": 15650, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_20.jpg", "length": 14839, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_21.jpg", "length": 15677, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_00.jpg", "length": 17778, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_01.jpg", "length": 17261, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_02.jpg", "length": 17112, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_03.jpg", "length": 17438, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_04.jpg", "length": 16879, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_05.jpg", "length": 17137, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_06.jpg", "length": 16774, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_07.jpg", "length": 17291, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_08.jpg", "length": 16541, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_09.jpg", "length": 16387, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_10.jpg", "length": 16329, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_11.jpg", "length": 16791, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_12.jpg", "length": 16772, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_13.jpg", "length": 17185, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_14.jpg", "length": 16633, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_15.jpg", "length": 17281, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_16.jpg", "length": 16872, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_17.jpg", "length": 16899, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_18.jpg", "length": 16980, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_19.jpg", "length": 17340, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0028/files/pocket_01.pdb", "length": 15276, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0028/files/pocket_02.pdb", "length": 14539, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0028/files/pocket_03.pdb", "length": 5293, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0028", "accession": "A0028", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WQJ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WQJ"], "FORCED_REFERENCES": null, "REFERENCES": ["P22692", "P05019"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PETLCGAELVDALQFVCGDRGFYFNKPTGYGSSSRRAPQTGIVDECCFRSCDLRRLEMYCAP", "AIHCPPCSEEKLARCRPPVGCEELVREPGCGCCATCALGLGMPCGVYTPRCGSGLRCYPPRGVEKPLHTLMHGQGVCMEL"], "NUCLSEQ": [], "DOMAINS": ["Insulin-like growth factor-binding protein 4", "IGFBP N-terminal", "Insulin-like growth factor 1", "B", "C", "A", "D"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2080, "SYSTRES": 142, "PROTATS": 2080, "PROTRES": 142, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.60371, "BOXSIZEY": 8.60371, "BOXSIZEZ": 6.0882, "mdName": "replica 1", "mdAtoms": 2080, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0028/files/topology.tpr", "length": 875412, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0028/files/screenshot.jpg", "length": 17233, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0028/files/trajectory.bin", "length": 124824960, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 5001, "atoms": 2080}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_01.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_02.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_03.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_04.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_05.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_06.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_07.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_08.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_09.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_10.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0028/files/pca_trajectory_11.bin", "length": 102240, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0, "frames": 20, "atoms": 426}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0028/files/structure.pdb", "length": 168515, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0028/files/trajectory.xtc", "length": 39945396, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_00.jpg", "length": 16404, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_01.jpg", "length": 15867, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_02.jpg", "length": 16198, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_03.jpg", "length": 15868, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_04.jpg", "length": 15832, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_05.jpg", "length": 15784, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_06.jpg", "length": 15168, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_07.jpg", "length": 15861, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_08.jpg", "length": 15831, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_09.jpg", "length": 15607, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_10.jpg", "length": 15658, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_11.jpg", "length": 16055, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_12.jpg", "length": 15258, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_13.jpg", "length": 15622, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_14.jpg", "length": 15839, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_15.jpg", "length": 16005, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_16.jpg", "length": 15586, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_17.jpg", "length": 16212, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_18.jpg", "length": 15855, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_19.jpg", "length": 15650, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_20.jpg", "length": 14839, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0028/files/clusters_00_screenshot_21.jpg", "length": 15677, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_00.jpg", "length": 17778, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_01.jpg", "length": 17261, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_02.jpg", "length": 17112, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_03.jpg", "length": 17438, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_04.jpg", "length": 16879, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_05.jpg", "length": 17137, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_06.jpg", "length": 16774, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_07.jpg", "length": 17291, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_08.jpg", "length": 16541, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_09.jpg", "length": 16387, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_10.jpg", "length": 16329, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_11.jpg", "length": 16791, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_12.jpg", "length": 16772, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_13.jpg", "length": 17185, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_14.jpg", "length": 16633, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_15.jpg", "length": 17281, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_16.jpg", "length": 16872, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_17.jpg", "length": 16899, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_18.jpg", "length": 16980, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0028/files/clusters_01_screenshot_19.jpg", "length": 17340, "contentType": "application/octet-stream", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0028/files/pocket_01.pdb", "length": 15276, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0028/files/pocket_02.pdb", "length": 14539, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0028/files/pocket_03.pdb", "length": 5293, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7c7cdf7837a592e2fc5b", "md": 0}}]}
|
data/files/A0029/project.json
ADDED
|
@@ -0,0 +1,196 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A0029",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1WR6",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1WR6"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9NZ52",
|
| 31 |
+
"P0CH28"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR",
|
| 38 |
+
"VTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQ"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"ADP-ribosylation factor-binding protein GGA3",
|
| 43 |
+
"GAT",
|
| 44 |
+
"Binds to ARF1 (in long isoform)",
|
| 45 |
+
"Unstructured hinge",
|
| 46 |
+
"Ubiquitin",
|
| 47 |
+
"Ubiquitin-like 2"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 2615,
|
| 59 |
+
"SYSTRES": 162,
|
| 60 |
+
"PROTATS": 2615,
|
| 61 |
+
"PROTRES": 162,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
}
|
| 82 |
+
],
|
| 83 |
+
"PBC_SELECTION": null,
|
| 84 |
+
"CHAINNAMES": null,
|
| 85 |
+
"MEMBRANES": null,
|
| 86 |
+
"CUSTOMS": null,
|
| 87 |
+
"ORIENTATION": null,
|
| 88 |
+
"PTM": [],
|
| 89 |
+
"MULTIMERIC": null,
|
| 90 |
+
"COLLECTIONS": "dynarepo",
|
| 91 |
+
"WARNINGS": [],
|
| 92 |
+
"BOXSIZEX": 8.49232,
|
| 93 |
+
"BOXSIZEY": 8.49232,
|
| 94 |
+
"BOXSIZEZ": 5.98384,
|
| 95 |
+
"mdName": "replica 1",
|
| 96 |
+
"mdAtoms": 2615,
|
| 97 |
+
"mdFrames": 5001
|
| 98 |
+
},
|
| 99 |
+
"mds": [
|
| 100 |
+
"replica 1",
|
| 101 |
+
"replica 2",
|
| 102 |
+
"replica 3"
|
| 103 |
+
],
|
| 104 |
+
"mdref": 0,
|
| 105 |
+
"files": [
|
| 106 |
+
"topology.tpr",
|
| 107 |
+
"screenshot.jpg",
|
| 108 |
+
"trajectory.bin",
|
| 109 |
+
"pca_trajectory_01.bin",
|
| 110 |
+
"pca_trajectory_02.bin",
|
| 111 |
+
"pca_trajectory_03.bin",
|
| 112 |
+
"pca_trajectory_04.bin",
|
| 113 |
+
"pca_trajectory_05.bin",
|
| 114 |
+
"pca_trajectory_06.bin",
|
| 115 |
+
"pca_trajectory_07.bin",
|
| 116 |
+
"pca_trajectory_08.bin",
|
| 117 |
+
"pca_trajectory_09.bin",
|
| 118 |
+
"pca_trajectory_10.bin",
|
| 119 |
+
"pca_trajectory_11.bin",
|
| 120 |
+
"pca_trajectory_12.bin",
|
| 121 |
+
"pca_trajectory_13.bin",
|
| 122 |
+
"structure.pdb",
|
| 123 |
+
"trajectory.xtc",
|
| 124 |
+
"clusters_00_screenshot_00.jpg",
|
| 125 |
+
"clusters_00_screenshot_01.jpg",
|
| 126 |
+
"clusters_00_screenshot_02.jpg",
|
| 127 |
+
"clusters_00_screenshot_03.jpg",
|
| 128 |
+
"clusters_00_screenshot_04.jpg",
|
| 129 |
+
"clusters_00_screenshot_05.jpg",
|
| 130 |
+
"clusters_00_screenshot_06.jpg",
|
| 131 |
+
"clusters_00_screenshot_07.jpg",
|
| 132 |
+
"clusters_00_screenshot_08.jpg",
|
| 133 |
+
"clusters_00_screenshot_09.jpg",
|
| 134 |
+
"clusters_00_screenshot_10.jpg",
|
| 135 |
+
"clusters_00_screenshot_11.jpg",
|
| 136 |
+
"clusters_00_screenshot_12.jpg",
|
| 137 |
+
"clusters_00_screenshot_13.jpg",
|
| 138 |
+
"clusters_00_screenshot_14.jpg",
|
| 139 |
+
"clusters_00_screenshot_15.jpg",
|
| 140 |
+
"clusters_00_screenshot_16.jpg",
|
| 141 |
+
"clusters_00_screenshot_17.jpg",
|
| 142 |
+
"clusters_00_screenshot_18.jpg",
|
| 143 |
+
"clusters_00_screenshot_19.jpg",
|
| 144 |
+
"clusters_00_screenshot_20.jpg",
|
| 145 |
+
"clusters_00_screenshot_21.jpg",
|
| 146 |
+
"clusters_00_screenshot_22.jpg",
|
| 147 |
+
"clusters_00_screenshot_23.jpg",
|
| 148 |
+
"clusters_00_screenshot_24.jpg",
|
| 149 |
+
"clusters_01_screenshot_00.jpg",
|
| 150 |
+
"clusters_01_screenshot_01.jpg",
|
| 151 |
+
"clusters_01_screenshot_02.jpg",
|
| 152 |
+
"clusters_01_screenshot_03.jpg",
|
| 153 |
+
"clusters_01_screenshot_04.jpg",
|
| 154 |
+
"clusters_01_screenshot_05.jpg",
|
| 155 |
+
"clusters_01_screenshot_06.jpg",
|
| 156 |
+
"clusters_01_screenshot_07.jpg",
|
| 157 |
+
"clusters_01_screenshot_08.jpg",
|
| 158 |
+
"clusters_01_screenshot_09.jpg",
|
| 159 |
+
"clusters_01_screenshot_10.jpg",
|
| 160 |
+
"clusters_01_screenshot_11.jpg",
|
| 161 |
+
"clusters_01_screenshot_12.jpg",
|
| 162 |
+
"clusters_01_screenshot_13.jpg",
|
| 163 |
+
"clusters_01_screenshot_14.jpg",
|
| 164 |
+
"clusters_01_screenshot_15.jpg",
|
| 165 |
+
"clusters_01_screenshot_16.jpg",
|
| 166 |
+
"clusters_01_screenshot_17.jpg",
|
| 167 |
+
"clusters_01_screenshot_18.jpg",
|
| 168 |
+
"clusters_01_screenshot_19.jpg",
|
| 169 |
+
"pocket_01.pdb",
|
| 170 |
+
"pocket_02.pdb"
|
| 171 |
+
],
|
| 172 |
+
"analyses": [
|
| 173 |
+
"clusters",
|
| 174 |
+
"clusters-00",
|
| 175 |
+
"clusters-01",
|
| 176 |
+
"dist-perres",
|
| 177 |
+
"energies",
|
| 178 |
+
"fluctuation",
|
| 179 |
+
"hbonds",
|
| 180 |
+
"interactions",
|
| 181 |
+
"pca",
|
| 182 |
+
"pockets",
|
| 183 |
+
"rgyr",
|
| 184 |
+
"rmsd-pairwise",
|
| 185 |
+
"rmsd-perres",
|
| 186 |
+
"rmsds",
|
| 187 |
+
"sasa",
|
| 188 |
+
"tmscores"
|
| 189 |
+
],
|
| 190 |
+
"mdIndex": 0,
|
| 191 |
+
"mdNumber": 1,
|
| 192 |
+
"refframe": 0,
|
| 193 |
+
"internalId": "683f7d5d13505ed724cd3ed8",
|
| 194 |
+
"creationDate": "2025-06-03T22:55:25.000Z",
|
| 195 |
+
"identifier": "A0029"
|
| 196 |
+
}
|
data/files/A0029/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0029", "accession": "A0029", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WR6", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WR6"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZ52", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR", "VTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQ"], "NUCLSEQ": [], "DOMAINS": ["ADP-ribosylation factor-binding protein GGA3", "GAT", "Binds to ARF1 (in long isoform)", "Unstructured hinge", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2615, "SYSTRES": 162, "PROTATS": 2615, "PROTRES": 162, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.49232, "BOXSIZEY": 8.49232, "BOXSIZEZ": 5.98384, "mdName": "replica 1", "mdAtoms": 2615, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0029/files/topology.tpr", "length": 1007260, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0029/files/screenshot.jpg", "length": 18249, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0029/files/trajectory.bin", "length": 156931380, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 5001, "atoms": 2615}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_01.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_02.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_03.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_04.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_05.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_06.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_07.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_08.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_09.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_10.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_11.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_12.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_13.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0029/files/structure.pdb", "length": 211850, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0029/files/trajectory.xtc", "length": 50010620, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_00.jpg", "length": 18608, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_01.jpg", "length": 18438, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_02.jpg", "length": 17867, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_03.jpg", "length": 18669, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_04.jpg", "length": 18193, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_05.jpg", "length": 18464, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_06.jpg", "length": 18732, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_07.jpg", "length": 18186, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_08.jpg", "length": 18301, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_09.jpg", "length": 18208, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_10.jpg", "length": 17916, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_11.jpg", "length": 18475, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_12.jpg", "length": 19040, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_13.jpg", "length": 18582, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_14.jpg", "length": 18581, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_15.jpg", "length": 18413, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_16.jpg", "length": 18873, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_17.jpg", "length": 18470, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_18.jpg", "length": 18551, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_19.jpg", "length": 19126, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_20.jpg", "length": 18877, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_21.jpg", "length": 18702, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_22.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_22.jpg", "length": 18452, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_23.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_23.jpg", "length": 18993, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_24.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_24.jpg", "length": 18720, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_00.jpg", "length": 18704, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_01.jpg", "length": 18800, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_02.jpg", "length": 18347, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_03.jpg", "length": 18949, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_04.jpg", "length": 18768, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_05.jpg", "length": 19092, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_06.jpg", "length": 18731, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_07.jpg", "length": 18696, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_08.jpg", "length": 19051, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_09.jpg", "length": 19207, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_10.jpg", "length": 19299, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_11.jpg", "length": 18826, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_12.jpg", "length": 19410, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_13.jpg", "length": 19128, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_14.jpg", "length": 18777, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_15.jpg", "length": 19425, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_16.jpg", "length": 18606, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_17.jpg", "length": 18791, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_18.jpg", "length": 19774, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_19.jpg", "length": 19064, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0029/files/pocket_01.pdb", "length": 11256, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0029/files/pocket_02.pdb", "length": 8040, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A0029", "accession": "A0029", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WR6", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WR6"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZ52", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR", "VTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQ"], "NUCLSEQ": [], "DOMAINS": ["ADP-ribosylation factor-binding protein GGA3", "GAT", "Binds to ARF1 (in long isoform)", "Unstructured hinge", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2615, "SYSTRES": 162, "PROTATS": 2615, "PROTRES": 162, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.49232, "BOXSIZEY": 8.49232, "BOXSIZEZ": 5.98384, "mdName": "replica 1", "mdAtoms": 2615, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0029/files/topology.tpr", "length": 1007260, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0029/files/screenshot.jpg", "length": 18249, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0029/files/trajectory.bin", "length": 156931380, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 5001, "atoms": 2615}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_01.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_02.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_03.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_04.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_05.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_06.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_07.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_08.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_09.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_10.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_11.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_12.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_13.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0029/files/structure.pdb", "length": 211850, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0029/files/trajectory.xtc", "length": 50010620, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_00.jpg", "length": 18608, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_01.jpg", "length": 18438, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_02.jpg", "length": 17867, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_03.jpg", "length": 18669, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_04.jpg", "length": 18193, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_05.jpg", "length": 18464, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_06.jpg", "length": 18732, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_07.jpg", "length": 18186, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_08.jpg", "length": 18301, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_09.jpg", "length": 18208, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_10.jpg", "length": 17916, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_11.jpg", "length": 18475, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_12.jpg", "length": 19040, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_13.jpg", "length": 18582, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_14.jpg", "length": 18581, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_15.jpg", "length": 18413, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_16.jpg", "length": 18873, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_17.jpg", "length": 18470, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_18.jpg", "length": 18551, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_19.jpg", "length": 19126, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_20.jpg", "length": 18877, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_21.jpg", "length": 18702, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_22.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_22.jpg", "length": 18452, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_23.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_23.jpg", "length": 18993, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_24.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_24.jpg", "length": 18720, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_00.jpg", "length": 18704, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_01.jpg", "length": 18800, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_02.jpg", "length": 18347, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_03.jpg", "length": 18949, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_04.jpg", "length": 18768, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_05.jpg", "length": 19092, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_06.jpg", "length": 18731, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_07.jpg", "length": 18696, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_08.jpg", "length": 19051, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_09.jpg", "length": 19207, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_10.jpg", "length": 19299, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_11.jpg", "length": 18826, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_12.jpg", "length": 19410, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_13.jpg", "length": 19128, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_14.jpg", "length": 18777, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_15.jpg", "length": 19425, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_16.jpg", "length": 18606, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_17.jpg", "length": 18791, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_18.jpg", "length": 19774, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_19.jpg", "length": 19064, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0029/files/pocket_01.pdb", "length": 11256, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0029/files/pocket_02.pdb", "length": 8040, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A0029", "accession": "A0029", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WR6", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WR6"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZ52", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR", "VTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQ"], "NUCLSEQ": [], "DOMAINS": ["ADP-ribosylation factor-binding protein GGA3", "GAT", "Binds to ARF1 (in long isoform)", "Unstructured hinge", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2615, "SYSTRES": 162, "PROTATS": 2615, "PROTRES": 162, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.49232, "BOXSIZEY": 8.49232, "BOXSIZEZ": 5.98384, "mdName": "replica 1", "mdAtoms": 2615, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0029/files/topology.tpr", "length": 1007260, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0029/files/screenshot.jpg", "length": 18249, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0029/files/trajectory.bin", "length": 156931380, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 5001, "atoms": 2615}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_01.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_02.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_03.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_04.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_05.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_06.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_07.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_08.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_09.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_10.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_11.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_12.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0029/files/pca_trajectory_13.bin", "length": 116640, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0, "frames": 20, "atoms": 486}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0029/files/structure.pdb", "length": 211850, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0029/files/trajectory.xtc", "length": 50010620, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_00.jpg", "length": 18608, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_01.jpg", "length": 18438, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_02.jpg", "length": 17867, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_03.jpg", "length": 18669, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_04.jpg", "length": 18193, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_05.jpg", "length": 18464, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_06.jpg", "length": 18732, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_07.jpg", "length": 18186, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_08.jpg", "length": 18301, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_09.jpg", "length": 18208, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_10.jpg", "length": 17916, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_11.jpg", "length": 18475, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_12.jpg", "length": 19040, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_13.jpg", "length": 18582, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_14.jpg", "length": 18581, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_15.jpg", "length": 18413, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_16.jpg", "length": 18873, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_17.jpg", "length": 18470, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_18.jpg", "length": 18551, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_19.jpg", "length": 19126, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_20.jpg", "length": 18877, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_21.jpg", "length": 18702, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_22.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_22.jpg", "length": 18452, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_23.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_23.jpg", "length": 18993, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_00_screenshot_24.jpg", "downloadUrl": "/projects/A0029/files/clusters_00_screenshot_24.jpg", "length": 18720, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_00.jpg", "length": 18704, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_01.jpg", "length": 18800, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_02.jpg", "length": 18347, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_03.jpg", "length": 18949, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_04.jpg", "length": 18768, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_05.jpg", "length": 19092, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_06.jpg", "length": 18731, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_07.jpg", "length": 18696, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_08.jpg", "length": 19051, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_09.jpg", "length": 19207, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_10.jpg", "length": 19299, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_11.jpg", "length": 18826, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_12.jpg", "length": 19410, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_13.jpg", "length": 19128, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_14.jpg", "length": 18777, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_15.jpg", "length": 19425, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_16.jpg", "length": 18606, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_17.jpg", "length": 18791, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_18.jpg", "length": 19774, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0029/files/clusters_01_screenshot_19.jpg", "length": 19064, "contentType": "application/octet-stream", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0029/files/pocket_01.pdb", "length": 11256, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0029/files/pocket_02.pdb", "length": 8040, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7d5d13505ed724cd3ed8", "md": 0}}]}
|
data/files/A002A/project.json
ADDED
|
@@ -0,0 +1,191 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002A",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1WRD",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1WRD"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O60784",
|
| 31 |
+
"P0CH28"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
|
| 38 |
+
"GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Target of Myb1 membrane trafficking protein",
|
| 43 |
+
"GAT",
|
| 44 |
+
"Disordered",
|
| 45 |
+
"Ubiquitin",
|
| 46 |
+
"Ubiquitin-like 2"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 2816,
|
| 58 |
+
"SYSTRES": 174,
|
| 59 |
+
"PROTATS": 2816,
|
| 60 |
+
"PROTRES": 174,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 8.13965,
|
| 92 |
+
"BOXSIZEY": 8.13965,
|
| 93 |
+
"BOXSIZEZ": 5.73787,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 2816,
|
| 96 |
+
"mdFrames": 5001
|
| 97 |
+
},
|
| 98 |
+
"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
+
"mdref": 0,
|
| 104 |
+
"files": [
|
| 105 |
+
"topology.tpr",
|
| 106 |
+
"screenshot.jpg",
|
| 107 |
+
"trajectory.bin",
|
| 108 |
+
"pca_trajectory_01.bin",
|
| 109 |
+
"pca_trajectory_02.bin",
|
| 110 |
+
"pca_trajectory_03.bin",
|
| 111 |
+
"pca_trajectory_04.bin",
|
| 112 |
+
"pca_trajectory_05.bin",
|
| 113 |
+
"pca_trajectory_06.bin",
|
| 114 |
+
"pca_trajectory_07.bin",
|
| 115 |
+
"pca_trajectory_08.bin",
|
| 116 |
+
"pca_trajectory_09.bin",
|
| 117 |
+
"pca_trajectory_10.bin",
|
| 118 |
+
"pca_trajectory_11.bin",
|
| 119 |
+
"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.bin",
|
| 121 |
+
"structure.pdb",
|
| 122 |
+
"trajectory.xtc",
|
| 123 |
+
"clusters_00_screenshot_00.jpg",
|
| 124 |
+
"clusters_00_screenshot_01.jpg",
|
| 125 |
+
"clusters_00_screenshot_02.jpg",
|
| 126 |
+
"clusters_00_screenshot_03.jpg",
|
| 127 |
+
"clusters_00_screenshot_04.jpg",
|
| 128 |
+
"clusters_00_screenshot_05.jpg",
|
| 129 |
+
"clusters_00_screenshot_06.jpg",
|
| 130 |
+
"clusters_00_screenshot_07.jpg",
|
| 131 |
+
"clusters_00_screenshot_08.jpg",
|
| 132 |
+
"clusters_00_screenshot_09.jpg",
|
| 133 |
+
"clusters_00_screenshot_10.jpg",
|
| 134 |
+
"clusters_00_screenshot_11.jpg",
|
| 135 |
+
"clusters_00_screenshot_12.jpg",
|
| 136 |
+
"clusters_00_screenshot_13.jpg",
|
| 137 |
+
"clusters_00_screenshot_14.jpg",
|
| 138 |
+
"clusters_00_screenshot_15.jpg",
|
| 139 |
+
"clusters_00_screenshot_16.jpg",
|
| 140 |
+
"clusters_00_screenshot_17.jpg",
|
| 141 |
+
"clusters_00_screenshot_18.jpg",
|
| 142 |
+
"clusters_00_screenshot_19.jpg",
|
| 143 |
+
"clusters_01_screenshot_00.jpg",
|
| 144 |
+
"clusters_01_screenshot_01.jpg",
|
| 145 |
+
"clusters_01_screenshot_02.jpg",
|
| 146 |
+
"clusters_01_screenshot_03.jpg",
|
| 147 |
+
"clusters_01_screenshot_04.jpg",
|
| 148 |
+
"clusters_01_screenshot_05.jpg",
|
| 149 |
+
"clusters_01_screenshot_06.jpg",
|
| 150 |
+
"clusters_01_screenshot_07.jpg",
|
| 151 |
+
"clusters_01_screenshot_08.jpg",
|
| 152 |
+
"clusters_01_screenshot_09.jpg",
|
| 153 |
+
"clusters_01_screenshot_10.jpg",
|
| 154 |
+
"clusters_01_screenshot_11.jpg",
|
| 155 |
+
"clusters_01_screenshot_12.jpg",
|
| 156 |
+
"clusters_01_screenshot_13.jpg",
|
| 157 |
+
"clusters_01_screenshot_14.jpg",
|
| 158 |
+
"clusters_01_screenshot_15.jpg",
|
| 159 |
+
"clusters_01_screenshot_16.jpg",
|
| 160 |
+
"clusters_01_screenshot_17.jpg",
|
| 161 |
+
"clusters_01_screenshot_18.jpg",
|
| 162 |
+
"clusters_01_screenshot_19.jpg",
|
| 163 |
+
"clusters_01_screenshot_20.jpg",
|
| 164 |
+
"pocket_01.pdb",
|
| 165 |
+
"pocket_02.pdb"
|
| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
+
"clusters",
|
| 169 |
+
"clusters-00",
|
| 170 |
+
"clusters-01",
|
| 171 |
+
"dist-perres",
|
| 172 |
+
"energies",
|
| 173 |
+
"fluctuation",
|
| 174 |
+
"hbonds",
|
| 175 |
+
"interactions",
|
| 176 |
+
"pca",
|
| 177 |
+
"pockets",
|
| 178 |
+
"rgyr",
|
| 179 |
+
"rmsd-pairwise",
|
| 180 |
+
"rmsd-perres",
|
| 181 |
+
"rmsds",
|
| 182 |
+
"sasa",
|
| 183 |
+
"tmscores"
|
| 184 |
+
],
|
| 185 |
+
"mdIndex": 0,
|
| 186 |
+
"mdNumber": 1,
|
| 187 |
+
"refframe": 0,
|
| 188 |
+
"internalId": "683f7e53033ad70f2bcb1da1",
|
| 189 |
+
"creationDate": "2025-06-03T22:59:31.000Z",
|
| 190 |
+
"identifier": "A002A"
|
| 191 |
+
}
|
data/files/A002A/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002A", "accession": "A002A", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WRD", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WRD"], "FORCED_REFERENCES": null, "REFERENCES": ["O60784", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"], "NUCLSEQ": [], "DOMAINS": ["Target of Myb1 membrane trafficking protein", "GAT", "Disordered", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 174, "PROTATS": 2816, "PROTRES": 174, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.13965, "BOXSIZEY": 8.13965, "BOXSIZEZ": 5.73787, "mdName": "replica 1", "mdAtoms": 2816, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002A/files/topology.tpr", "length": 1048380, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002A/files/screenshot.jpg", "length": 19440, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002A/files/trajectory.bin", "length": 168993792, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 5001, "atoms": 2816}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_01.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_02.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_03.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_04.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_05.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_06.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_07.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_08.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_09.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_10.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_11.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_12.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_13.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002A/files/structure.pdb", "length": 228131, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002A/files/trajectory.xtc", "length": 53825612, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_00.jpg", "length": 19805, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_01.jpg", "length": 19505, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_02.jpg", "length": 19848, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_03.jpg", "length": 19407, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_04.jpg", "length": 19623, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_05.jpg", "length": 19060, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_06.jpg", "length": 20155, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_07.jpg", "length": 19354, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_08.jpg", "length": 18817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_09.jpg", "length": 19701, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_10.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_11.jpg", "length": 20265, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_12.jpg", "length": 19672, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_13.jpg", "length": 19500, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_14.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_15.jpg", "length": 19541, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_16.jpg", "length": 19730, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_17.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_18.jpg", "length": 20102, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_19.jpg", "length": 19629, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_00.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_01.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_02.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_03.jpg", "length": 21314, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_04.jpg", "length": 20980, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_05.jpg", "length": 20540, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_06.jpg", "length": 20162, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_07.jpg", "length": 20831, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_08.jpg", "length": 21204, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_09.jpg", "length": 21403, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_10.jpg", "length": 20775, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_11.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_12.jpg", "length": 20717, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_13.jpg", "length": 21232, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_14.jpg", "length": 21114, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_15.jpg", "length": 20099, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_16.jpg", "length": 19885, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_17.jpg", "length": 20853, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_18.jpg", "length": 20655, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_19.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_20.jpg", "length": 21297, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002A/files/pocket_01.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002A/files/pocket_02.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002A", "accession": "A002A", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WRD", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WRD"], "FORCED_REFERENCES": null, "REFERENCES": ["O60784", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"], "NUCLSEQ": [], "DOMAINS": ["Target of Myb1 membrane trafficking protein", "GAT", "Disordered", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 174, "PROTATS": 2816, "PROTRES": 174, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.13965, "BOXSIZEY": 8.13965, "BOXSIZEZ": 5.73787, "mdName": "replica 1", "mdAtoms": 2816, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002A/files/topology.tpr", "length": 1048380, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002A/files/screenshot.jpg", "length": 19440, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002A/files/trajectory.bin", "length": 168993792, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 5001, "atoms": 2816}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_01.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_02.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_03.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_04.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_05.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_06.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_07.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_08.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_09.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_10.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_11.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_12.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_13.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002A/files/structure.pdb", "length": 228131, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002A/files/trajectory.xtc", "length": 53825612, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_00.jpg", "length": 19805, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_01.jpg", "length": 19505, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_02.jpg", "length": 19848, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_03.jpg", "length": 19407, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_04.jpg", "length": 19623, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_05.jpg", "length": 19060, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_06.jpg", "length": 20155, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_07.jpg", "length": 19354, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_08.jpg", "length": 18817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_09.jpg", "length": 19701, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_10.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_11.jpg", "length": 20265, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_12.jpg", "length": 19672, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_13.jpg", "length": 19500, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_14.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_15.jpg", "length": 19541, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_16.jpg", "length": 19730, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_17.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_18.jpg", "length": 20102, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_19.jpg", "length": 19629, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_00.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_01.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_02.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_03.jpg", "length": 21314, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_04.jpg", "length": 20980, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_05.jpg", "length": 20540, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_06.jpg", "length": 20162, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_07.jpg", "length": 20831, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_08.jpg", "length": 21204, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_09.jpg", "length": 21403, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_10.jpg", "length": 20775, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_11.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_12.jpg", "length": 20717, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_13.jpg", "length": 21232, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_14.jpg", "length": 21114, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_15.jpg", "length": 20099, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_16.jpg", "length": 19885, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_17.jpg", "length": 20853, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_18.jpg", "length": 20655, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_19.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_20.jpg", "length": 21297, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002A/files/pocket_01.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002A/files/pocket_02.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002A", "accession": "A002A", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WRD", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WRD"], "FORCED_REFERENCES": null, "REFERENCES": ["O60784", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"], "NUCLSEQ": [], "DOMAINS": ["Target of Myb1 membrane trafficking protein", "GAT", "Disordered", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 174, "PROTATS": 2816, "PROTRES": 174, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.13965, "BOXSIZEY": 8.13965, "BOXSIZEZ": 5.73787, "mdName": "replica 1", "mdAtoms": 2816, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002A/files/topology.tpr", "length": 1048380, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002A/files/screenshot.jpg", "length": 19440, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002A/files/trajectory.bin", "length": 168993792, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 5001, "atoms": 2816}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_01.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_02.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_03.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_04.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_05.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_06.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_07.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_08.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_09.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_10.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_11.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_12.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_13.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002A/files/structure.pdb", "length": 228131, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002A/files/trajectory.xtc", "length": 53825612, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_00.jpg", "length": 19805, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_01.jpg", "length": 19505, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_02.jpg", "length": 19848, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_03.jpg", "length": 19407, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_04.jpg", "length": 19623, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_05.jpg", "length": 19060, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_06.jpg", "length": 20155, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_07.jpg", "length": 19354, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_08.jpg", "length": 18817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_09.jpg", "length": 19701, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_10.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_11.jpg", "length": 20265, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_12.jpg", "length": 19672, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_13.jpg", "length": 19500, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_14.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_15.jpg", "length": 19541, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_16.jpg", "length": 19730, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_17.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_18.jpg", "length": 20102, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_19.jpg", "length": 19629, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_00.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_01.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_02.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_03.jpg", "length": 21314, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_04.jpg", "length": 20980, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_05.jpg", "length": 20540, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_06.jpg", "length": 20162, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_07.jpg", "length": 20831, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_08.jpg", "length": 21204, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_09.jpg", "length": 21403, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_10.jpg", "length": 20775, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_11.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_12.jpg", "length": 20717, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_13.jpg", "length": 21232, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_14.jpg", "length": 21114, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_15.jpg", "length": 20099, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_16.jpg", "length": 19885, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_17.jpg", "length": 20853, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_18.jpg", "length": 20655, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_19.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_20.jpg", "length": 21297, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002A/files/pocket_01.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002A/files/pocket_02.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}]}
|
data/files/A002B/project.json
ADDED
|
@@ -0,0 +1,255 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002B",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1WVE",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1WVE"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P09788",
|
| 31 |
+
"P09787"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"AVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF",
|
| 38 |
+
"SQWGSGKNLYDKVCGHCHKPEVGVGPVLEGRGLPEAYIKDIVRNGFRAMPAFPASYVDDESLTQVAEYLSSLPAP"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"4-cresol dehydrogenase [hydroxylating] flavoprotein subunit",
|
| 43 |
+
"FAD-binding PCMH-type",
|
| 44 |
+
"4-cresol dehydrogenase [hydroxylating] cytochrome c subunit"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 18230,
|
| 56 |
+
"SYSTRES": 1180,
|
| 57 |
+
"PROTATS": 18230,
|
| 58 |
+
"PROTRES": 1180,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
},
|
| 79 |
+
{
|
| 80 |
+
"name": "chain A-chain C interaction",
|
| 81 |
+
"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain C",
|
| 83 |
+
"selection_1": "chain A",
|
| 84 |
+
"selection_2": "chain C",
|
| 85 |
+
"type": "protein-protein"
|
| 86 |
+
},
|
| 87 |
+
{
|
| 88 |
+
"name": "chain C-chain D interaction",
|
| 89 |
+
"agent_1": "chain C",
|
| 90 |
+
"agent_2": "chain D",
|
| 91 |
+
"selection_1": "chain A",
|
| 92 |
+
"selection_2": "chain D",
|
| 93 |
+
"type": "protein-protein"
|
| 94 |
+
}
|
| 95 |
+
],
|
| 96 |
+
"PBC_SELECTION": null,
|
| 97 |
+
"CHAINNAMES": null,
|
| 98 |
+
"MEMBRANES": null,
|
| 99 |
+
"CUSTOMS": null,
|
| 100 |
+
"ORIENTATION": null,
|
| 101 |
+
"PTM": [],
|
| 102 |
+
"MULTIMERIC": null,
|
| 103 |
+
"COLLECTIONS": "dynarepo",
|
| 104 |
+
"WARNINGS": [],
|
| 105 |
+
"BOXSIZEX": 12.7005,
|
| 106 |
+
"BOXSIZEY": 12.7005,
|
| 107 |
+
"BOXSIZEZ": 9.00348,
|
| 108 |
+
"mdName": "replica 1",
|
| 109 |
+
"mdAtoms": 18230,
|
| 110 |
+
"mdFrames": 5001
|
| 111 |
+
},
|
| 112 |
+
"mds": [
|
| 113 |
+
"replica 1",
|
| 114 |
+
"replica 2",
|
| 115 |
+
"replica 3"
|
| 116 |
+
],
|
| 117 |
+
"mdref": 0,
|
| 118 |
+
"files": [
|
| 119 |
+
"topology.tpr",
|
| 120 |
+
"screenshot.jpg",
|
| 121 |
+
"trajectory.bin",
|
| 122 |
+
"pca_trajectory_01.bin",
|
| 123 |
+
"pca_trajectory_02.bin",
|
| 124 |
+
"pca_trajectory_03.bin",
|
| 125 |
+
"pca_trajectory_04.bin",
|
| 126 |
+
"pca_trajectory_05.bin",
|
| 127 |
+
"pca_trajectory_06.bin",
|
| 128 |
+
"pca_trajectory_07.bin",
|
| 129 |
+
"pca_trajectory_08.bin",
|
| 130 |
+
"pca_trajectory_09.bin",
|
| 131 |
+
"pca_trajectory_10.bin",
|
| 132 |
+
"pca_trajectory_11.bin",
|
| 133 |
+
"pca_trajectory_12.bin",
|
| 134 |
+
"pca_trajectory_13.bin",
|
| 135 |
+
"pca_trajectory_14.bin",
|
| 136 |
+
"pca_trajectory_15.bin",
|
| 137 |
+
"structure.pdb",
|
| 138 |
+
"trajectory.xtc",
|
| 139 |
+
"clusters_00_screenshot_00.jpg",
|
| 140 |
+
"clusters_00_screenshot_01.jpg",
|
| 141 |
+
"clusters_00_screenshot_02.jpg",
|
| 142 |
+
"clusters_00_screenshot_03.jpg",
|
| 143 |
+
"clusters_00_screenshot_04.jpg",
|
| 144 |
+
"clusters_00_screenshot_05.jpg",
|
| 145 |
+
"clusters_00_screenshot_06.jpg",
|
| 146 |
+
"clusters_00_screenshot_07.jpg",
|
| 147 |
+
"clusters_00_screenshot_08.jpg",
|
| 148 |
+
"clusters_00_screenshot_09.jpg",
|
| 149 |
+
"clusters_00_screenshot_10.jpg",
|
| 150 |
+
"clusters_00_screenshot_11.jpg",
|
| 151 |
+
"clusters_00_screenshot_12.jpg",
|
| 152 |
+
"clusters_00_screenshot_13.jpg",
|
| 153 |
+
"clusters_00_screenshot_14.jpg",
|
| 154 |
+
"clusters_00_screenshot_15.jpg",
|
| 155 |
+
"clusters_00_screenshot_16.jpg",
|
| 156 |
+
"clusters_00_screenshot_17.jpg",
|
| 157 |
+
"clusters_00_screenshot_18.jpg",
|
| 158 |
+
"clusters_01_screenshot_00.jpg",
|
| 159 |
+
"clusters_01_screenshot_01.jpg",
|
| 160 |
+
"clusters_01_screenshot_02.jpg",
|
| 161 |
+
"clusters_01_screenshot_03.jpg",
|
| 162 |
+
"clusters_01_screenshot_04.jpg",
|
| 163 |
+
"clusters_01_screenshot_05.jpg",
|
| 164 |
+
"clusters_01_screenshot_06.jpg",
|
| 165 |
+
"clusters_01_screenshot_07.jpg",
|
| 166 |
+
"clusters_01_screenshot_08.jpg",
|
| 167 |
+
"clusters_01_screenshot_09.jpg",
|
| 168 |
+
"clusters_01_screenshot_10.jpg",
|
| 169 |
+
"clusters_01_screenshot_11.jpg",
|
| 170 |
+
"clusters_01_screenshot_12.jpg",
|
| 171 |
+
"clusters_01_screenshot_13.jpg",
|
| 172 |
+
"clusters_01_screenshot_14.jpg",
|
| 173 |
+
"clusters_01_screenshot_15.jpg",
|
| 174 |
+
"clusters_01_screenshot_16.jpg",
|
| 175 |
+
"clusters_01_screenshot_17.jpg",
|
| 176 |
+
"clusters_01_screenshot_18.jpg",
|
| 177 |
+
"clusters_01_screenshot_19.jpg",
|
| 178 |
+
"clusters_02_screenshot_00.jpg",
|
| 179 |
+
"clusters_02_screenshot_01.jpg",
|
| 180 |
+
"clusters_02_screenshot_02.jpg",
|
| 181 |
+
"clusters_02_screenshot_03.jpg",
|
| 182 |
+
"clusters_02_screenshot_04.jpg",
|
| 183 |
+
"clusters_02_screenshot_05.jpg",
|
| 184 |
+
"clusters_02_screenshot_06.jpg",
|
| 185 |
+
"clusters_02_screenshot_07.jpg",
|
| 186 |
+
"clusters_02_screenshot_08.jpg",
|
| 187 |
+
"clusters_02_screenshot_09.jpg",
|
| 188 |
+
"clusters_02_screenshot_10.jpg",
|
| 189 |
+
"clusters_02_screenshot_11.jpg",
|
| 190 |
+
"clusters_02_screenshot_12.jpg",
|
| 191 |
+
"clusters_02_screenshot_13.jpg",
|
| 192 |
+
"clusters_02_screenshot_14.jpg",
|
| 193 |
+
"clusters_02_screenshot_15.jpg",
|
| 194 |
+
"clusters_02_screenshot_16.jpg",
|
| 195 |
+
"clusters_02_screenshot_17.jpg",
|
| 196 |
+
"clusters_03_screenshot_00.jpg",
|
| 197 |
+
"clusters_03_screenshot_01.jpg",
|
| 198 |
+
"clusters_03_screenshot_02.jpg",
|
| 199 |
+
"clusters_03_screenshot_03.jpg",
|
| 200 |
+
"clusters_03_screenshot_04.jpg",
|
| 201 |
+
"clusters_03_screenshot_05.jpg",
|
| 202 |
+
"clusters_03_screenshot_06.jpg",
|
| 203 |
+
"clusters_03_screenshot_07.jpg",
|
| 204 |
+
"clusters_03_screenshot_08.jpg",
|
| 205 |
+
"clusters_03_screenshot_09.jpg",
|
| 206 |
+
"clusters_03_screenshot_10.jpg",
|
| 207 |
+
"clusters_03_screenshot_11.jpg",
|
| 208 |
+
"clusters_03_screenshot_12.jpg",
|
| 209 |
+
"clusters_03_screenshot_13.jpg",
|
| 210 |
+
"clusters_03_screenshot_14.jpg",
|
| 211 |
+
"clusters_03_screenshot_15.jpg",
|
| 212 |
+
"clusters_03_screenshot_16.jpg",
|
| 213 |
+
"clusters_03_screenshot_17.jpg",
|
| 214 |
+
"clusters_03_screenshot_18.jpg",
|
| 215 |
+
"clusters_03_screenshot_19.jpg",
|
| 216 |
+
"clusters_03_screenshot_20.jpg",
|
| 217 |
+
"clusters_03_screenshot_21.jpg",
|
| 218 |
+
"pocket_01.pdb",
|
| 219 |
+
"pocket_02.pdb",
|
| 220 |
+
"pocket_03.pdb",
|
| 221 |
+
"pocket_04.pdb",
|
| 222 |
+
"pocket_05.pdb",
|
| 223 |
+
"pocket_06.pdb",
|
| 224 |
+
"pocket_07.pdb",
|
| 225 |
+
"pocket_08.pdb",
|
| 226 |
+
"pocket_09.pdb",
|
| 227 |
+
"pocket_10.pdb"
|
| 228 |
+
],
|
| 229 |
+
"analyses": [
|
| 230 |
+
"clusters",
|
| 231 |
+
"clusters-00",
|
| 232 |
+
"clusters-01",
|
| 233 |
+
"clusters-02",
|
| 234 |
+
"clusters-03",
|
| 235 |
+
"dist-perres",
|
| 236 |
+
"energies",
|
| 237 |
+
"fluctuation",
|
| 238 |
+
"hbonds",
|
| 239 |
+
"interactions",
|
| 240 |
+
"pca",
|
| 241 |
+
"pockets",
|
| 242 |
+
"rgyr",
|
| 243 |
+
"rmsd-pairwise",
|
| 244 |
+
"rmsd-perres",
|
| 245 |
+
"rmsds",
|
| 246 |
+
"sasa",
|
| 247 |
+
"tmscores"
|
| 248 |
+
],
|
| 249 |
+
"mdIndex": 0,
|
| 250 |
+
"mdNumber": 1,
|
| 251 |
+
"refframe": 9,
|
| 252 |
+
"internalId": "683f80f91f4ac25e2c41474e",
|
| 253 |
+
"creationDate": "2025-06-03T23:10:49.000Z",
|
| 254 |
+
"identifier": "A002B"
|
| 255 |
+
}
|
data/files/A002B/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002B", "accession": "A002B", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WVE", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WVE"], "FORCED_REFERENCES": null, "REFERENCES": ["P09788", "P09787"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF", "SQWGSGKNLYDKVCGHCHKPEVGVGPVLEGRGLPEAYIKDIVRNGFRAMPAFPASYVDDESLTQVAEYLSSLPAP"], "NUCLSEQ": [], "DOMAINS": ["4-cresol dehydrogenase [hydroxylating] flavoprotein subunit", "FAD-binding PCMH-type", "4-cresol dehydrogenase [hydroxylating] cytochrome c subunit"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 18230, "SYSTRES": 1180, "PROTATS": 18230, "PROTRES": 1180, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain C-chain D interaction", "agent_1": "chain C", "agent_2": "chain D", "selection_1": "chain A", "selection_2": "chain D", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.7005, "BOXSIZEY": 12.7005, "BOXSIZEZ": 9.00348, "mdName": "replica 1", "mdAtoms": 18230, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002B/files/topology.tpr", "length": 5205668, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002B/files/screenshot.jpg", "length": 30130, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002B/files/trajectory.bin", "length": 1094018760, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 5001, "atoms": 18230}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_01.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_02.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_03.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_04.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_05.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_06.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_07.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_08.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_09.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_10.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_11.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_12.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_13.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_14.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_15.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002B/files/structure.pdb", "length": 1476665, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002B/files/trajectory.xtc", "length": 345984472, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_00.jpg", "length": 29621, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_01.jpg", "length": 29910, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_02.jpg", "length": 30096, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_03.jpg", "length": 30258, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_04.jpg", "length": 30034, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_05.jpg", "length": 30101, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_06.jpg", "length": 30265, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_07.jpg", "length": 30272, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_08.jpg", "length": 30268, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_09.jpg", "length": 29954, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_10.jpg", "length": 29912, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_11.jpg", "length": 30540, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_12.jpg", "length": 30530, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_13.jpg", "length": 30260, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_14.jpg", "length": 30223, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_15.jpg", "length": 30800, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_16.jpg", "length": 30323, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_17.jpg", "length": 30775, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_18.jpg", "length": 30248, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_00.jpg", "length": 30816, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_01.jpg", "length": 30537, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_02.jpg", "length": 30795, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_03.jpg", "length": 30699, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_04.jpg", "length": 30545, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_05.jpg", "length": 30707, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_06.jpg", "length": 31036, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_07.jpg", "length": 31071, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_08.jpg", "length": 31025, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_09.jpg", "length": 31066, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_10.jpg", "length": 30784, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_11.jpg", "length": 31322, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_12.jpg", "length": 30795, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_13.jpg", "length": 31221, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_14.jpg", "length": 30955, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_15.jpg", "length": 30676, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_16.jpg", "length": 30791, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_17.jpg", "length": 30623, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_18.jpg", "length": 30581, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_19.jpg", "length": 31287, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_00.jpg", "length": 30749, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_01.jpg", "length": 30502, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_02.jpg", "length": 30757, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_03.jpg", "length": 30818, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_04.jpg", "length": 30864, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_05.jpg", "length": 30972, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_06.jpg", "length": 31191, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_07.jpg", "length": 30740, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_08.jpg", "length": 30926, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_09.jpg", "length": 30812, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_10.jpg", "length": 31071, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_11.jpg", "length": 30887, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_12.jpg", "length": 30818, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_13.jpg", "length": 31036, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_14.jpg", "length": 30775, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_15.jpg", "length": 30907, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_16.jpg", "length": 30866, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_17.jpg", "length": 30748, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_00.jpg", "length": 29209, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_01.jpg", "length": 29356, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_02.jpg", "length": 29516, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_03.jpg", "length": 29586, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_04.jpg", "length": 29579, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_05.jpg", "length": 29696, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_06.jpg", "length": 29721, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_07.jpg", "length": 29489, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_08.jpg", "length": 29332, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_09.jpg", "length": 29410, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_10.jpg", "length": 29880, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_11.jpg", "length": 29413, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_12.jpg", "length": 29587, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_13.jpg", "length": 29081, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_14.jpg", "length": 29336, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_15.jpg", "length": 29580, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_16.jpg", "length": 29325, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_17.jpg", "length": 29595, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_18.jpg", "length": 29958, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_19.jpg", "length": 29718, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_20.jpg", "length": 29442, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_21.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_21.jpg", "length": 29588, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002B/files/pocket_01.pdb", "length": 87234, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002B/files/pocket_02.pdb", "length": 36314, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002B/files/pocket_03.pdb", "length": 34773, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002B/files/pocket_04.pdb", "length": 33567, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002B/files/pocket_05.pdb", "length": 27001, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002B/files/pocket_06.pdb", "length": 22981, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002B/files/pocket_07.pdb", "length": 20301, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002B/files/pocket_08.pdb", "length": 15879, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002B/files/pocket_09.pdb", "length": 15611, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002B/files/pocket_10.pdb", "length": 15410, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002B", "accession": "A002B", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WVE", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WVE"], "FORCED_REFERENCES": null, "REFERENCES": ["P09788", "P09787"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF", "SQWGSGKNLYDKVCGHCHKPEVGVGPVLEGRGLPEAYIKDIVRNGFRAMPAFPASYVDDESLTQVAEYLSSLPAP"], "NUCLSEQ": [], "DOMAINS": ["4-cresol dehydrogenase [hydroxylating] flavoprotein subunit", "FAD-binding PCMH-type", "4-cresol dehydrogenase [hydroxylating] cytochrome c subunit"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 18230, "SYSTRES": 1180, "PROTATS": 18230, "PROTRES": 1180, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain C-chain D interaction", "agent_1": "chain C", "agent_2": "chain D", "selection_1": "chain A", "selection_2": "chain D", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.7005, "BOXSIZEY": 12.7005, "BOXSIZEZ": 9.00348, "mdName": "replica 1", "mdAtoms": 18230, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002B/files/topology.tpr", "length": 5205668, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002B/files/screenshot.jpg", "length": 30130, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002B/files/trajectory.bin", "length": 1094018760, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 5001, "atoms": 18230}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_01.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_02.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_03.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_04.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_05.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_06.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_07.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_08.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_09.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_10.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_11.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_12.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_13.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_14.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_15.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002B/files/structure.pdb", "length": 1476665, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002B/files/trajectory.xtc", "length": 345984472, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_00.jpg", "length": 29621, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_01.jpg", "length": 29910, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_02.jpg", "length": 30096, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_03.jpg", "length": 30258, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_04.jpg", "length": 30034, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_05.jpg", "length": 30101, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_06.jpg", "length": 30265, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_07.jpg", "length": 30272, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_08.jpg", "length": 30268, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_09.jpg", "length": 29954, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_10.jpg", "length": 29912, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_11.jpg", "length": 30540, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_12.jpg", "length": 30530, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_13.jpg", "length": 30260, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_14.jpg", "length": 30223, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_15.jpg", "length": 30800, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_16.jpg", "length": 30323, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_17.jpg", "length": 30775, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_18.jpg", "length": 30248, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_00.jpg", "length": 30816, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_01.jpg", "length": 30537, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_02.jpg", "length": 30795, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_03.jpg", "length": 30699, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_04.jpg", "length": 30545, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_05.jpg", "length": 30707, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_06.jpg", "length": 31036, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_07.jpg", "length": 31071, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_08.jpg", "length": 31025, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_09.jpg", "length": 31066, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_10.jpg", "length": 30784, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_11.jpg", "length": 31322, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_12.jpg", "length": 30795, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_13.jpg", "length": 31221, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_14.jpg", "length": 30955, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_15.jpg", "length": 30676, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_16.jpg", "length": 30791, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_17.jpg", "length": 30623, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_18.jpg", "length": 30581, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_19.jpg", "length": 31287, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_00.jpg", "length": 30749, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_01.jpg", "length": 30502, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_02.jpg", "length": 30757, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_03.jpg", "length": 30818, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_04.jpg", "length": 30864, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_05.jpg", "length": 30972, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_06.jpg", "length": 31191, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_07.jpg", "length": 30740, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_08.jpg", "length": 30926, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_09.jpg", "length": 30812, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_10.jpg", "length": 31071, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_11.jpg", "length": 30887, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_12.jpg", "length": 30818, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_13.jpg", "length": 31036, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_14.jpg", "length": 30775, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_15.jpg", "length": 30907, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_16.jpg", "length": 30866, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_17.jpg", "length": 30748, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_00.jpg", "length": 29209, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_01.jpg", "length": 29356, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_02.jpg", "length": 29516, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_03.jpg", "length": 29586, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_04.jpg", "length": 29579, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_05.jpg", "length": 29696, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_06.jpg", "length": 29721, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_07.jpg", "length": 29489, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_08.jpg", "length": 29332, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_09.jpg", "length": 29410, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_10.jpg", "length": 29880, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_11.jpg", "length": 29413, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_12.jpg", "length": 29587, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_13.jpg", "length": 29081, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_14.jpg", "length": 29336, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_15.jpg", "length": 29580, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_16.jpg", "length": 29325, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_17.jpg", "length": 29595, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_18.jpg", "length": 29958, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_19.jpg", "length": 29718, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_20.jpg", "length": 29442, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_21.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_21.jpg", "length": 29588, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002B/files/pocket_01.pdb", "length": 87234, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002B/files/pocket_02.pdb", "length": 36314, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002B/files/pocket_03.pdb", "length": 34773, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002B/files/pocket_04.pdb", "length": 33567, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002B/files/pocket_05.pdb", "length": 27001, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002B/files/pocket_06.pdb", "length": 22981, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002B/files/pocket_07.pdb", "length": 20301, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002B/files/pocket_08.pdb", "length": 15879, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002B/files/pocket_09.pdb", "length": 15611, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002B/files/pocket_10.pdb", "length": 15410, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002B", "accession": "A002B", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WVE", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1WVE"], "FORCED_REFERENCES": null, "REFERENCES": ["P09788", "P09787"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["AVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF", "SQWGSGKNLYDKVCGHCHKPEVGVGPVLEGRGLPEAYIKDIVRNGFRAMPAFPASYVDDESLTQVAEYLSSLPAP"], "NUCLSEQ": [], "DOMAINS": ["4-cresol dehydrogenase [hydroxylating] flavoprotein subunit", "FAD-binding PCMH-type", "4-cresol dehydrogenase [hydroxylating] cytochrome c subunit"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 18230, "SYSTRES": 1180, "PROTATS": 18230, "PROTRES": 1180, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain C-chain D interaction", "agent_1": "chain C", "agent_2": "chain D", "selection_1": "chain A", "selection_2": "chain D", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.7005, "BOXSIZEY": 12.7005, "BOXSIZEZ": 9.00348, "mdName": "replica 1", "mdAtoms": 18230, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002B/files/topology.tpr", "length": 5205668, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002B/files/screenshot.jpg", "length": 30130, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002B/files/trajectory.bin", "length": 1094018760, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 5001, "atoms": 18230}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_01.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_02.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_03.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_04.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_05.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_06.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_07.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_08.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_09.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_10.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_11.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_12.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_13.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_14.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002B/files/pca_trajectory_15.bin", "length": 849600, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0, "frames": 20, "atoms": 3540}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002B/files/structure.pdb", "length": 1476665, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002B/files/trajectory.xtc", "length": 345984472, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_00.jpg", "length": 29621, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_01.jpg", "length": 29910, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_02.jpg", "length": 30096, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_03.jpg", "length": 30258, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_04.jpg", "length": 30034, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_05.jpg", "length": 30101, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_06.jpg", "length": 30265, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_07.jpg", "length": 30272, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_08.jpg", "length": 30268, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_09.jpg", "length": 29954, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_10.jpg", "length": 29912, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_11.jpg", "length": 30540, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_12.jpg", "length": 30530, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_13.jpg", "length": 30260, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_14.jpg", "length": 30223, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_15.jpg", "length": 30800, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_16.jpg", "length": 30323, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_17.jpg", "length": 30775, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_00_screenshot_18.jpg", "length": 30248, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_00.jpg", "length": 30816, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_01.jpg", "length": 30537, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_02.jpg", "length": 30795, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_03.jpg", "length": 30699, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_04.jpg", "length": 30545, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_05.jpg", "length": 30707, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_06.jpg", "length": 31036, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_07.jpg", "length": 31071, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_08.jpg", "length": 31025, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_09.jpg", "length": 31066, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_10.jpg", "length": 30784, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_11.jpg", "length": 31322, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_12.jpg", "length": 30795, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_13.jpg", "length": 31221, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_14.jpg", "length": 30955, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_15.jpg", "length": 30676, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_16.jpg", "length": 30791, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_17.jpg", "length": 30623, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_18.jpg", "length": 30581, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002B/files/clusters_01_screenshot_19.jpg", "length": 31287, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_00.jpg", "length": 30749, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_01.jpg", "length": 30502, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_02.jpg", "length": 30757, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_03.jpg", "length": 30818, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_04.jpg", "length": 30864, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_05.jpg", "length": 30972, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_06.jpg", "length": 31191, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_07.jpg", "length": 30740, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_08.jpg", "length": 30926, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_09.jpg", "length": 30812, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_10.jpg", "length": 31071, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_11.jpg", "length": 30887, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_12.jpg", "length": 30818, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_13.jpg", "length": 31036, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_14.jpg", "length": 30775, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_15.jpg", "length": 30907, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_16.jpg", "length": 30866, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_02_screenshot_17.jpg", "length": 30748, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_00.jpg", "length": 29209, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_01.jpg", "length": 29356, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_02.jpg", "length": 29516, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_03.jpg", "length": 29586, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_04.jpg", "length": 29579, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_05.jpg", "length": 29696, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_06.jpg", "length": 29721, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_07.jpg", "length": 29489, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_08.jpg", "length": 29332, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_09.jpg", "length": 29410, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_10.jpg", "length": 29880, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_11.jpg", "length": 29413, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_12.jpg", "length": 29587, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_13.jpg", "length": 29081, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_14.jpg", "length": 29336, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_15.jpg", "length": 29580, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_16.jpg", "length": 29325, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_17.jpg", "length": 29595, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_18.jpg", "length": 29958, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_19.jpg", "length": 29718, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_20.jpg", "length": 29442, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "clusters_03_screenshot_21.jpg", "downloadUrl": "/projects/A002B/files/clusters_03_screenshot_21.jpg", "length": 29588, "contentType": "application/octet-stream", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002B/files/pocket_01.pdb", "length": 87234, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002B/files/pocket_02.pdb", "length": 36314, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002B/files/pocket_03.pdb", "length": 34773, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002B/files/pocket_04.pdb", "length": 33567, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002B/files/pocket_05.pdb", "length": 27001, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002B/files/pocket_06.pdb", "length": 22981, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002B/files/pocket_07.pdb", "length": 20301, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002B/files/pocket_08.pdb", "length": 15879, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002B/files/pocket_09.pdb", "length": 15611, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002B/files/pocket_10.pdb", "length": 15410, "contentType": "chemical/x-pdb", "metadata": {"project": "683f80f91f4ac25e2c41474e", "md": 0}}]}
|
data/files/A002C/project.json
ADDED
|
@@ -0,0 +1,340 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002C",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1X75",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1X75"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0AES4",
|
| 31 |
+
"P62554"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI",
|
| 38 |
+
"TRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGS"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"DNA gyrase subunit A",
|
| 43 |
+
"Topo IIA-type catalytic",
|
| 44 |
+
"Toxin CcdB"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 7552,
|
| 56 |
+
"SYSTRES": 466,
|
| 57 |
+
"PROTATS": 7552,
|
| 58 |
+
"PROTRES": 466,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
},
|
| 79 |
+
{
|
| 80 |
+
"name": "chain A-chain C interaction",
|
| 81 |
+
"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain C",
|
| 83 |
+
"selection_1": "chain A",
|
| 84 |
+
"selection_2": "chain C",
|
| 85 |
+
"type": "protein-protein"
|
| 86 |
+
},
|
| 87 |
+
{
|
| 88 |
+
"name": "chain A-chain D interaction",
|
| 89 |
+
"agent_1": "chain A",
|
| 90 |
+
"agent_2": "chain D",
|
| 91 |
+
"selection_1": "chain A",
|
| 92 |
+
"selection_2": "chain D",
|
| 93 |
+
"type": "protein-protein"
|
| 94 |
+
},
|
| 95 |
+
{
|
| 96 |
+
"name": "chain B-chain C interaction",
|
| 97 |
+
"agent_1": "chain B",
|
| 98 |
+
"agent_2": "chain C",
|
| 99 |
+
"selection_1": "chain B",
|
| 100 |
+
"selection_2": "chain C",
|
| 101 |
+
"type": "protein-protein"
|
| 102 |
+
},
|
| 103 |
+
{
|
| 104 |
+
"name": "chain B-chain D interaction",
|
| 105 |
+
"agent_1": "chain B",
|
| 106 |
+
"agent_2": "chain D",
|
| 107 |
+
"selection_1": "chain B",
|
| 108 |
+
"selection_2": "chain D",
|
| 109 |
+
"type": "protein-protein"
|
| 110 |
+
},
|
| 111 |
+
{
|
| 112 |
+
"name": "chain C-chain D interaction",
|
| 113 |
+
"agent_1": "chain C",
|
| 114 |
+
"agent_2": "chain D",
|
| 115 |
+
"selection_1": "chain C",
|
| 116 |
+
"selection_2": "chain D",
|
| 117 |
+
"type": "protein-protein"
|
| 118 |
+
}
|
| 119 |
+
],
|
| 120 |
+
"PBC_SELECTION": null,
|
| 121 |
+
"CHAINNAMES": null,
|
| 122 |
+
"MEMBRANES": null,
|
| 123 |
+
"CUSTOMS": null,
|
| 124 |
+
"ORIENTATION": null,
|
| 125 |
+
"PTM": [],
|
| 126 |
+
"MULTIMERIC": null,
|
| 127 |
+
"COLLECTIONS": "dynarepo",
|
| 128 |
+
"WARNINGS": [],
|
| 129 |
+
"BOXSIZEX": 10.8343,
|
| 130 |
+
"BOXSIZEY": 10.8343,
|
| 131 |
+
"BOXSIZEZ": 7.6382,
|
| 132 |
+
"mdName": "replica 1",
|
| 133 |
+
"mdAtoms": 7552,
|
| 134 |
+
"mdFrames": 5001
|
| 135 |
+
},
|
| 136 |
+
"mds": [
|
| 137 |
+
"replica 1",
|
| 138 |
+
"replica 2",
|
| 139 |
+
"replica 3"
|
| 140 |
+
],
|
| 141 |
+
"mdref": 0,
|
| 142 |
+
"files": [
|
| 143 |
+
"topology.tpr",
|
| 144 |
+
"screenshot.jpg",
|
| 145 |
+
"trajectory.bin",
|
| 146 |
+
"pca_trajectory_01.bin",
|
| 147 |
+
"pca_trajectory_02.bin",
|
| 148 |
+
"pca_trajectory_03.bin",
|
| 149 |
+
"pca_trajectory_04.bin",
|
| 150 |
+
"pca_trajectory_05.bin",
|
| 151 |
+
"pca_trajectory_06.bin",
|
| 152 |
+
"pca_trajectory_07.bin",
|
| 153 |
+
"pca_trajectory_08.bin",
|
| 154 |
+
"pca_trajectory_09.bin",
|
| 155 |
+
"pca_trajectory_10.bin",
|
| 156 |
+
"pca_trajectory_11.bin",
|
| 157 |
+
"pca_trajectory_12.bin",
|
| 158 |
+
"pca_trajectory_13.bin",
|
| 159 |
+
"pca_trajectory_14.bin",
|
| 160 |
+
"pca_trajectory_15.bin",
|
| 161 |
+
"structure.pdb",
|
| 162 |
+
"trajectory.xtc",
|
| 163 |
+
"clusters_00_screenshot_00.jpg",
|
| 164 |
+
"clusters_00_screenshot_01.jpg",
|
| 165 |
+
"clusters_00_screenshot_02.jpg",
|
| 166 |
+
"clusters_00_screenshot_03.jpg",
|
| 167 |
+
"clusters_00_screenshot_04.jpg",
|
| 168 |
+
"clusters_00_screenshot_05.jpg",
|
| 169 |
+
"clusters_00_screenshot_06.jpg",
|
| 170 |
+
"clusters_00_screenshot_07.jpg",
|
| 171 |
+
"clusters_00_screenshot_08.jpg",
|
| 172 |
+
"clusters_00_screenshot_09.jpg",
|
| 173 |
+
"clusters_00_screenshot_10.jpg",
|
| 174 |
+
"clusters_00_screenshot_11.jpg",
|
| 175 |
+
"clusters_00_screenshot_12.jpg",
|
| 176 |
+
"clusters_00_screenshot_13.jpg",
|
| 177 |
+
"clusters_00_screenshot_14.jpg",
|
| 178 |
+
"clusters_00_screenshot_15.jpg",
|
| 179 |
+
"clusters_00_screenshot_16.jpg",
|
| 180 |
+
"clusters_00_screenshot_17.jpg",
|
| 181 |
+
"clusters_00_screenshot_18.jpg",
|
| 182 |
+
"clusters_01_screenshot_00.jpg",
|
| 183 |
+
"clusters_01_screenshot_01.jpg",
|
| 184 |
+
"clusters_01_screenshot_02.jpg",
|
| 185 |
+
"clusters_01_screenshot_03.jpg",
|
| 186 |
+
"clusters_01_screenshot_04.jpg",
|
| 187 |
+
"clusters_01_screenshot_05.jpg",
|
| 188 |
+
"clusters_01_screenshot_06.jpg",
|
| 189 |
+
"clusters_01_screenshot_07.jpg",
|
| 190 |
+
"clusters_01_screenshot_08.jpg",
|
| 191 |
+
"clusters_01_screenshot_09.jpg",
|
| 192 |
+
"clusters_01_screenshot_10.jpg",
|
| 193 |
+
"clusters_01_screenshot_11.jpg",
|
| 194 |
+
"clusters_01_screenshot_12.jpg",
|
| 195 |
+
"clusters_01_screenshot_13.jpg",
|
| 196 |
+
"clusters_01_screenshot_14.jpg",
|
| 197 |
+
"clusters_01_screenshot_15.jpg",
|
| 198 |
+
"clusters_01_screenshot_16.jpg",
|
| 199 |
+
"clusters_01_screenshot_17.jpg",
|
| 200 |
+
"clusters_01_screenshot_18.jpg",
|
| 201 |
+
"clusters_02_screenshot_00.jpg",
|
| 202 |
+
"clusters_02_screenshot_01.jpg",
|
| 203 |
+
"clusters_02_screenshot_02.jpg",
|
| 204 |
+
"clusters_02_screenshot_03.jpg",
|
| 205 |
+
"clusters_02_screenshot_04.jpg",
|
| 206 |
+
"clusters_02_screenshot_05.jpg",
|
| 207 |
+
"clusters_02_screenshot_06.jpg",
|
| 208 |
+
"clusters_02_screenshot_07.jpg",
|
| 209 |
+
"clusters_02_screenshot_08.jpg",
|
| 210 |
+
"clusters_02_screenshot_09.jpg",
|
| 211 |
+
"clusters_02_screenshot_10.jpg",
|
| 212 |
+
"clusters_02_screenshot_11.jpg",
|
| 213 |
+
"clusters_02_screenshot_12.jpg",
|
| 214 |
+
"clusters_02_screenshot_13.jpg",
|
| 215 |
+
"clusters_02_screenshot_14.jpg",
|
| 216 |
+
"clusters_02_screenshot_15.jpg",
|
| 217 |
+
"clusters_02_screenshot_16.jpg",
|
| 218 |
+
"clusters_02_screenshot_17.jpg",
|
| 219 |
+
"clusters_02_screenshot_18.jpg",
|
| 220 |
+
"clusters_02_screenshot_19.jpg",
|
| 221 |
+
"clusters_03_screenshot_00.jpg",
|
| 222 |
+
"clusters_03_screenshot_01.jpg",
|
| 223 |
+
"clusters_03_screenshot_02.jpg",
|
| 224 |
+
"clusters_03_screenshot_03.jpg",
|
| 225 |
+
"clusters_03_screenshot_04.jpg",
|
| 226 |
+
"clusters_03_screenshot_05.jpg",
|
| 227 |
+
"clusters_03_screenshot_06.jpg",
|
| 228 |
+
"clusters_03_screenshot_07.jpg",
|
| 229 |
+
"clusters_03_screenshot_08.jpg",
|
| 230 |
+
"clusters_03_screenshot_09.jpg",
|
| 231 |
+
"clusters_03_screenshot_10.jpg",
|
| 232 |
+
"clusters_03_screenshot_11.jpg",
|
| 233 |
+
"clusters_03_screenshot_12.jpg",
|
| 234 |
+
"clusters_03_screenshot_13.jpg",
|
| 235 |
+
"clusters_03_screenshot_14.jpg",
|
| 236 |
+
"clusters_03_screenshot_15.jpg",
|
| 237 |
+
"clusters_03_screenshot_16.jpg",
|
| 238 |
+
"clusters_03_screenshot_17.jpg",
|
| 239 |
+
"clusters_03_screenshot_18.jpg",
|
| 240 |
+
"clusters_04_screenshot_00.jpg",
|
| 241 |
+
"clusters_04_screenshot_01.jpg",
|
| 242 |
+
"clusters_04_screenshot_02.jpg",
|
| 243 |
+
"clusters_04_screenshot_03.jpg",
|
| 244 |
+
"clusters_04_screenshot_04.jpg",
|
| 245 |
+
"clusters_04_screenshot_05.jpg",
|
| 246 |
+
"clusters_04_screenshot_06.jpg",
|
| 247 |
+
"clusters_04_screenshot_07.jpg",
|
| 248 |
+
"clusters_04_screenshot_08.jpg",
|
| 249 |
+
"clusters_04_screenshot_09.jpg",
|
| 250 |
+
"clusters_04_screenshot_10.jpg",
|
| 251 |
+
"clusters_04_screenshot_11.jpg",
|
| 252 |
+
"clusters_04_screenshot_12.jpg",
|
| 253 |
+
"clusters_04_screenshot_13.jpg",
|
| 254 |
+
"clusters_04_screenshot_14.jpg",
|
| 255 |
+
"clusters_04_screenshot_15.jpg",
|
| 256 |
+
"clusters_04_screenshot_16.jpg",
|
| 257 |
+
"clusters_04_screenshot_17.jpg",
|
| 258 |
+
"clusters_04_screenshot_18.jpg",
|
| 259 |
+
"clusters_05_screenshot_00.jpg",
|
| 260 |
+
"clusters_05_screenshot_01.jpg",
|
| 261 |
+
"clusters_05_screenshot_02.jpg",
|
| 262 |
+
"clusters_05_screenshot_03.jpg",
|
| 263 |
+
"clusters_05_screenshot_04.jpg",
|
| 264 |
+
"clusters_05_screenshot_05.jpg",
|
| 265 |
+
"clusters_05_screenshot_06.jpg",
|
| 266 |
+
"clusters_05_screenshot_07.jpg",
|
| 267 |
+
"clusters_05_screenshot_08.jpg",
|
| 268 |
+
"clusters_05_screenshot_09.jpg",
|
| 269 |
+
"clusters_05_screenshot_10.jpg",
|
| 270 |
+
"clusters_05_screenshot_11.jpg",
|
| 271 |
+
"clusters_05_screenshot_12.jpg",
|
| 272 |
+
"clusters_05_screenshot_13.jpg",
|
| 273 |
+
"clusters_05_screenshot_14.jpg",
|
| 274 |
+
"clusters_05_screenshot_15.jpg",
|
| 275 |
+
"clusters_05_screenshot_16.jpg",
|
| 276 |
+
"clusters_05_screenshot_17.jpg",
|
| 277 |
+
"clusters_05_screenshot_18.jpg",
|
| 278 |
+
"clusters_06_screenshot_00.jpg",
|
| 279 |
+
"clusters_06_screenshot_01.jpg",
|
| 280 |
+
"clusters_06_screenshot_02.jpg",
|
| 281 |
+
"clusters_06_screenshot_03.jpg",
|
| 282 |
+
"clusters_06_screenshot_04.jpg",
|
| 283 |
+
"clusters_06_screenshot_05.jpg",
|
| 284 |
+
"clusters_06_screenshot_06.jpg",
|
| 285 |
+
"clusters_06_screenshot_07.jpg",
|
| 286 |
+
"clusters_06_screenshot_08.jpg",
|
| 287 |
+
"clusters_06_screenshot_09.jpg",
|
| 288 |
+
"clusters_06_screenshot_10.jpg",
|
| 289 |
+
"clusters_06_screenshot_11.jpg",
|
| 290 |
+
"clusters_06_screenshot_12.jpg",
|
| 291 |
+
"clusters_06_screenshot_13.jpg",
|
| 292 |
+
"clusters_06_screenshot_14.jpg",
|
| 293 |
+
"clusters_06_screenshot_15.jpg",
|
| 294 |
+
"clusters_06_screenshot_16.jpg",
|
| 295 |
+
"clusters_06_screenshot_17.jpg",
|
| 296 |
+
"clusters_06_screenshot_18.jpg",
|
| 297 |
+
"clusters_06_screenshot_19.jpg",
|
| 298 |
+
"clusters_06_screenshot_20.jpg",
|
| 299 |
+
"clusters_06_screenshot_21.jpg",
|
| 300 |
+
"pocket_01.pdb",
|
| 301 |
+
"pocket_02.pdb",
|
| 302 |
+
"pocket_03.pdb",
|
| 303 |
+
"pocket_04.pdb",
|
| 304 |
+
"pocket_05.pdb",
|
| 305 |
+
"pocket_06.pdb",
|
| 306 |
+
"pocket_07.pdb",
|
| 307 |
+
"pocket_08.pdb",
|
| 308 |
+
"pocket_09.pdb",
|
| 309 |
+
"pocket_10.pdb"
|
| 310 |
+
],
|
| 311 |
+
"analyses": [
|
| 312 |
+
"clusters",
|
| 313 |
+
"clusters-00",
|
| 314 |
+
"clusters-01",
|
| 315 |
+
"clusters-02",
|
| 316 |
+
"clusters-03",
|
| 317 |
+
"clusters-04",
|
| 318 |
+
"clusters-05",
|
| 319 |
+
"clusters-06",
|
| 320 |
+
"dist-perres",
|
| 321 |
+
"energies",
|
| 322 |
+
"fluctuation",
|
| 323 |
+
"hbonds",
|
| 324 |
+
"interactions",
|
| 325 |
+
"pca",
|
| 326 |
+
"pockets",
|
| 327 |
+
"rgyr",
|
| 328 |
+
"rmsd-pairwise",
|
| 329 |
+
"rmsd-perres",
|
| 330 |
+
"rmsds",
|
| 331 |
+
"sasa",
|
| 332 |
+
"tmscores"
|
| 333 |
+
],
|
| 334 |
+
"mdIndex": 0,
|
| 335 |
+
"mdNumber": 1,
|
| 336 |
+
"refframe": 0,
|
| 337 |
+
"internalId": "683f8487bdc6adc8d9b5fd17",
|
| 338 |
+
"creationDate": "2025-06-03T23:25:59.000Z",
|
| 339 |
+
"identifier": "A002C"
|
| 340 |
+
}
|
data/files/A002C/records.jsonl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
data/files/A002D/project.json
ADDED
|
@@ -0,0 +1,201 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002D",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1XD3",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1XD3"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P15374",
|
| 31 |
+
"P0CG48"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG",
|
| 38 |
+
"EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ubiquitin carboxyl-terminal hydrolase isozyme L3",
|
| 43 |
+
"UCH catalytic",
|
| 44 |
+
"Interaction with ubiquitin",
|
| 45 |
+
"Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site",
|
| 46 |
+
"Transition state stabilizer",
|
| 47 |
+
"Important for enzyme activity",
|
| 48 |
+
"Ubiquitin",
|
| 49 |
+
"Ubiquitin-like 1",
|
| 50 |
+
"Interacts with activating enzyme",
|
| 51 |
+
"Essential for function"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
+
"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 4837,
|
| 63 |
+
"SYSTRES": 304,
|
| 64 |
+
"PROTATS": 4837,
|
| 65 |
+
"PROTRES": 304,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "chain A-chain B interaction",
|
| 80 |
+
"agent_1": "chain A",
|
| 81 |
+
"agent_2": "chain B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
}
|
| 86 |
+
],
|
| 87 |
+
"PBC_SELECTION": null,
|
| 88 |
+
"CHAINNAMES": null,
|
| 89 |
+
"MEMBRANES": null,
|
| 90 |
+
"CUSTOMS": null,
|
| 91 |
+
"ORIENTATION": null,
|
| 92 |
+
"PTM": [],
|
| 93 |
+
"MULTIMERIC": null,
|
| 94 |
+
"COLLECTIONS": "dynarepo",
|
| 95 |
+
"WARNINGS": [],
|
| 96 |
+
"BOXSIZEX": 8.91256,
|
| 97 |
+
"BOXSIZEY": 8.91256,
|
| 98 |
+
"BOXSIZEZ": 6.30984,
|
| 99 |
+
"mdName": "replica 1",
|
| 100 |
+
"mdAtoms": 4837,
|
| 101 |
+
"mdFrames": 5001
|
| 102 |
+
},
|
| 103 |
+
"mds": [
|
| 104 |
+
"replica 1",
|
| 105 |
+
"replica 2",
|
| 106 |
+
"replica 3"
|
| 107 |
+
],
|
| 108 |
+
"mdref": 0,
|
| 109 |
+
"files": [
|
| 110 |
+
"topology.tpr",
|
| 111 |
+
"screenshot.jpg",
|
| 112 |
+
"trajectory.bin",
|
| 113 |
+
"pca_trajectory_01.bin",
|
| 114 |
+
"pca_trajectory_02.bin",
|
| 115 |
+
"pca_trajectory_03.bin",
|
| 116 |
+
"pca_trajectory_04.bin",
|
| 117 |
+
"pca_trajectory_05.bin",
|
| 118 |
+
"pca_trajectory_06.bin",
|
| 119 |
+
"pca_trajectory_07.bin",
|
| 120 |
+
"pca_trajectory_08.bin",
|
| 121 |
+
"pca_trajectory_09.bin",
|
| 122 |
+
"pca_trajectory_10.bin",
|
| 123 |
+
"pca_trajectory_11.bin",
|
| 124 |
+
"pca_trajectory_12.bin",
|
| 125 |
+
"pca_trajectory_13.bin",
|
| 126 |
+
"pca_trajectory_14.bin",
|
| 127 |
+
"pca_trajectory_15.bin",
|
| 128 |
+
"structure.pdb",
|
| 129 |
+
"trajectory.xtc",
|
| 130 |
+
"clusters_00_screenshot_00.jpg",
|
| 131 |
+
"clusters_00_screenshot_01.jpg",
|
| 132 |
+
"clusters_00_screenshot_02.jpg",
|
| 133 |
+
"clusters_00_screenshot_03.jpg",
|
| 134 |
+
"clusters_00_screenshot_04.jpg",
|
| 135 |
+
"clusters_00_screenshot_05.jpg",
|
| 136 |
+
"clusters_00_screenshot_06.jpg",
|
| 137 |
+
"clusters_00_screenshot_07.jpg",
|
| 138 |
+
"clusters_00_screenshot_08.jpg",
|
| 139 |
+
"clusters_00_screenshot_09.jpg",
|
| 140 |
+
"clusters_00_screenshot_10.jpg",
|
| 141 |
+
"clusters_00_screenshot_11.jpg",
|
| 142 |
+
"clusters_00_screenshot_12.jpg",
|
| 143 |
+
"clusters_00_screenshot_13.jpg",
|
| 144 |
+
"clusters_00_screenshot_14.jpg",
|
| 145 |
+
"clusters_00_screenshot_15.jpg",
|
| 146 |
+
"clusters_00_screenshot_16.jpg",
|
| 147 |
+
"clusters_00_screenshot_17.jpg",
|
| 148 |
+
"clusters_00_screenshot_18.jpg",
|
| 149 |
+
"clusters_00_screenshot_19.jpg",
|
| 150 |
+
"clusters_01_screenshot_00.jpg",
|
| 151 |
+
"clusters_01_screenshot_01.jpg",
|
| 152 |
+
"clusters_01_screenshot_02.jpg",
|
| 153 |
+
"clusters_01_screenshot_03.jpg",
|
| 154 |
+
"clusters_01_screenshot_04.jpg",
|
| 155 |
+
"clusters_01_screenshot_05.jpg",
|
| 156 |
+
"clusters_01_screenshot_06.jpg",
|
| 157 |
+
"clusters_01_screenshot_07.jpg",
|
| 158 |
+
"clusters_01_screenshot_08.jpg",
|
| 159 |
+
"clusters_01_screenshot_09.jpg",
|
| 160 |
+
"clusters_01_screenshot_10.jpg",
|
| 161 |
+
"clusters_01_screenshot_11.jpg",
|
| 162 |
+
"clusters_01_screenshot_12.jpg",
|
| 163 |
+
"clusters_01_screenshot_13.jpg",
|
| 164 |
+
"clusters_01_screenshot_14.jpg",
|
| 165 |
+
"clusters_01_screenshot_15.jpg",
|
| 166 |
+
"clusters_01_screenshot_16.jpg",
|
| 167 |
+
"clusters_01_screenshot_17.jpg",
|
| 168 |
+
"clusters_01_screenshot_18.jpg",
|
| 169 |
+
"clusters_01_screenshot_19.jpg",
|
| 170 |
+
"pocket_01.pdb",
|
| 171 |
+
"pocket_02.pdb",
|
| 172 |
+
"pocket_03.pdb",
|
| 173 |
+
"pocket_04.pdb",
|
| 174 |
+
"pocket_05.pdb",
|
| 175 |
+
"pocket_06.pdb"
|
| 176 |
+
],
|
| 177 |
+
"analyses": [
|
| 178 |
+
"clusters",
|
| 179 |
+
"clusters-00",
|
| 180 |
+
"clusters-01",
|
| 181 |
+
"dist-perres",
|
| 182 |
+
"energies",
|
| 183 |
+
"fluctuation",
|
| 184 |
+
"hbonds",
|
| 185 |
+
"interactions",
|
| 186 |
+
"pca",
|
| 187 |
+
"pockets",
|
| 188 |
+
"rgyr",
|
| 189 |
+
"rmsd-pairwise",
|
| 190 |
+
"rmsd-perres",
|
| 191 |
+
"rmsds",
|
| 192 |
+
"sasa",
|
| 193 |
+
"tmscores"
|
| 194 |
+
],
|
| 195 |
+
"mdIndex": 0,
|
| 196 |
+
"mdNumber": 1,
|
| 197 |
+
"refframe": 1,
|
| 198 |
+
"internalId": "683f86d96181f7ce44a52a0b",
|
| 199 |
+
"creationDate": "2025-06-03T23:35:53.000Z",
|
| 200 |
+
"identifier": "A002D"
|
| 201 |
+
}
|
data/files/A002D/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002D", "accession": "A002D", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XD3", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XD3"], "FORCED_REFERENCES": null, "REFERENCES": ["P15374", "P0CG48"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG", "EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA"], "NUCLSEQ": [], "DOMAINS": ["Ubiquitin carboxyl-terminal hydrolase isozyme L3", "UCH catalytic", "Interaction with ubiquitin", "Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site", "Transition state stabilizer", "Important for enzyme activity", "Ubiquitin", "Ubiquitin-like 1", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4837, "SYSTRES": 304, "PROTATS": 4837, "PROTRES": 304, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.91256, "BOXSIZEY": 8.91256, "BOXSIZEZ": 6.30984, "mdName": "replica 1", "mdAtoms": 4837, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002D/files/topology.tpr", "length": 1595952, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002D/files/screenshot.jpg", "length": 23133, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002D/files/trajectory.bin", "length": 290278044, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 5001, "atoms": 4837}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_01.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_02.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_03.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_04.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_05.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_06.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_07.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_08.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_09.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_10.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_11.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_12.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_13.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_14.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_15.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002D/files/structure.pdb", "length": 391832, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002D/files/trajectory.xtc", "length": 92271700, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_00.jpg", "length": 24057, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_01.jpg", "length": 24228, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_02.jpg", "length": 24015, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_03.jpg", "length": 23661, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_04.jpg", "length": 24027, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_05.jpg", "length": 23527, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_06.jpg", "length": 23756, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_07.jpg", "length": 24655, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_08.jpg", "length": 24392, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_09.jpg", "length": 23206, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_10.jpg", "length": 24330, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_11.jpg", "length": 24566, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_12.jpg", "length": 23724, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_13.jpg", "length": 24256, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_14.jpg", "length": 23764, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_15.jpg", "length": 24100, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_16.jpg", "length": 24730, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_17.jpg", "length": 24904, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_18.jpg", "length": 24461, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_19.jpg", "length": 24462, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_00.jpg", "length": 24027, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_01.jpg", "length": 24071, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_02.jpg", "length": 24099, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_03.jpg", "length": 23752, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_04.jpg", "length": 23892, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_05.jpg", "length": 24035, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_06.jpg", "length": 24166, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_07.jpg", "length": 24178, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_08.jpg", "length": 24058, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_09.jpg", "length": 24046, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_10.jpg", "length": 24119, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_11.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_12.jpg", "length": 24176, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_13.jpg", "length": 23857, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_14.jpg", "length": 24479, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_15.jpg", "length": 24515, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_16.jpg", "length": 24411, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_17.jpg", "length": 24682, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_18.jpg", "length": 24511, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_19.jpg", "length": 24301, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002D/files/pocket_01.pdb", "length": 22914, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002D/files/pocket_02.pdb", "length": 7303, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002D/files/pocket_03.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002D/files/pocket_04.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002D/files/pocket_05.pdb", "length": 4824, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002D/files/pocket_06.pdb", "length": 4422, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002D", "accession": "A002D", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XD3", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XD3"], "FORCED_REFERENCES": null, "REFERENCES": ["P15374", "P0CG48"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG", "EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA"], "NUCLSEQ": [], "DOMAINS": ["Ubiquitin carboxyl-terminal hydrolase isozyme L3", "UCH catalytic", "Interaction with ubiquitin", "Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site", "Transition state stabilizer", "Important for enzyme activity", "Ubiquitin", "Ubiquitin-like 1", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4837, "SYSTRES": 304, "PROTATS": 4837, "PROTRES": 304, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.91256, "BOXSIZEY": 8.91256, "BOXSIZEZ": 6.30984, "mdName": "replica 1", "mdAtoms": 4837, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002D/files/topology.tpr", "length": 1595952, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002D/files/screenshot.jpg", "length": 23133, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002D/files/trajectory.bin", "length": 290278044, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 5001, "atoms": 4837}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_01.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_02.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_03.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_04.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_05.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_06.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_07.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_08.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_09.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_10.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_11.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_12.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_13.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_14.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_15.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002D/files/structure.pdb", "length": 391832, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002D/files/trajectory.xtc", "length": 92271700, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_00.jpg", "length": 24057, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_01.jpg", "length": 24228, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_02.jpg", "length": 24015, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_03.jpg", "length": 23661, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_04.jpg", "length": 24027, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_05.jpg", "length": 23527, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_06.jpg", "length": 23756, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_07.jpg", "length": 24655, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_08.jpg", "length": 24392, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_09.jpg", "length": 23206, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_10.jpg", "length": 24330, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_11.jpg", "length": 24566, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_12.jpg", "length": 23724, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_13.jpg", "length": 24256, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_14.jpg", "length": 23764, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_15.jpg", "length": 24100, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_16.jpg", "length": 24730, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_17.jpg", "length": 24904, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_18.jpg", "length": 24461, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_19.jpg", "length": 24462, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_00.jpg", "length": 24027, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_01.jpg", "length": 24071, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_02.jpg", "length": 24099, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_03.jpg", "length": 23752, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_04.jpg", "length": 23892, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_05.jpg", "length": 24035, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_06.jpg", "length": 24166, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_07.jpg", "length": 24178, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_08.jpg", "length": 24058, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_09.jpg", "length": 24046, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_10.jpg", "length": 24119, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_11.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_12.jpg", "length": 24176, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_13.jpg", "length": 23857, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_14.jpg", "length": 24479, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_15.jpg", "length": 24515, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_16.jpg", "length": 24411, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_17.jpg", "length": 24682, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_18.jpg", "length": 24511, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_19.jpg", "length": 24301, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002D/files/pocket_01.pdb", "length": 22914, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002D/files/pocket_02.pdb", "length": 7303, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002D/files/pocket_03.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002D/files/pocket_04.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002D/files/pocket_05.pdb", "length": 4824, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002D/files/pocket_06.pdb", "length": 4422, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002D", "accession": "A002D", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XD3", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XD3"], "FORCED_REFERENCES": null, "REFERENCES": ["P15374", "P0CG48"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG", "EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA"], "NUCLSEQ": [], "DOMAINS": ["Ubiquitin carboxyl-terminal hydrolase isozyme L3", "UCH catalytic", "Interaction with ubiquitin", "Interaction with ubiquitin. Crossover loop which restricts access of large ubiquitin adducts to the active site", "Transition state stabilizer", "Important for enzyme activity", "Ubiquitin", "Ubiquitin-like 1", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4837, "SYSTRES": 304, "PROTATS": 4837, "PROTRES": 304, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.91256, "BOXSIZEY": 8.91256, "BOXSIZEZ": 6.30984, "mdName": "replica 1", "mdAtoms": 4837, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002D/files/topology.tpr", "length": 1595952, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002D/files/screenshot.jpg", "length": 23133, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002D/files/trajectory.bin", "length": 290278044, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 5001, "atoms": 4837}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_01.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_02.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_03.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_04.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_05.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_06.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_07.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_08.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_09.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_10.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_11.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_12.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_13.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_14.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002D/files/pca_trajectory_15.bin", "length": 218880, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0, "frames": 20, "atoms": 912}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002D/files/structure.pdb", "length": 391832, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002D/files/trajectory.xtc", "length": 92271700, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_00.jpg", "length": 24057, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_01.jpg", "length": 24228, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_02.jpg", "length": 24015, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_03.jpg", "length": 23661, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_04.jpg", "length": 24027, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_05.jpg", "length": 23527, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_06.jpg", "length": 23756, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_07.jpg", "length": 24655, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_08.jpg", "length": 24392, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_09.jpg", "length": 23206, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_10.jpg", "length": 24330, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_11.jpg", "length": 24566, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_12.jpg", "length": 23724, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_13.jpg", "length": 24256, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_14.jpg", "length": 23764, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_15.jpg", "length": 24100, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_16.jpg", "length": 24730, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_17.jpg", "length": 24904, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_18.jpg", "length": 24461, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002D/files/clusters_00_screenshot_19.jpg", "length": 24462, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_00.jpg", "length": 24027, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_01.jpg", "length": 24071, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_02.jpg", "length": 24099, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_03.jpg", "length": 23752, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_04.jpg", "length": 23892, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_05.jpg", "length": 24035, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_06.jpg", "length": 24166, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_07.jpg", "length": 24178, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_08.jpg", "length": 24058, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_09.jpg", "length": 24046, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_10.jpg", "length": 24119, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_11.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_12.jpg", "length": 24176, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_13.jpg", "length": 23857, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_14.jpg", "length": 24479, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_15.jpg", "length": 24515, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_16.jpg", "length": 24411, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_17.jpg", "length": 24682, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_18.jpg", "length": 24511, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002D/files/clusters_01_screenshot_19.jpg", "length": 24301, "contentType": "application/octet-stream", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002D/files/pocket_01.pdb", "length": 22914, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002D/files/pocket_02.pdb", "length": 7303, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002D/files/pocket_03.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002D/files/pocket_04.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002D/files/pocket_05.pdb", "length": 4824, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002D/files/pocket_06.pdb", "length": 4422, "contentType": "chemical/x-pdb", "metadata": {"project": "683f86d96181f7ce44a52a0b", "md": 0}}]}
|
data/files/A002E/project.json
ADDED
|
@@ -0,0 +1,178 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002E",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1XG2",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1XG2"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P14280",
|
| 31 |
+
"P83326"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"FENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTNQATDPKLKGRYETCSENYADAIDSLGQAKQFLTSGDYNSLNIYASAAFDGAGTCEDSFEGPPNIPTQLHQADLKLEDLCDIVLVISNLLP",
|
| 38 |
+
"IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVAYVDGLYD"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Pectinesterase 1",
|
| 43 |
+
"Transition state stabilizer",
|
| 44 |
+
"Pectinesterase inhibitor"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 7088,
|
| 56 |
+
"SYSTRES": 468,
|
| 57 |
+
"PROTATS": 7088,
|
| 58 |
+
"PROTRES": 468,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 10.2753,
|
| 90 |
+
"BOXSIZEY": 10.2753,
|
| 91 |
+
"BOXSIZEZ": 7.21184,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 7088,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"structure.pdb",
|
| 112 |
+
"trajectory.xtc",
|
| 113 |
+
"clusters_00_screenshot_00.jpg",
|
| 114 |
+
"clusters_00_screenshot_01.jpg",
|
| 115 |
+
"clusters_00_screenshot_02.jpg",
|
| 116 |
+
"clusters_00_screenshot_03.jpg",
|
| 117 |
+
"clusters_00_screenshot_04.jpg",
|
| 118 |
+
"clusters_00_screenshot_05.jpg",
|
| 119 |
+
"clusters_00_screenshot_06.jpg",
|
| 120 |
+
"clusters_00_screenshot_07.jpg",
|
| 121 |
+
"clusters_00_screenshot_08.jpg",
|
| 122 |
+
"clusters_00_screenshot_09.jpg",
|
| 123 |
+
"clusters_00_screenshot_10.jpg",
|
| 124 |
+
"clusters_00_screenshot_11.jpg",
|
| 125 |
+
"clusters_00_screenshot_12.jpg",
|
| 126 |
+
"clusters_00_screenshot_13.jpg",
|
| 127 |
+
"clusters_00_screenshot_14.jpg",
|
| 128 |
+
"clusters_00_screenshot_15.jpg",
|
| 129 |
+
"clusters_00_screenshot_16.jpg",
|
| 130 |
+
"clusters_00_screenshot_17.jpg",
|
| 131 |
+
"clusters_00_screenshot_18.jpg",
|
| 132 |
+
"clusters_00_screenshot_19.jpg",
|
| 133 |
+
"clusters_01_screenshot_00.jpg",
|
| 134 |
+
"clusters_01_screenshot_01.jpg",
|
| 135 |
+
"clusters_01_screenshot_02.jpg",
|
| 136 |
+
"clusters_01_screenshot_03.jpg",
|
| 137 |
+
"clusters_01_screenshot_04.jpg",
|
| 138 |
+
"clusters_01_screenshot_05.jpg",
|
| 139 |
+
"clusters_01_screenshot_06.jpg",
|
| 140 |
+
"clusters_01_screenshot_07.jpg",
|
| 141 |
+
"clusters_01_screenshot_08.jpg",
|
| 142 |
+
"clusters_01_screenshot_09.jpg",
|
| 143 |
+
"clusters_01_screenshot_10.jpg",
|
| 144 |
+
"clusters_01_screenshot_11.jpg",
|
| 145 |
+
"clusters_01_screenshot_12.jpg",
|
| 146 |
+
"clusters_01_screenshot_13.jpg",
|
| 147 |
+
"clusters_01_screenshot_14.jpg",
|
| 148 |
+
"clusters_01_screenshot_15.jpg",
|
| 149 |
+
"clusters_01_screenshot_16.jpg",
|
| 150 |
+
"clusters_01_screenshot_17.jpg",
|
| 151 |
+
"clusters_01_screenshot_18.jpg",
|
| 152 |
+
"clusters_01_screenshot_19.jpg"
|
| 153 |
+
],
|
| 154 |
+
"analyses": [
|
| 155 |
+
"mem-map",
|
| 156 |
+
"clusters",
|
| 157 |
+
"clusters-00",
|
| 158 |
+
"clusters-01",
|
| 159 |
+
"dist-perres",
|
| 160 |
+
"energies",
|
| 161 |
+
"fluctuation",
|
| 162 |
+
"hbonds",
|
| 163 |
+
"interactions",
|
| 164 |
+
"pca",
|
| 165 |
+
"rgyr",
|
| 166 |
+
"rmsd-pairwise",
|
| 167 |
+
"rmsd-perres",
|
| 168 |
+
"rmsds",
|
| 169 |
+
"sasa",
|
| 170 |
+
"tmscores"
|
| 171 |
+
],
|
| 172 |
+
"mdIndex": 0,
|
| 173 |
+
"mdNumber": 1,
|
| 174 |
+
"refframe": 0,
|
| 175 |
+
"internalId": "683f890c5318eaebd29115c1",
|
| 176 |
+
"creationDate": "2025-06-03T23:45:16.000Z",
|
| 177 |
+
"identifier": "A002E"
|
| 178 |
+
}
|
data/files/A002E/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002E", "accession": "A002E", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XG2", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XG2"], "FORCED_REFERENCES": null, "REFERENCES": ["P14280", "P83326"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["FENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTNQATDPKLKGRYETCSENYADAIDSLGQAKQFLTSGDYNSLNIYASAAFDGAGTCEDSFEGPPNIPTQLHQADLKLEDLCDIVLVISNLLP", "IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVAYVDGLYD"], "NUCLSEQ": [], "DOMAINS": ["Pectinesterase 1", "Transition state stabilizer", "Pectinesterase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7088, "SYSTRES": 468, "PROTATS": 7088, "PROTRES": 468, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.2753, "BOXSIZEY": 10.2753, "BOXSIZEZ": 7.21184, "mdName": "replica 1", "mdAtoms": 7088, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002E/files/topology.tpr", "length": 2210984, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002E/files/screenshot.jpg", "length": 29643, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002E/files/trajectory.bin", "length": 425365056, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 5001, "atoms": 7088}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_01.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_02.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_03.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_04.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_05.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002E/files/structure.pdb", "length": 574163, "contentType": "chemical/x-pdb", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002E/files/trajectory.xtc", "length": 135107596, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_00.jpg", "length": 28894, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_01.jpg", "length": 28605, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_02.jpg", "length": 30039, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_03.jpg", "length": 28849, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_04.jpg", "length": 27331, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_05.jpg", "length": 29044, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_06.jpg", "length": 28523, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_07.jpg", "length": 28425, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_08.jpg", "length": 29064, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_09.jpg", "length": 27586, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_10.jpg", "length": 27462, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_11.jpg", "length": 28426, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_12.jpg", "length": 27440, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_13.jpg", "length": 28384, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_14.jpg", "length": 28452, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_15.jpg", "length": 28814, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_16.jpg", "length": 29198, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_17.jpg", "length": 28115, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_18.jpg", "length": 29349, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_19.jpg", "length": 29731, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_00.jpg", "length": 26382, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_01.jpg", "length": 26970, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_02.jpg", "length": 25977, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_03.jpg", "length": 28292, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_04.jpg", "length": 29089, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_05.jpg", "length": 28084, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_06.jpg", "length": 27296, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_07.jpg", "length": 27722, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_08.jpg", "length": 28957, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_09.jpg", "length": 27455, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_10.jpg", "length": 26734, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_11.jpg", "length": 27945, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_12.jpg", "length": 27269, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_13.jpg", "length": 28762, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_14.jpg", "length": 29525, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_15.jpg", "length": 28818, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_16.jpg", "length": 30702, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_17.jpg", "length": 27397, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_18.jpg", "length": 27889, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_19.jpg", "length": 27473, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002E", "accession": "A002E", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XG2", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XG2"], "FORCED_REFERENCES": null, "REFERENCES": ["P14280", "P83326"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["FENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTNQATDPKLKGRYETCSENYADAIDSLGQAKQFLTSGDYNSLNIYASAAFDGAGTCEDSFEGPPNIPTQLHQADLKLEDLCDIVLVISNLLP", "IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVAYVDGLYD"], "NUCLSEQ": [], "DOMAINS": ["Pectinesterase 1", "Transition state stabilizer", "Pectinesterase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7088, "SYSTRES": 468, "PROTATS": 7088, "PROTRES": 468, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.2753, "BOXSIZEY": 10.2753, "BOXSIZEZ": 7.21184, "mdName": "replica 1", "mdAtoms": 7088, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002E/files/topology.tpr", "length": 2210984, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002E/files/screenshot.jpg", "length": 29643, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002E/files/trajectory.bin", "length": 425365056, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 5001, "atoms": 7088}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_01.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_02.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_03.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_04.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_05.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002E/files/structure.pdb", "length": 574163, "contentType": "chemical/x-pdb", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002E/files/trajectory.xtc", "length": 135107596, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_00.jpg", "length": 28894, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_01.jpg", "length": 28605, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_02.jpg", "length": 30039, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_03.jpg", "length": 28849, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_04.jpg", "length": 27331, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_05.jpg", "length": 29044, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_06.jpg", "length": 28523, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_07.jpg", "length": 28425, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_08.jpg", "length": 29064, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_09.jpg", "length": 27586, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_10.jpg", "length": 27462, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_11.jpg", "length": 28426, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_12.jpg", "length": 27440, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_13.jpg", "length": 28384, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_14.jpg", "length": 28452, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_15.jpg", "length": 28814, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_16.jpg", "length": 29198, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_17.jpg", "length": 28115, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_18.jpg", "length": 29349, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_19.jpg", "length": 29731, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_00.jpg", "length": 26382, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_01.jpg", "length": 26970, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_02.jpg", "length": 25977, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_03.jpg", "length": 28292, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_04.jpg", "length": 29089, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_05.jpg", "length": 28084, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_06.jpg", "length": 27296, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_07.jpg", "length": 27722, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_08.jpg", "length": 28957, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_09.jpg", "length": 27455, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_10.jpg", "length": 26734, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_11.jpg", "length": 27945, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_12.jpg", "length": 27269, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_13.jpg", "length": 28762, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_14.jpg", "length": 29525, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_15.jpg", "length": 28818, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_16.jpg", "length": 30702, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_17.jpg", "length": 27397, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_18.jpg", "length": 27889, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_19.jpg", "length": 27473, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002E", "accession": "A002E", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XG2", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XG2"], "FORCED_REFERENCES": null, "REFERENCES": ["P14280", "P83326"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["FENHLISEICPKTRNPSLCLQALESDPRSASKDLKGLGQFSIDIAQASAKQTSKIIASLTNQATDPKLKGRYETCSENYADAIDSLGQAKQFLTSGDYNSLNIYASAAFDGAGTCEDSFEGPPNIPTQLHQADLKLEDLCDIVLVISNLLP", "IIANAVVAQDGTGDYQTLAEAVAAAPDKSKTRYVIYVKRGTYKENVEVASNKMNLMIVGDGMYATTITGSLNVVDGSTTFRSATLAAVGQGFILQDICIQNTAGPAKDQAVALRVGADMSVINRCRIDAYQDTLYAHSQRQFYRDSYVTGTVDFIFGNAAVVFQKCQLVARKPGKYQQNMVTAQGRTDPNQATGTSIQFCNIIASSDLEPVLKEFPTYLGRPWKEYSRTVVMESYLGGLINPAGWAEWDGDFALKTLYYGEFMNNGPGAGTSKRVKWPGYHVITDPAKAMPFTVAKLIQGGSWLRSTGVAYVDGLYD"], "NUCLSEQ": [], "DOMAINS": ["Pectinesterase 1", "Transition state stabilizer", "Pectinesterase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7088, "SYSTRES": 468, "PROTATS": 7088, "PROTRES": 468, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.2753, "BOXSIZEY": 10.2753, "BOXSIZEZ": 7.21184, "mdName": "replica 1", "mdAtoms": 7088, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002E/files/topology.tpr", "length": 2210984, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002E/files/screenshot.jpg", "length": 29643, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002E/files/trajectory.bin", "length": 425365056, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 5001, "atoms": 7088}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_01.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_02.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_03.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_04.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002E/files/pca_trajectory_05.bin", "length": 336960, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0, "frames": 20, "atoms": 1404}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002E/files/structure.pdb", "length": 574163, "contentType": "chemical/x-pdb", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002E/files/trajectory.xtc", "length": 135107596, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_00.jpg", "length": 28894, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_01.jpg", "length": 28605, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_02.jpg", "length": 30039, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_03.jpg", "length": 28849, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_04.jpg", "length": 27331, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_05.jpg", "length": 29044, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_06.jpg", "length": 28523, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_07.jpg", "length": 28425, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_08.jpg", "length": 29064, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_09.jpg", "length": 27586, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_10.jpg", "length": 27462, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_11.jpg", "length": 28426, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_12.jpg", "length": 27440, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_13.jpg", "length": 28384, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_14.jpg", "length": 28452, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_15.jpg", "length": 28814, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_16.jpg", "length": 29198, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_17.jpg", "length": 28115, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_18.jpg", "length": 29349, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002E/files/clusters_00_screenshot_19.jpg", "length": 29731, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_00.jpg", "length": 26382, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_01.jpg", "length": 26970, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_02.jpg", "length": 25977, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_03.jpg", "length": 28292, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_04.jpg", "length": 29089, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_05.jpg", "length": 28084, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_06.jpg", "length": 27296, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_07.jpg", "length": 27722, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_08.jpg", "length": 28957, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_09.jpg", "length": 27455, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_10.jpg", "length": 26734, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_11.jpg", "length": 27945, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_12.jpg", "length": 27269, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_13.jpg", "length": 28762, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_14.jpg", "length": 29525, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_15.jpg", "length": 28818, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_16.jpg", "length": 30702, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_17.jpg", "length": 27397, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_18.jpg", "length": 27889, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002E/files/clusters_01_screenshot_19.jpg", "length": 27473, "contentType": "application/octet-stream", "metadata": {"project": "683f890c5318eaebd29115c1", "md": 0}}]}
|
data/files/A002F/project.json
ADDED
|
@@ -0,0 +1,192 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1XQS",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1XQS"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9NZL4",
|
| 31 |
+
"P0DMV8"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"RGEVEQMKSCLRVLSQPMPPTAGEAEQAADQQEREGALELLADLCENMDNAADFCQLSGMHLLVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLGLGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFLRLDGFSVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTLCSMGMVQQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRECREPELGLEELLRHRCQLLQQHEEYQEELEFCEKLLQTCFS",
|
| 38 |
+
"ERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Hsp70-binding protein 1",
|
| 43 |
+
"Heat shock 70 kDa protein 1A",
|
| 44 |
+
"Nucleotide-binding domain (NBD)"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 6783,
|
| 56 |
+
"SYSTRES": 429,
|
| 57 |
+
"PROTATS": 6783,
|
| 58 |
+
"PROTRES": 429,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 11.0148,
|
| 90 |
+
"BOXSIZEY": 11.0148,
|
| 91 |
+
"BOXSIZEZ": 7.73571,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 6783,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"structure.pdb",
|
| 115 |
+
"trajectory.xtc",
|
| 116 |
+
"clusters_00_screenshot_00.jpg",
|
| 117 |
+
"clusters_00_screenshot_01.jpg",
|
| 118 |
+
"clusters_00_screenshot_02.jpg",
|
| 119 |
+
"clusters_00_screenshot_03.jpg",
|
| 120 |
+
"clusters_00_screenshot_04.jpg",
|
| 121 |
+
"clusters_00_screenshot_05.jpg",
|
| 122 |
+
"clusters_00_screenshot_06.jpg",
|
| 123 |
+
"clusters_00_screenshot_07.jpg",
|
| 124 |
+
"clusters_00_screenshot_08.jpg",
|
| 125 |
+
"clusters_00_screenshot_09.jpg",
|
| 126 |
+
"clusters_00_screenshot_10.jpg",
|
| 127 |
+
"clusters_00_screenshot_11.jpg",
|
| 128 |
+
"clusters_00_screenshot_12.jpg",
|
| 129 |
+
"clusters_00_screenshot_13.jpg",
|
| 130 |
+
"clusters_00_screenshot_14.jpg",
|
| 131 |
+
"clusters_00_screenshot_15.jpg",
|
| 132 |
+
"clusters_00_screenshot_16.jpg",
|
| 133 |
+
"clusters_00_screenshot_17.jpg",
|
| 134 |
+
"clusters_00_screenshot_18.jpg",
|
| 135 |
+
"clusters_00_screenshot_19.jpg",
|
| 136 |
+
"clusters_00_screenshot_20.jpg",
|
| 137 |
+
"clusters_01_screenshot_00.jpg",
|
| 138 |
+
"clusters_01_screenshot_01.jpg",
|
| 139 |
+
"clusters_01_screenshot_02.jpg",
|
| 140 |
+
"clusters_01_screenshot_03.jpg",
|
| 141 |
+
"clusters_01_screenshot_04.jpg",
|
| 142 |
+
"clusters_01_screenshot_05.jpg",
|
| 143 |
+
"clusters_01_screenshot_06.jpg",
|
| 144 |
+
"clusters_01_screenshot_07.jpg",
|
| 145 |
+
"clusters_01_screenshot_08.jpg",
|
| 146 |
+
"clusters_01_screenshot_09.jpg",
|
| 147 |
+
"clusters_01_screenshot_10.jpg",
|
| 148 |
+
"clusters_01_screenshot_11.jpg",
|
| 149 |
+
"clusters_01_screenshot_12.jpg",
|
| 150 |
+
"clusters_01_screenshot_13.jpg",
|
| 151 |
+
"clusters_01_screenshot_14.jpg",
|
| 152 |
+
"clusters_01_screenshot_15.jpg",
|
| 153 |
+
"clusters_01_screenshot_16.jpg",
|
| 154 |
+
"clusters_01_screenshot_17.jpg",
|
| 155 |
+
"clusters_01_screenshot_18.jpg",
|
| 156 |
+
"clusters_01_screenshot_19.jpg",
|
| 157 |
+
"clusters_01_screenshot_20.jpg",
|
| 158 |
+
"clusters_01_screenshot_21.jpg",
|
| 159 |
+
"pocket_01.pdb",
|
| 160 |
+
"pocket_02.pdb",
|
| 161 |
+
"pocket_03.pdb",
|
| 162 |
+
"pocket_04.pdb",
|
| 163 |
+
"pocket_05.pdb",
|
| 164 |
+
"pocket_06.pdb",
|
| 165 |
+
"pocket_07.pdb",
|
| 166 |
+
"pocket_08.pdb"
|
| 167 |
+
],
|
| 168 |
+
"analyses": [
|
| 169 |
+
"clusters",
|
| 170 |
+
"clusters-00",
|
| 171 |
+
"clusters-01",
|
| 172 |
+
"dist-perres",
|
| 173 |
+
"energies",
|
| 174 |
+
"fluctuation",
|
| 175 |
+
"hbonds",
|
| 176 |
+
"interactions",
|
| 177 |
+
"pca",
|
| 178 |
+
"pockets",
|
| 179 |
+
"rgyr",
|
| 180 |
+
"rmsd-pairwise",
|
| 181 |
+
"rmsd-perres",
|
| 182 |
+
"rmsds",
|
| 183 |
+
"sasa",
|
| 184 |
+
"tmscores"
|
| 185 |
+
],
|
| 186 |
+
"mdIndex": 0,
|
| 187 |
+
"mdNumber": 1,
|
| 188 |
+
"refframe": 0,
|
| 189 |
+
"internalId": "683f8b9943a9d19eee6f9bd1",
|
| 190 |
+
"creationDate": "2025-06-03T23:56:09.000Z",
|
| 191 |
+
"identifier": "A002F"
|
| 192 |
+
}
|
data/files/A002F/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002F", "accession": "A002F", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XQS", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XQS"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZL4", "P0DMV8"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["RGEVEQMKSCLRVLSQPMPPTAGEAEQAADQQEREGALELLADLCENMDNAADFCQLSGMHLLVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLGLGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFLRLDGFSVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTLCSMGMVQQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRECREPELGLEELLRHRCQLLQQHEEYQEELEFCEKLLQTCFS", "ERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNG"], "NUCLSEQ": [], "DOMAINS": ["Hsp70-binding protein 1", "Heat shock 70 kDa protein 1A", "Nucleotide-binding domain (NBD)"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6783, "SYSTRES": 429, "PROTATS": 6783, "PROTRES": 429, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0148, "BOXSIZEY": 11.0148, "BOXSIZEZ": 7.73571, "mdName": "replica 1", "mdAtoms": 6783, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002F/files/topology.tpr", "length": 2161896, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002F/files/screenshot.jpg", "length": 23008, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002F/files/trajectory.bin", "length": 407061396, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 5001, "atoms": 6783}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_01.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_02.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_03.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_04.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_05.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_06.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_07.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_08.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002F/files/structure.pdb", "length": 549458, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002F/files/trajectory.xtc", "length": 129399608, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_00.jpg", "length": 20553, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_01.jpg", "length": 20141, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_02.jpg", "length": 20463, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_03.jpg", "length": 20769, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_04.jpg", "length": 21181, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_05.jpg", "length": 20388, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_06.jpg", "length": 21194, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_07.jpg", "length": 21941, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_08.jpg", "length": 22828, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_09.jpg", "length": 22770, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_10.jpg", "length": 21284, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_11.jpg", "length": 21372, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_12.jpg", "length": 22686, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_13.jpg", "length": 20937, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_14.jpg", "length": 21833, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_15.jpg", "length": 22509, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_16.jpg", "length": 21545, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_17.jpg", "length": 22330, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_18.jpg", "length": 20429, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_19.jpg", "length": 20274, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_20.jpg", "length": 19777, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_00.jpg", "length": 19883, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_01.jpg", "length": 20763, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_02.jpg", "length": 20999, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_03.jpg", "length": 20373, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_04.jpg", "length": 20558, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_05.jpg", "length": 19999, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_06.jpg", "length": 21575, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_07.jpg", "length": 22045, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_08.jpg", "length": 22132, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_09.jpg", "length": 21638, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_10.jpg", "length": 21463, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_11.jpg", "length": 22239, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_12.jpg", "length": 21641, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_13.jpg", "length": 22106, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_14.jpg", "length": 21677, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_15.jpg", "length": 21359, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_16.jpg", "length": 20650, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_17.jpg", "length": 21503, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_18.jpg", "length": 20458, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_19.jpg", "length": 22279, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_20.jpg", "length": 20023, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_21.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_21.jpg", "length": 20797, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002F/files/pocket_01.pdb", "length": 27336, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002F/files/pocket_02.pdb", "length": 21574, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002F/files/pocket_03.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002F/files/pocket_04.pdb", "length": 9179, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002F/files/pocket_05.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002F/files/pocket_06.pdb", "length": 4757, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002F/files/pocket_07.pdb", "length": 4355, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002F/files/pocket_08.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002F", "accession": "A002F", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XQS", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XQS"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZL4", "P0DMV8"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["RGEVEQMKSCLRVLSQPMPPTAGEAEQAADQQEREGALELLADLCENMDNAADFCQLSGMHLLVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLGLGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFLRLDGFSVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTLCSMGMVQQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRECREPELGLEELLRHRCQLLQQHEEYQEELEFCEKLLQTCFS", "ERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNG"], "NUCLSEQ": [], "DOMAINS": ["Hsp70-binding protein 1", "Heat shock 70 kDa protein 1A", "Nucleotide-binding domain (NBD)"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6783, "SYSTRES": 429, "PROTATS": 6783, "PROTRES": 429, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0148, "BOXSIZEY": 11.0148, "BOXSIZEZ": 7.73571, "mdName": "replica 1", "mdAtoms": 6783, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002F/files/topology.tpr", "length": 2161896, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002F/files/screenshot.jpg", "length": 23008, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002F/files/trajectory.bin", "length": 407061396, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 5001, "atoms": 6783}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_01.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_02.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_03.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_04.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_05.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_06.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_07.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_08.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002F/files/structure.pdb", "length": 549458, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002F/files/trajectory.xtc", "length": 129399608, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_00.jpg", "length": 20553, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_01.jpg", "length": 20141, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_02.jpg", "length": 20463, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_03.jpg", "length": 20769, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_04.jpg", "length": 21181, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_05.jpg", "length": 20388, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_06.jpg", "length": 21194, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_07.jpg", "length": 21941, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_08.jpg", "length": 22828, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_09.jpg", "length": 22770, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_10.jpg", "length": 21284, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_11.jpg", "length": 21372, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_12.jpg", "length": 22686, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_13.jpg", "length": 20937, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_14.jpg", "length": 21833, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_15.jpg", "length": 22509, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_16.jpg", "length": 21545, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_17.jpg", "length": 22330, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_18.jpg", "length": 20429, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_19.jpg", "length": 20274, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_20.jpg", "length": 19777, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_00.jpg", "length": 19883, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_01.jpg", "length": 20763, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_02.jpg", "length": 20999, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_03.jpg", "length": 20373, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_04.jpg", "length": 20558, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_05.jpg", "length": 19999, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_06.jpg", "length": 21575, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_07.jpg", "length": 22045, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_08.jpg", "length": 22132, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_09.jpg", "length": 21638, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_10.jpg", "length": 21463, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_11.jpg", "length": 22239, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_12.jpg", "length": 21641, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_13.jpg", "length": 22106, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_14.jpg", "length": 21677, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_15.jpg", "length": 21359, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_16.jpg", "length": 20650, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_17.jpg", "length": 21503, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_18.jpg", "length": 20458, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_19.jpg", "length": 22279, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_20.jpg", "length": 20023, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_21.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_21.jpg", "length": 20797, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002F/files/pocket_01.pdb", "length": 27336, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002F/files/pocket_02.pdb", "length": 21574, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002F/files/pocket_03.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002F/files/pocket_04.pdb", "length": 9179, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002F/files/pocket_05.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002F/files/pocket_06.pdb", "length": 4757, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002F/files/pocket_07.pdb", "length": 4355, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002F/files/pocket_08.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002F", "accession": "A002F", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XQS", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XQS"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZL4", "P0DMV8"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["RGEVEQMKSCLRVLSQPMPPTAGEAEQAADQQEREGALELLADLCENMDNAADFCQLSGMHLLVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLGLGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFLRLDGFSVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTLCSMGMVQQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRECREPELGLEELLRHRCQLLQQHEEYQEELEFCEKLLQTCFS", "ERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNG"], "NUCLSEQ": [], "DOMAINS": ["Hsp70-binding protein 1", "Heat shock 70 kDa protein 1A", "Nucleotide-binding domain (NBD)"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6783, "SYSTRES": 429, "PROTATS": 6783, "PROTRES": 429, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0148, "BOXSIZEY": 11.0148, "BOXSIZEZ": 7.73571, "mdName": "replica 1", "mdAtoms": 6783, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002F/files/topology.tpr", "length": 2161896, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002F/files/screenshot.jpg", "length": 23008, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002F/files/trajectory.bin", "length": 407061396, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 5001, "atoms": 6783}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_01.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_02.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_03.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_04.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_05.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_06.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_07.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002F/files/pca_trajectory_08.bin", "length": 308880, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0, "frames": 20, "atoms": 1287}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002F/files/structure.pdb", "length": 549458, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002F/files/trajectory.xtc", "length": 129399608, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_00.jpg", "length": 20553, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_01.jpg", "length": 20141, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_02.jpg", "length": 20463, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_03.jpg", "length": 20769, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_04.jpg", "length": 21181, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_05.jpg", "length": 20388, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_06.jpg", "length": 21194, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_07.jpg", "length": 21941, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_08.jpg", "length": 22828, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_09.jpg", "length": 22770, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_10.jpg", "length": 21284, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_11.jpg", "length": 21372, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_12.jpg", "length": 22686, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_13.jpg", "length": 20937, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_14.jpg", "length": 21833, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_15.jpg", "length": 22509, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_16.jpg", "length": 21545, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_17.jpg", "length": 22330, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_18.jpg", "length": 20429, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_19.jpg", "length": 20274, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002F/files/clusters_00_screenshot_20.jpg", "length": 19777, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_00.jpg", "length": 19883, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_01.jpg", "length": 20763, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_02.jpg", "length": 20999, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_03.jpg", "length": 20373, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_04.jpg", "length": 20558, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_05.jpg", "length": 19999, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_06.jpg", "length": 21575, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_07.jpg", "length": 22045, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_08.jpg", "length": 22132, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_09.jpg", "length": 21638, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_10.jpg", "length": 21463, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_11.jpg", "length": 22239, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_12.jpg", "length": 21641, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_13.jpg", "length": 22106, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_14.jpg", "length": 21677, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_15.jpg", "length": 21359, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_16.jpg", "length": 20650, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_17.jpg", "length": 21503, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_18.jpg", "length": 20458, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_19.jpg", "length": 22279, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_20.jpg", "length": 20023, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "clusters_01_screenshot_21.jpg", "downloadUrl": "/projects/A002F/files/clusters_01_screenshot_21.jpg", "length": 20797, "contentType": "application/octet-stream", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002F/files/pocket_01.pdb", "length": 27336, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002F/files/pocket_02.pdb", "length": 21574, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002F/files/pocket_03.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002F/files/pocket_04.pdb", "length": 9179, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002F/files/pocket_05.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002F/files/pocket_06.pdb", "length": 4757, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002F/files/pocket_07.pdb", "length": 4355, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002F/files/pocket_08.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8b9943a9d19eee6f9bd1", "md": 0}}]}
|
data/files/A002G/project.json
ADDED
|
@@ -0,0 +1,256 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002G",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1XWD",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1XWD"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01215",
|
| 31 |
+
"P01225",
|
| 32 |
+
"P23945"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"DVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS",
|
| 39 |
+
"CELTNITIAIEKEECRFCISINTTWCAGYCYTRDLVYKDPARPKIQKTCTFKELVYETVRVPGCAHHADSLYTYPVATQCHCGKCDSDSTDCTVRGLGPSYCSFG",
|
| 40 |
+
"CHHRICHCSNRVFLCQESKVTEIPSDLPRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLE"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Glycoprotein hormones alpha chain",
|
| 45 |
+
"Follitropin subunit beta",
|
| 46 |
+
"Follicle-stimulating hormone receptor",
|
| 47 |
+
"LRRNT"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 6860,
|
| 59 |
+
"SYSTRES": 437,
|
| 60 |
+
"PROTATS": 6860,
|
| 61 |
+
"PROTRES": 437,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"name": "chain A-chain C interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain C",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "chain B-chain C interaction",
|
| 92 |
+
"agent_1": "chain B",
|
| 93 |
+
"agent_2": "chain C",
|
| 94 |
+
"selection_1": "chain B",
|
| 95 |
+
"selection_2": "chain C",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
}
|
| 98 |
+
],
|
| 99 |
+
"PBC_SELECTION": null,
|
| 100 |
+
"CHAINNAMES": null,
|
| 101 |
+
"MEMBRANES": null,
|
| 102 |
+
"CUSTOMS": null,
|
| 103 |
+
"ORIENTATION": null,
|
| 104 |
+
"PTM": [],
|
| 105 |
+
"MULTIMERIC": null,
|
| 106 |
+
"COLLECTIONS": "dynarepo",
|
| 107 |
+
"WARNINGS": [],
|
| 108 |
+
"BOXSIZEX": 10.4989,
|
| 109 |
+
"BOXSIZEY": 10.4989,
|
| 110 |
+
"BOXSIZEZ": 7.4077,
|
| 111 |
+
"mdName": "replica 1",
|
| 112 |
+
"mdAtoms": 6860,
|
| 113 |
+
"mdFrames": 5001
|
| 114 |
+
},
|
| 115 |
+
"mds": [
|
| 116 |
+
"replica 1",
|
| 117 |
+
"replica 2",
|
| 118 |
+
"replica 3"
|
| 119 |
+
],
|
| 120 |
+
"mdref": 0,
|
| 121 |
+
"files": [
|
| 122 |
+
"topology.tpr",
|
| 123 |
+
"screenshot.jpg",
|
| 124 |
+
"trajectory.bin",
|
| 125 |
+
"pca_trajectory_01.bin",
|
| 126 |
+
"pca_trajectory_02.bin",
|
| 127 |
+
"pca_trajectory_03.bin",
|
| 128 |
+
"pca_trajectory_04.bin",
|
| 129 |
+
"pca_trajectory_05.bin",
|
| 130 |
+
"pca_trajectory_06.bin",
|
| 131 |
+
"pca_trajectory_07.bin",
|
| 132 |
+
"pca_trajectory_08.bin",
|
| 133 |
+
"pca_trajectory_09.bin",
|
| 134 |
+
"pca_trajectory_10.bin",
|
| 135 |
+
"pca_trajectory_11.bin",
|
| 136 |
+
"structure.pdb",
|
| 137 |
+
"trajectory.xtc",
|
| 138 |
+
"clusters_00_screenshot_00.jpg",
|
| 139 |
+
"clusters_00_screenshot_01.jpg",
|
| 140 |
+
"clusters_00_screenshot_02.jpg",
|
| 141 |
+
"clusters_00_screenshot_03.jpg",
|
| 142 |
+
"clusters_00_screenshot_04.jpg",
|
| 143 |
+
"clusters_00_screenshot_05.jpg",
|
| 144 |
+
"clusters_00_screenshot_06.jpg",
|
| 145 |
+
"clusters_00_screenshot_07.jpg",
|
| 146 |
+
"clusters_00_screenshot_08.jpg",
|
| 147 |
+
"clusters_00_screenshot_09.jpg",
|
| 148 |
+
"clusters_00_screenshot_10.jpg",
|
| 149 |
+
"clusters_00_screenshot_11.jpg",
|
| 150 |
+
"clusters_00_screenshot_12.jpg",
|
| 151 |
+
"clusters_00_screenshot_13.jpg",
|
| 152 |
+
"clusters_00_screenshot_14.jpg",
|
| 153 |
+
"clusters_00_screenshot_15.jpg",
|
| 154 |
+
"clusters_00_screenshot_16.jpg",
|
| 155 |
+
"clusters_00_screenshot_17.jpg",
|
| 156 |
+
"clusters_00_screenshot_18.jpg",
|
| 157 |
+
"clusters_00_screenshot_19.jpg",
|
| 158 |
+
"clusters_00_screenshot_20.jpg",
|
| 159 |
+
"clusters_01_screenshot_00.jpg",
|
| 160 |
+
"clusters_01_screenshot_01.jpg",
|
| 161 |
+
"clusters_01_screenshot_02.jpg",
|
| 162 |
+
"clusters_01_screenshot_03.jpg",
|
| 163 |
+
"clusters_01_screenshot_04.jpg",
|
| 164 |
+
"clusters_01_screenshot_05.jpg",
|
| 165 |
+
"clusters_01_screenshot_06.jpg",
|
| 166 |
+
"clusters_01_screenshot_07.jpg",
|
| 167 |
+
"clusters_01_screenshot_08.jpg",
|
| 168 |
+
"clusters_01_screenshot_09.jpg",
|
| 169 |
+
"clusters_01_screenshot_10.jpg",
|
| 170 |
+
"clusters_01_screenshot_11.jpg",
|
| 171 |
+
"clusters_01_screenshot_12.jpg",
|
| 172 |
+
"clusters_01_screenshot_13.jpg",
|
| 173 |
+
"clusters_01_screenshot_14.jpg",
|
| 174 |
+
"clusters_01_screenshot_15.jpg",
|
| 175 |
+
"clusters_01_screenshot_16.jpg",
|
| 176 |
+
"clusters_01_screenshot_17.jpg",
|
| 177 |
+
"clusters_01_screenshot_18.jpg",
|
| 178 |
+
"clusters_02_screenshot_00.jpg",
|
| 179 |
+
"clusters_02_screenshot_01.jpg",
|
| 180 |
+
"clusters_02_screenshot_02.jpg",
|
| 181 |
+
"clusters_02_screenshot_03.jpg",
|
| 182 |
+
"clusters_02_screenshot_04.jpg",
|
| 183 |
+
"clusters_02_screenshot_05.jpg",
|
| 184 |
+
"clusters_02_screenshot_06.jpg",
|
| 185 |
+
"clusters_02_screenshot_07.jpg",
|
| 186 |
+
"clusters_02_screenshot_08.jpg",
|
| 187 |
+
"clusters_02_screenshot_09.jpg",
|
| 188 |
+
"clusters_02_screenshot_10.jpg",
|
| 189 |
+
"clusters_02_screenshot_11.jpg",
|
| 190 |
+
"clusters_02_screenshot_12.jpg",
|
| 191 |
+
"clusters_02_screenshot_13.jpg",
|
| 192 |
+
"clusters_02_screenshot_14.jpg",
|
| 193 |
+
"clusters_02_screenshot_15.jpg",
|
| 194 |
+
"clusters_02_screenshot_16.jpg",
|
| 195 |
+
"clusters_02_screenshot_17.jpg",
|
| 196 |
+
"clusters_02_screenshot_18.jpg",
|
| 197 |
+
"clusters_02_screenshot_19.jpg",
|
| 198 |
+
"clusters_03_screenshot_00.jpg",
|
| 199 |
+
"clusters_03_screenshot_01.jpg",
|
| 200 |
+
"clusters_03_screenshot_02.jpg",
|
| 201 |
+
"clusters_03_screenshot_03.jpg",
|
| 202 |
+
"clusters_03_screenshot_04.jpg",
|
| 203 |
+
"clusters_03_screenshot_05.jpg",
|
| 204 |
+
"clusters_03_screenshot_06.jpg",
|
| 205 |
+
"clusters_03_screenshot_07.jpg",
|
| 206 |
+
"clusters_03_screenshot_08.jpg",
|
| 207 |
+
"clusters_03_screenshot_09.jpg",
|
| 208 |
+
"clusters_03_screenshot_10.jpg",
|
| 209 |
+
"clusters_03_screenshot_11.jpg",
|
| 210 |
+
"clusters_03_screenshot_12.jpg",
|
| 211 |
+
"clusters_03_screenshot_13.jpg",
|
| 212 |
+
"clusters_03_screenshot_14.jpg",
|
| 213 |
+
"clusters_03_screenshot_15.jpg",
|
| 214 |
+
"clusters_03_screenshot_16.jpg",
|
| 215 |
+
"clusters_03_screenshot_17.jpg",
|
| 216 |
+
"clusters_03_screenshot_18.jpg",
|
| 217 |
+
"clusters_03_screenshot_19.jpg",
|
| 218 |
+
"clusters_03_screenshot_20.jpg",
|
| 219 |
+
"pocket_01.pdb",
|
| 220 |
+
"pocket_02.pdb",
|
| 221 |
+
"pocket_03.pdb",
|
| 222 |
+
"pocket_04.pdb",
|
| 223 |
+
"pocket_05.pdb",
|
| 224 |
+
"pocket_06.pdb",
|
| 225 |
+
"pocket_07.pdb",
|
| 226 |
+
"pocket_08.pdb",
|
| 227 |
+
"pocket_09.pdb",
|
| 228 |
+
"pocket_10.pdb"
|
| 229 |
+
],
|
| 230 |
+
"analyses": [
|
| 231 |
+
"clusters",
|
| 232 |
+
"clusters-00",
|
| 233 |
+
"clusters-01",
|
| 234 |
+
"clusters-02",
|
| 235 |
+
"clusters-03",
|
| 236 |
+
"dist-perres",
|
| 237 |
+
"energies",
|
| 238 |
+
"fluctuation",
|
| 239 |
+
"hbonds",
|
| 240 |
+
"interactions",
|
| 241 |
+
"pca",
|
| 242 |
+
"pockets",
|
| 243 |
+
"rgyr",
|
| 244 |
+
"rmsd-pairwise",
|
| 245 |
+
"rmsd-perres",
|
| 246 |
+
"rmsds",
|
| 247 |
+
"sasa",
|
| 248 |
+
"tmscores"
|
| 249 |
+
],
|
| 250 |
+
"mdIndex": 0,
|
| 251 |
+
"mdNumber": 1,
|
| 252 |
+
"refframe": 0,
|
| 253 |
+
"internalId": "683f8e0633451f98db78e62b",
|
| 254 |
+
"creationDate": "2025-06-04T00:06:30.000Z",
|
| 255 |
+
"identifier": "A002G"
|
| 256 |
+
}
|
data/files/A002G/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002G", "accession": "A002G", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XWD", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XWD"], "FORCED_REFERENCES": null, "REFERENCES": ["P01215", "P01225", "P23945"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS", "CELTNITIAIEKEECRFCISINTTWCAGYCYTRDLVYKDPARPKIQKTCTFKELVYETVRVPGCAHHADSLYTYPVATQCHCGKCDSDSTDCTVRGLGPSYCSFG", "CHHRICHCSNRVFLCQESKVTEIPSDLPRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLE"], "NUCLSEQ": [], "DOMAINS": ["Glycoprotein hormones alpha chain", "Follitropin subunit beta", "Follicle-stimulating hormone receptor", "LRRNT"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6860, "SYSTRES": 437, "PROTATS": 6860, "PROTRES": 437, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.4989, "BOXSIZEY": 10.4989, "BOXSIZEZ": 7.4077, "mdName": "replica 1", "mdAtoms": 6860, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002G/files/topology.tpr", "length": 2187668, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002G/files/screenshot.jpg", "length": 23813, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002G/files/trajectory.bin", "length": 411682320, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 5001, "atoms": 6860}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_01.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_02.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_03.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_04.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_05.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_06.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_07.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_08.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_09.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_10.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_11.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002G/files/structure.pdb", "length": 555695, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002G/files/trajectory.xtc", "length": 130414556, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_00.jpg", "length": 23832, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_01.jpg", "length": 24330, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_02.jpg", "length": 23711, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_03.jpg", "length": 23524, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_04.jpg", "length": 23301, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_05.jpg", "length": 23617, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_06.jpg", "length": 23949, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_07.jpg", "length": 23676, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_08.jpg", "length": 23873, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_09.jpg", "length": 23693, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_10.jpg", "length": 23565, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_11.jpg", "length": 23614, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_12.jpg", "length": 23882, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_13.jpg", "length": 23673, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_14.jpg", "length": 23531, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_15.jpg", "length": 23292, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_16.jpg", "length": 24008, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_17.jpg", "length": 23557, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_18.jpg", "length": 23200, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_19.jpg", "length": 23663, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_20.jpg", "length": 23773, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_00.jpg", "length": 23656, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_01.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_02.jpg", "length": 23885, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_03.jpg", "length": 23770, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_04.jpg", "length": 23833, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_05.jpg", "length": 23954, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_06.jpg", "length": 23555, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_07.jpg", "length": 23487, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_08.jpg", "length": 24236, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_09.jpg", "length": 24079, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_10.jpg", "length": 24043, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_11.jpg", "length": 23894, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_12.jpg", "length": 23903, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_13.jpg", "length": 23775, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_14.jpg", "length": 23977, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_15.jpg", "length": 23761, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_16.jpg", "length": 23572, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_17.jpg", "length": 23950, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_18.jpg", "length": 24263, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_00.jpg", "length": 23556, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_01.jpg", "length": 23833, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_02.jpg", "length": 23441, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_03.jpg", "length": 23333, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_04.jpg", "length": 23705, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_05.jpg", "length": 23063, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_06.jpg", "length": 22677, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_07.jpg", "length": 23407, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_08.jpg", "length": 22924, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_09.jpg", "length": 23199, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_10.jpg", "length": 23239, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_11.jpg", "length": 23088, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_12.jpg", "length": 23152, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_13.jpg", "length": 23042, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_14.jpg", "length": 22753, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_15.jpg", "length": 23113, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_16.jpg", "length": 23122, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_17.jpg", "length": 22989, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_18.jpg", "length": 23201, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_19.jpg", "length": 22686, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_00.jpg", "length": 23774, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_01.jpg", "length": 24381, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_02.jpg", "length": 23679, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_03.jpg", "length": 23526, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_04.jpg", "length": 24180, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_05.jpg", "length": 23436, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_06.jpg", "length": 23035, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_07.jpg", "length": 23799, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_08.jpg", "length": 23010, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_09.jpg", "length": 23718, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_10.jpg", "length": 23903, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_11.jpg", "length": 24010, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_12.jpg", "length": 23575, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_13.jpg", "length": 23810, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_14.jpg", "length": 23820, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_15.jpg", "length": 23553, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_16.jpg", "length": 23502, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_17.jpg", "length": 23620, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_18.jpg", "length": 23372, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_19.jpg", "length": 22926, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_20.jpg", "length": 23565, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002G/files/pocket_01.pdb", "length": 49647, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002G/files/pocket_02.pdb", "length": 31892, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002G/files/pocket_03.pdb", "length": 13869, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002G/files/pocket_04.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002G/files/pocket_05.pdb", "length": 10251, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002G/files/pocket_06.pdb", "length": 9983, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002G/files/pocket_07.pdb", "length": 9313, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002G/files/pocket_08.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002G/files/pocket_09.pdb", "length": 6834, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002G/files/pocket_10.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002G", "accession": "A002G", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XWD", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XWD"], "FORCED_REFERENCES": null, "REFERENCES": ["P01215", "P01225", "P23945"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS", "CELTNITIAIEKEECRFCISINTTWCAGYCYTRDLVYKDPARPKIQKTCTFKELVYETVRVPGCAHHADSLYTYPVATQCHCGKCDSDSTDCTVRGLGPSYCSFG", "CHHRICHCSNRVFLCQESKVTEIPSDLPRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLE"], "NUCLSEQ": [], "DOMAINS": ["Glycoprotein hormones alpha chain", "Follitropin subunit beta", "Follicle-stimulating hormone receptor", "LRRNT"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6860, "SYSTRES": 437, "PROTATS": 6860, "PROTRES": 437, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.4989, "BOXSIZEY": 10.4989, "BOXSIZEZ": 7.4077, "mdName": "replica 1", "mdAtoms": 6860, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002G/files/topology.tpr", "length": 2187668, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002G/files/screenshot.jpg", "length": 23813, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002G/files/trajectory.bin", "length": 411682320, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 5001, "atoms": 6860}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_01.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_02.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_03.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_04.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_05.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_06.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_07.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_08.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_09.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_10.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_11.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002G/files/structure.pdb", "length": 555695, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002G/files/trajectory.xtc", "length": 130414556, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_00.jpg", "length": 23832, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_01.jpg", "length": 24330, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_02.jpg", "length": 23711, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_03.jpg", "length": 23524, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_04.jpg", "length": 23301, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_05.jpg", "length": 23617, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_06.jpg", "length": 23949, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_07.jpg", "length": 23676, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_08.jpg", "length": 23873, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_09.jpg", "length": 23693, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_10.jpg", "length": 23565, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_11.jpg", "length": 23614, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_12.jpg", "length": 23882, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_13.jpg", "length": 23673, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_14.jpg", "length": 23531, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_15.jpg", "length": 23292, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_16.jpg", "length": 24008, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_17.jpg", "length": 23557, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_18.jpg", "length": 23200, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_19.jpg", "length": 23663, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_20.jpg", "length": 23773, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_00.jpg", "length": 23656, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_01.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_02.jpg", "length": 23885, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_03.jpg", "length": 23770, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_04.jpg", "length": 23833, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_05.jpg", "length": 23954, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_06.jpg", "length": 23555, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_07.jpg", "length": 23487, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_08.jpg", "length": 24236, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_09.jpg", "length": 24079, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_10.jpg", "length": 24043, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_11.jpg", "length": 23894, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_12.jpg", "length": 23903, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_13.jpg", "length": 23775, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_14.jpg", "length": 23977, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_15.jpg", "length": 23761, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_16.jpg", "length": 23572, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_17.jpg", "length": 23950, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_18.jpg", "length": 24263, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_00.jpg", "length": 23556, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_01.jpg", "length": 23833, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_02.jpg", "length": 23441, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_03.jpg", "length": 23333, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_04.jpg", "length": 23705, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_05.jpg", "length": 23063, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_06.jpg", "length": 22677, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_07.jpg", "length": 23407, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_08.jpg", "length": 22924, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_09.jpg", "length": 23199, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_10.jpg", "length": 23239, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_11.jpg", "length": 23088, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_12.jpg", "length": 23152, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_13.jpg", "length": 23042, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_14.jpg", "length": 22753, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_15.jpg", "length": 23113, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_16.jpg", "length": 23122, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_17.jpg", "length": 22989, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_18.jpg", "length": 23201, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_19.jpg", "length": 22686, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_00.jpg", "length": 23774, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_01.jpg", "length": 24381, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_02.jpg", "length": 23679, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_03.jpg", "length": 23526, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_04.jpg", "length": 24180, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_05.jpg", "length": 23436, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_06.jpg", "length": 23035, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_07.jpg", "length": 23799, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_08.jpg", "length": 23010, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_09.jpg", "length": 23718, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_10.jpg", "length": 23903, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_11.jpg", "length": 24010, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_12.jpg", "length": 23575, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_13.jpg", "length": 23810, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_14.jpg", "length": 23820, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_15.jpg", "length": 23553, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_16.jpg", "length": 23502, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_17.jpg", "length": 23620, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_18.jpg", "length": 23372, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_19.jpg", "length": 22926, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_20.jpg", "length": 23565, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002G/files/pocket_01.pdb", "length": 49647, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002G/files/pocket_02.pdb", "length": 31892, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002G/files/pocket_03.pdb", "length": 13869, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002G/files/pocket_04.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002G/files/pocket_05.pdb", "length": 10251, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002G/files/pocket_06.pdb", "length": 9983, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002G/files/pocket_07.pdb", "length": 9313, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002G/files/pocket_08.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002G/files/pocket_09.pdb", "length": 6834, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002G/files/pocket_10.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002G", "accession": "A002G", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1XWD", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1XWD"], "FORCED_REFERENCES": null, "REFERENCES": ["P01215", "P01225", "P23945"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS", "CELTNITIAIEKEECRFCISINTTWCAGYCYTRDLVYKDPARPKIQKTCTFKELVYETVRVPGCAHHADSLYTYPVATQCHCGKCDSDSTDCTVRGLGPSYCSFG", "CHHRICHCSNRVFLCQESKVTEIPSDLPRNAIELRFVLTKLRVIQKGAFSGFGDLEKIEISQNDVLEVIEADVFSNLPKLHEIRIEKANNLLYINPEAFQNLPNLQYLLISNTGIKHLPDVHKIHSLQKVLLDIQDNINIHTIERNSFVGLSFESVILWLNKNGIQEIHNCAFNGTQLDELNLSDNNNLEELPNDVFHGASGPVILDISRTRIHSLPSYGLENLKKLRARSTYNLKKLPTLE"], "NUCLSEQ": [], "DOMAINS": ["Glycoprotein hormones alpha chain", "Follitropin subunit beta", "Follicle-stimulating hormone receptor", "LRRNT"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6860, "SYSTRES": 437, "PROTATS": 6860, "PROTRES": 437, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.4989, "BOXSIZEY": 10.4989, "BOXSIZEZ": 7.4077, "mdName": "replica 1", "mdAtoms": 6860, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002G/files/topology.tpr", "length": 2187668, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002G/files/screenshot.jpg", "length": 23813, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002G/files/trajectory.bin", "length": 411682320, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 5001, "atoms": 6860}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_01.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_02.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_03.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_04.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_05.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_06.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_07.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_08.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_09.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_10.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002G/files/pca_trajectory_11.bin", "length": 314640, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0, "frames": 20, "atoms": 1311}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002G/files/structure.pdb", "length": 555695, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002G/files/trajectory.xtc", "length": 130414556, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_00.jpg", "length": 23832, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_01.jpg", "length": 24330, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_02.jpg", "length": 23711, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_03.jpg", "length": 23524, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_04.jpg", "length": 23301, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_05.jpg", "length": 23617, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_06.jpg", "length": 23949, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_07.jpg", "length": 23676, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_08.jpg", "length": 23873, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_09.jpg", "length": 23693, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_10.jpg", "length": 23565, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_11.jpg", "length": 23614, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_12.jpg", "length": 23882, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_13.jpg", "length": 23673, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_14.jpg", "length": 23531, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_15.jpg", "length": 23292, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_16.jpg", "length": 24008, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_17.jpg", "length": 23557, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_18.jpg", "length": 23200, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_19.jpg", "length": 23663, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002G/files/clusters_00_screenshot_20.jpg", "length": 23773, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_00.jpg", "length": 23656, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_01.jpg", "length": 24097, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_02.jpg", "length": 23885, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_03.jpg", "length": 23770, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_04.jpg", "length": 23833, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_05.jpg", "length": 23954, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_06.jpg", "length": 23555, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_07.jpg", "length": 23487, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_08.jpg", "length": 24236, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_09.jpg", "length": 24079, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_10.jpg", "length": 24043, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_11.jpg", "length": 23894, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_12.jpg", "length": 23903, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_13.jpg", "length": 23775, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_14.jpg", "length": 23977, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_15.jpg", "length": 23761, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_16.jpg", "length": 23572, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_17.jpg", "length": 23950, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_01_screenshot_18.jpg", "length": 24263, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_00.jpg", "length": 23556, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_01.jpg", "length": 23833, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_02.jpg", "length": 23441, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_03.jpg", "length": 23333, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_04.jpg", "length": 23705, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_05.jpg", "length": 23063, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_06.jpg", "length": 22677, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_07.jpg", "length": 23407, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_08.jpg", "length": 22924, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_09.jpg", "length": 23199, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_10.jpg", "length": 23239, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_11.jpg", "length": 23088, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_12.jpg", "length": 23152, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_13.jpg", "length": 23042, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_14.jpg", "length": 22753, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_15.jpg", "length": 23113, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_16.jpg", "length": 23122, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_17.jpg", "length": 22989, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_18.jpg", "length": 23201, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_02_screenshot_19.jpg", "length": 22686, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_00.jpg", "length": 23774, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_01.jpg", "length": 24381, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_02.jpg", "length": 23679, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_03.jpg", "length": 23526, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_04.jpg", "length": 24180, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_05.jpg", "length": 23436, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_06.jpg", "length": 23035, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_07.jpg", "length": 23799, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_08.jpg", "length": 23010, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_09.jpg", "length": 23718, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_10.jpg", "length": 23903, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_11.jpg", "length": 24010, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_12.jpg", "length": 23575, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_13.jpg", "length": 23810, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_14.jpg", "length": 23820, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_15.jpg", "length": 23553, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_16.jpg", "length": 23502, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_17.jpg", "length": 23620, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_18.jpg", "length": 23372, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_19.jpg", "length": 22926, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002G/files/clusters_03_screenshot_20.jpg", "length": 23565, "contentType": "application/octet-stream", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002G/files/pocket_01.pdb", "length": 49647, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002G/files/pocket_02.pdb", "length": 31892, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002G/files/pocket_03.pdb", "length": 13869, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002G/files/pocket_04.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002G/files/pocket_05.pdb", "length": 10251, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002G/files/pocket_06.pdb", "length": 9983, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002G/files/pocket_07.pdb", "length": 9313, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002G/files/pocket_08.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002G/files/pocket_09.pdb", "length": 6834, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002G/files/pocket_10.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f8e0633451f98db78e62b", "md": 0}}]}
|
data/files/A002H/project.json
ADDED
|
@@ -0,0 +1,206 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002H",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1YCS",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1YCS"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P04637",
|
| 31 |
+
"Q13625"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRXPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMXNSSXMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEE",
|
| 38 |
+
"PLALLLDSSLEGEFDLVQRIIYEVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQFGVNVNAADSDGWTPLHCAASCNNVQVCKFLVESGAAVFAMTYSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGYVPRNLLGLYP"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Cellular tumor antigen p53",
|
| 43 |
+
"Interaction with CCAR2",
|
| 44 |
+
"Disordered",
|
| 45 |
+
"Interaction with WWOX",
|
| 46 |
+
"Interaction with HIPK1",
|
| 47 |
+
"Required for interaction with ZNF385A",
|
| 48 |
+
"Required for interaction with FBXO42",
|
| 49 |
+
"Interaction with AXIN1",
|
| 50 |
+
"Interaction with the 53BP2 SH3 domain",
|
| 51 |
+
"Interaction with E4F1",
|
| 52 |
+
"Interaction with DNA",
|
| 53 |
+
"Apoptosis-stimulating of p53 protein 2",
|
| 54 |
+
"SH3",
|
| 55 |
+
"Mediates interaction with APC2"
|
| 56 |
+
],
|
| 57 |
+
"FRAMESTEP": 0.1,
|
| 58 |
+
"TIMESTEP": 2,
|
| 59 |
+
"TEMP": 310,
|
| 60 |
+
"ENSEMBLE": "NPT",
|
| 61 |
+
"FF": [
|
| 62 |
+
"CHARMM36m"
|
| 63 |
+
],
|
| 64 |
+
"WAT": "TIP3P",
|
| 65 |
+
"BOXTYPE": "Dodecahedron",
|
| 66 |
+
"SYSTATS": 5917,
|
| 67 |
+
"SYSTRES": 384,
|
| 68 |
+
"PROTATS": 5917,
|
| 69 |
+
"PROTRES": 384,
|
| 70 |
+
"NUCLATS": 0,
|
| 71 |
+
"NUCLRES": 0,
|
| 72 |
+
"LIPIATS": 0,
|
| 73 |
+
"LIPIRES": 0,
|
| 74 |
+
"CARBATS": 0,
|
| 75 |
+
"CARBRES": 0,
|
| 76 |
+
"SOLVATS": 0,
|
| 77 |
+
"SOLVRES": 0,
|
| 78 |
+
"COUNCAT": 0,
|
| 79 |
+
"COUNANI": 0,
|
| 80 |
+
"COUNION": 0,
|
| 81 |
+
"INTERACTIONS": [
|
| 82 |
+
{
|
| 83 |
+
"name": "chain A-chain B interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain B",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain B",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
}
|
| 90 |
+
],
|
| 91 |
+
"PBC_SELECTION": null,
|
| 92 |
+
"CHAINNAMES": null,
|
| 93 |
+
"MEMBRANES": null,
|
| 94 |
+
"CUSTOMS": null,
|
| 95 |
+
"ORIENTATION": null,
|
| 96 |
+
"PTM": [],
|
| 97 |
+
"MULTIMERIC": null,
|
| 98 |
+
"COLLECTIONS": "dynarepo",
|
| 99 |
+
"WARNINGS": [],
|
| 100 |
+
"BOXSIZEX": 11.12,
|
| 101 |
+
"BOXSIZEY": 11.12,
|
| 102 |
+
"BOXSIZEZ": 7.81413,
|
| 103 |
+
"mdName": "replica 1",
|
| 104 |
+
"mdAtoms": 5917,
|
| 105 |
+
"mdFrames": 5001
|
| 106 |
+
},
|
| 107 |
+
"mds": [
|
| 108 |
+
"replica 1",
|
| 109 |
+
"replica 2",
|
| 110 |
+
"replica 3"
|
| 111 |
+
],
|
| 112 |
+
"mdref": 0,
|
| 113 |
+
"files": [
|
| 114 |
+
"topology.tpr",
|
| 115 |
+
"screenshot.jpg",
|
| 116 |
+
"trajectory.bin",
|
| 117 |
+
"pca_trajectory_01.bin",
|
| 118 |
+
"pca_trajectory_02.bin",
|
| 119 |
+
"pca_trajectory_03.bin",
|
| 120 |
+
"pca_trajectory_04.bin",
|
| 121 |
+
"pca_trajectory_05.bin",
|
| 122 |
+
"pca_trajectory_06.bin",
|
| 123 |
+
"pca_trajectory_07.bin",
|
| 124 |
+
"pca_trajectory_08.bin",
|
| 125 |
+
"pca_trajectory_09.bin",
|
| 126 |
+
"pca_trajectory_10.bin",
|
| 127 |
+
"pca_trajectory_11.bin",
|
| 128 |
+
"pca_trajectory_12.bin",
|
| 129 |
+
"pca_trajectory_13.bin",
|
| 130 |
+
"pca_trajectory_14.bin",
|
| 131 |
+
"pca_trajectory_15.bin",
|
| 132 |
+
"pca_trajectory_16.bin",
|
| 133 |
+
"structure.pdb",
|
| 134 |
+
"trajectory.xtc",
|
| 135 |
+
"clusters_00_screenshot_00.jpg",
|
| 136 |
+
"clusters_00_screenshot_01.jpg",
|
| 137 |
+
"clusters_00_screenshot_02.jpg",
|
| 138 |
+
"clusters_00_screenshot_03.jpg",
|
| 139 |
+
"clusters_00_screenshot_04.jpg",
|
| 140 |
+
"clusters_00_screenshot_05.jpg",
|
| 141 |
+
"clusters_00_screenshot_06.jpg",
|
| 142 |
+
"clusters_00_screenshot_07.jpg",
|
| 143 |
+
"clusters_00_screenshot_08.jpg",
|
| 144 |
+
"clusters_00_screenshot_09.jpg",
|
| 145 |
+
"clusters_00_screenshot_10.jpg",
|
| 146 |
+
"clusters_00_screenshot_11.jpg",
|
| 147 |
+
"clusters_00_screenshot_12.jpg",
|
| 148 |
+
"clusters_00_screenshot_13.jpg",
|
| 149 |
+
"clusters_00_screenshot_14.jpg",
|
| 150 |
+
"clusters_00_screenshot_15.jpg",
|
| 151 |
+
"clusters_00_screenshot_16.jpg",
|
| 152 |
+
"clusters_00_screenshot_17.jpg",
|
| 153 |
+
"clusters_00_screenshot_18.jpg",
|
| 154 |
+
"clusters_00_screenshot_19.jpg",
|
| 155 |
+
"clusters_01_screenshot_00.jpg",
|
| 156 |
+
"clusters_01_screenshot_01.jpg",
|
| 157 |
+
"clusters_01_screenshot_02.jpg",
|
| 158 |
+
"clusters_01_screenshot_03.jpg",
|
| 159 |
+
"clusters_01_screenshot_04.jpg",
|
| 160 |
+
"clusters_01_screenshot_05.jpg",
|
| 161 |
+
"clusters_01_screenshot_06.jpg",
|
| 162 |
+
"clusters_01_screenshot_07.jpg",
|
| 163 |
+
"clusters_01_screenshot_08.jpg",
|
| 164 |
+
"clusters_01_screenshot_09.jpg",
|
| 165 |
+
"clusters_01_screenshot_10.jpg",
|
| 166 |
+
"clusters_01_screenshot_11.jpg",
|
| 167 |
+
"clusters_01_screenshot_12.jpg",
|
| 168 |
+
"clusters_01_screenshot_13.jpg",
|
| 169 |
+
"clusters_01_screenshot_14.jpg",
|
| 170 |
+
"clusters_01_screenshot_15.jpg",
|
| 171 |
+
"clusters_01_screenshot_16.jpg",
|
| 172 |
+
"clusters_01_screenshot_17.jpg",
|
| 173 |
+
"clusters_01_screenshot_18.jpg",
|
| 174 |
+
"clusters_01_screenshot_19.jpg",
|
| 175 |
+
"pocket_01.pdb",
|
| 176 |
+
"pocket_02.pdb",
|
| 177 |
+
"pocket_03.pdb",
|
| 178 |
+
"pocket_04.pdb",
|
| 179 |
+
"pocket_05.pdb",
|
| 180 |
+
"pocket_06.pdb"
|
| 181 |
+
],
|
| 182 |
+
"analyses": [
|
| 183 |
+
"clusters",
|
| 184 |
+
"clusters-00",
|
| 185 |
+
"clusters-01",
|
| 186 |
+
"dist-perres",
|
| 187 |
+
"energies",
|
| 188 |
+
"fluctuation",
|
| 189 |
+
"hbonds",
|
| 190 |
+
"interactions",
|
| 191 |
+
"pca",
|
| 192 |
+
"pockets",
|
| 193 |
+
"rgyr",
|
| 194 |
+
"rmsd-pairwise",
|
| 195 |
+
"rmsd-perres",
|
| 196 |
+
"rmsds",
|
| 197 |
+
"sasa",
|
| 198 |
+
"tmscores"
|
| 199 |
+
],
|
| 200 |
+
"mdIndex": 0,
|
| 201 |
+
"mdNumber": 1,
|
| 202 |
+
"refframe": 0,
|
| 203 |
+
"internalId": "683f907c819d232493bd0815",
|
| 204 |
+
"creationDate": "2025-06-04T00:17:00.000Z",
|
| 205 |
+
"identifier": "A002H"
|
| 206 |
+
}
|
data/files/A002H/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002H", "accession": "A002H", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1YCS", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1YCS"], "FORCED_REFERENCES": null, "REFERENCES": ["P04637", "Q13625"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRXPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMXNSSXMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEE", "PLALLLDSSLEGEFDLVQRIIYEVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQFGVNVNAADSDGWTPLHCAASCNNVQVCKFLVESGAAVFAMTYSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGYVPRNLLGLYP"], "NUCLSEQ": [], "DOMAINS": ["Cellular tumor antigen p53", "Interaction with CCAR2", "Disordered", "Interaction with WWOX", "Interaction with HIPK1", "Required for interaction with ZNF385A", "Required for interaction with FBXO42", "Interaction with AXIN1", "Interaction with the 53BP2 SH3 domain", "Interaction with E4F1", "Interaction with DNA", "Apoptosis-stimulating of p53 protein 2", "SH3", "Mediates interaction with APC2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 5917, "SYSTRES": 384, "PROTATS": 5917, "PROTRES": 384, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.12, "BOXSIZEY": 11.12, "BOXSIZEZ": 7.81413, "mdName": "replica 1", "mdAtoms": 5917, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002H/files/topology.tpr", "length": 1961604, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002H/files/screenshot.jpg", "length": 22924, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002H/files/trajectory.bin", "length": 355091004, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 5001, "atoms": 5917}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_01.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_02.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_03.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_04.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_05.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_06.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_07.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_08.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_09.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_10.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_11.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_12.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_13.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_14.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_15.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_16.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002H/files/structure.pdb", "length": 479312, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002H/files/trajectory.xtc", "length": 112877796, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_00.jpg", "length": 25511, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_01.jpg", "length": 25026, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_02.jpg", "length": 25081, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_03.jpg", "length": 25184, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_04.jpg", "length": 26071, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_05.jpg", "length": 25231, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_06.jpg", "length": 25250, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_07.jpg", "length": 25664, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_08.jpg", "length": 25820, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_09.jpg", "length": 25973, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_10.jpg", "length": 25901, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_11.jpg", "length": 26187, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_12.jpg", "length": 25935, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_13.jpg", "length": 26200, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_14.jpg", "length": 25346, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_15.jpg", "length": 25650, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_16.jpg", "length": 25558, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_17.jpg", "length": 25557, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_18.jpg", "length": 25083, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_19.jpg", "length": 25400, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_00.jpg", "length": 23368, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_01.jpg", "length": 23254, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_02.jpg", "length": 23824, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_03.jpg", "length": 24188, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_04.jpg", "length": 24115, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_05.jpg", "length": 23798, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_06.jpg", "length": 23692, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_07.jpg", "length": 24254, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_08.jpg", "length": 24071, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_09.jpg", "length": 23603, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_10.jpg", "length": 24089, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_11.jpg", "length": 22900, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_12.jpg", "length": 23690, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_13.jpg", "length": 23447, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_14.jpg", "length": 24282, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_15.jpg", "length": 24101, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_16.jpg", "length": 24003, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_17.jpg", "length": 23985, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_18.jpg", "length": 23966, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_19.jpg", "length": 23492, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002H/files/pocket_01.pdb", "length": 19564, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002H/files/pocket_02.pdb", "length": 16817, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002H/files/pocket_03.pdb", "length": 11122, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002H/files/pocket_04.pdb", "length": 10854, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002H/files/pocket_05.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002H/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002H", "accession": "A002H", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1YCS", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1YCS"], "FORCED_REFERENCES": null, "REFERENCES": ["P04637", "Q13625"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRXPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMXNSSXMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEE", "PLALLLDSSLEGEFDLVQRIIYEVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQFGVNVNAADSDGWTPLHCAASCNNVQVCKFLVESGAAVFAMTYSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGYVPRNLLGLYP"], "NUCLSEQ": [], "DOMAINS": ["Cellular tumor antigen p53", "Interaction with CCAR2", "Disordered", "Interaction with WWOX", "Interaction with HIPK1", "Required for interaction with ZNF385A", "Required for interaction with FBXO42", "Interaction with AXIN1", "Interaction with the 53BP2 SH3 domain", "Interaction with E4F1", "Interaction with DNA", "Apoptosis-stimulating of p53 protein 2", "SH3", "Mediates interaction with APC2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 5917, "SYSTRES": 384, "PROTATS": 5917, "PROTRES": 384, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.12, "BOXSIZEY": 11.12, "BOXSIZEZ": 7.81413, "mdName": "replica 1", "mdAtoms": 5917, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002H/files/topology.tpr", "length": 1961604, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002H/files/screenshot.jpg", "length": 22924, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002H/files/trajectory.bin", "length": 355091004, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 5001, "atoms": 5917}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_01.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_02.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_03.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_04.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_05.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_06.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_07.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_08.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_09.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_10.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_11.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_12.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_13.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_14.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_15.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_16.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002H/files/structure.pdb", "length": 479312, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002H/files/trajectory.xtc", "length": 112877796, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_00.jpg", "length": 25511, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_01.jpg", "length": 25026, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_02.jpg", "length": 25081, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_03.jpg", "length": 25184, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_04.jpg", "length": 26071, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_05.jpg", "length": 25231, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_06.jpg", "length": 25250, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_07.jpg", "length": 25664, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_08.jpg", "length": 25820, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_09.jpg", "length": 25973, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_10.jpg", "length": 25901, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_11.jpg", "length": 26187, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_12.jpg", "length": 25935, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_13.jpg", "length": 26200, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_14.jpg", "length": 25346, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_15.jpg", "length": 25650, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_16.jpg", "length": 25558, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_17.jpg", "length": 25557, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_18.jpg", "length": 25083, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_19.jpg", "length": 25400, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_00.jpg", "length": 23368, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_01.jpg", "length": 23254, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_02.jpg", "length": 23824, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_03.jpg", "length": 24188, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_04.jpg", "length": 24115, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_05.jpg", "length": 23798, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_06.jpg", "length": 23692, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_07.jpg", "length": 24254, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_08.jpg", "length": 24071, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_09.jpg", "length": 23603, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_10.jpg", "length": 24089, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_11.jpg", "length": 22900, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_12.jpg", "length": 23690, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_13.jpg", "length": 23447, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_14.jpg", "length": 24282, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_15.jpg", "length": 24101, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_16.jpg", "length": 24003, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_17.jpg", "length": 23985, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_18.jpg", "length": 23966, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_19.jpg", "length": 23492, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002H/files/pocket_01.pdb", "length": 19564, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002H/files/pocket_02.pdb", "length": 16817, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002H/files/pocket_03.pdb", "length": 11122, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002H/files/pocket_04.pdb", "length": 10854, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002H/files/pocket_05.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002H/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002H", "accession": "A002H", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1YCS", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1YCS"], "FORCED_REFERENCES": null, "REFERENCES": ["P04637", "Q13625"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRXPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMXNSSXMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEE", "PLALLLDSSLEGEFDLVQRIIYEVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQFGVNVNAADSDGWTPLHCAASCNNVQVCKFLVESGAAVFAMTYSDMQTAADKCEEMEEGYTQCSQFLYGVQEKMGIMNKGVIYALWDYEPQNDDELPMKEGDCMTIIHREDEDEIEWWWARLNDKEGYVPRNLLGLYP"], "NUCLSEQ": [], "DOMAINS": ["Cellular tumor antigen p53", "Interaction with CCAR2", "Disordered", "Interaction with WWOX", "Interaction with HIPK1", "Required for interaction with ZNF385A", "Required for interaction with FBXO42", "Interaction with AXIN1", "Interaction with the 53BP2 SH3 domain", "Interaction with E4F1", "Interaction with DNA", "Apoptosis-stimulating of p53 protein 2", "SH3", "Mediates interaction with APC2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 5917, "SYSTRES": 384, "PROTATS": 5917, "PROTRES": 384, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.12, "BOXSIZEY": 11.12, "BOXSIZEZ": 7.81413, "mdName": "replica 1", "mdAtoms": 5917, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002H/files/topology.tpr", "length": 1961604, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002H/files/screenshot.jpg", "length": 22924, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002H/files/trajectory.bin", "length": 355091004, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 5001, "atoms": 5917}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_01.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_02.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_03.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_04.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_05.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_06.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_07.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_08.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_09.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_10.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_11.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_12.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_13.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_14.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_15.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A002H/files/pca_trajectory_16.bin", "length": 276480, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0, "frames": 20, "atoms": 1152}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002H/files/structure.pdb", "length": 479312, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002H/files/trajectory.xtc", "length": 112877796, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_00.jpg", "length": 25511, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_01.jpg", "length": 25026, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_02.jpg", "length": 25081, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_03.jpg", "length": 25184, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_04.jpg", "length": 26071, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_05.jpg", "length": 25231, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_06.jpg", "length": 25250, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_07.jpg", "length": 25664, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_08.jpg", "length": 25820, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_09.jpg", "length": 25973, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_10.jpg", "length": 25901, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_11.jpg", "length": 26187, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_12.jpg", "length": 25935, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_13.jpg", "length": 26200, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_14.jpg", "length": 25346, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_15.jpg", "length": 25650, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_16.jpg", "length": 25558, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_17.jpg", "length": 25557, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_18.jpg", "length": 25083, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002H/files/clusters_00_screenshot_19.jpg", "length": 25400, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_00.jpg", "length": 23368, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_01.jpg", "length": 23254, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_02.jpg", "length": 23824, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_03.jpg", "length": 24188, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_04.jpg", "length": 24115, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_05.jpg", "length": 23798, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_06.jpg", "length": 23692, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_07.jpg", "length": 24254, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_08.jpg", "length": 24071, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_09.jpg", "length": 23603, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_10.jpg", "length": 24089, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_11.jpg", "length": 22900, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_12.jpg", "length": 23690, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_13.jpg", "length": 23447, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_14.jpg", "length": 24282, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_15.jpg", "length": 24101, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_16.jpg", "length": 24003, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_17.jpg", "length": 23985, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_18.jpg", "length": 23966, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002H/files/clusters_01_screenshot_19.jpg", "length": 23492, "contentType": "application/octet-stream", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002H/files/pocket_01.pdb", "length": 19564, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002H/files/pocket_02.pdb", "length": 16817, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002H/files/pocket_03.pdb", "length": 11122, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002H/files/pocket_04.pdb", "length": 10854, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002H/files/pocket_05.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002H/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f907c819d232493bd0815", "md": 0}}]}
|
data/files/A002I/project.json
ADDED
|
@@ -0,0 +1,189 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002I",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1YD8",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1YD8"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0CH28",
|
| 31 |
+
"Q9NZ52"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"IQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG",
|
| 38 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ubiquitin",
|
| 43 |
+
"Ubiquitin-like 2",
|
| 44 |
+
"ADP-ribosylation factor-binding protein GGA3",
|
| 45 |
+
"GAT",
|
| 46 |
+
"Binds to ARF1 (in long isoform)",
|
| 47 |
+
"Unstructured hinge"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 2675,
|
| 59 |
+
"SYSTRES": 165,
|
| 60 |
+
"PROTATS": 2675,
|
| 61 |
+
"PROTRES": 165,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
}
|
| 82 |
+
],
|
| 83 |
+
"PBC_SELECTION": null,
|
| 84 |
+
"CHAINNAMES": null,
|
| 85 |
+
"MEMBRANES": null,
|
| 86 |
+
"CUSTOMS": null,
|
| 87 |
+
"ORIENTATION": null,
|
| 88 |
+
"PTM": [],
|
| 89 |
+
"MULTIMERIC": null,
|
| 90 |
+
"COLLECTIONS": "dynarepo",
|
| 91 |
+
"WARNINGS": [],
|
| 92 |
+
"BOXSIZEX": 8.29306,
|
| 93 |
+
"BOXSIZEY": 8.29306,
|
| 94 |
+
"BOXSIZEZ": 5.84923,
|
| 95 |
+
"mdName": "replica 1",
|
| 96 |
+
"mdAtoms": 2675,
|
| 97 |
+
"mdFrames": 5001
|
| 98 |
+
},
|
| 99 |
+
"mds": [
|
| 100 |
+
"replica 1",
|
| 101 |
+
"replica 2",
|
| 102 |
+
"replica 3"
|
| 103 |
+
],
|
| 104 |
+
"mdref": 0,
|
| 105 |
+
"files": [
|
| 106 |
+
"topology.tpr",
|
| 107 |
+
"screenshot.jpg",
|
| 108 |
+
"trajectory.bin",
|
| 109 |
+
"pca_trajectory_01.bin",
|
| 110 |
+
"pca_trajectory_02.bin",
|
| 111 |
+
"pca_trajectory_03.bin",
|
| 112 |
+
"pca_trajectory_04.bin",
|
| 113 |
+
"pca_trajectory_05.bin",
|
| 114 |
+
"pca_trajectory_06.bin",
|
| 115 |
+
"pca_trajectory_07.bin",
|
| 116 |
+
"pca_trajectory_08.bin",
|
| 117 |
+
"pca_trajectory_09.bin",
|
| 118 |
+
"pca_trajectory_10.bin",
|
| 119 |
+
"pca_trajectory_11.bin",
|
| 120 |
+
"pca_trajectory_12.bin",
|
| 121 |
+
"structure.pdb",
|
| 122 |
+
"trajectory.xtc",
|
| 123 |
+
"clusters_00_screenshot_00.jpg",
|
| 124 |
+
"clusters_00_screenshot_01.jpg",
|
| 125 |
+
"clusters_00_screenshot_02.jpg",
|
| 126 |
+
"clusters_00_screenshot_03.jpg",
|
| 127 |
+
"clusters_00_screenshot_04.jpg",
|
| 128 |
+
"clusters_00_screenshot_05.jpg",
|
| 129 |
+
"clusters_00_screenshot_06.jpg",
|
| 130 |
+
"clusters_00_screenshot_07.jpg",
|
| 131 |
+
"clusters_00_screenshot_08.jpg",
|
| 132 |
+
"clusters_00_screenshot_09.jpg",
|
| 133 |
+
"clusters_00_screenshot_10.jpg",
|
| 134 |
+
"clusters_00_screenshot_11.jpg",
|
| 135 |
+
"clusters_00_screenshot_12.jpg",
|
| 136 |
+
"clusters_00_screenshot_13.jpg",
|
| 137 |
+
"clusters_00_screenshot_14.jpg",
|
| 138 |
+
"clusters_00_screenshot_15.jpg",
|
| 139 |
+
"clusters_00_screenshot_16.jpg",
|
| 140 |
+
"clusters_00_screenshot_17.jpg",
|
| 141 |
+
"clusters_00_screenshot_18.jpg",
|
| 142 |
+
"clusters_00_screenshot_19.jpg",
|
| 143 |
+
"clusters_00_screenshot_20.jpg",
|
| 144 |
+
"clusters_00_screenshot_21.jpg",
|
| 145 |
+
"clusters_01_screenshot_00.jpg",
|
| 146 |
+
"clusters_01_screenshot_01.jpg",
|
| 147 |
+
"clusters_01_screenshot_02.jpg",
|
| 148 |
+
"clusters_01_screenshot_03.jpg",
|
| 149 |
+
"clusters_01_screenshot_04.jpg",
|
| 150 |
+
"clusters_01_screenshot_05.jpg",
|
| 151 |
+
"clusters_01_screenshot_06.jpg",
|
| 152 |
+
"clusters_01_screenshot_07.jpg",
|
| 153 |
+
"clusters_01_screenshot_08.jpg",
|
| 154 |
+
"clusters_01_screenshot_09.jpg",
|
| 155 |
+
"clusters_01_screenshot_10.jpg",
|
| 156 |
+
"clusters_01_screenshot_11.jpg",
|
| 157 |
+
"clusters_01_screenshot_12.jpg",
|
| 158 |
+
"clusters_01_screenshot_13.jpg",
|
| 159 |
+
"clusters_01_screenshot_14.jpg",
|
| 160 |
+
"clusters_01_screenshot_15.jpg",
|
| 161 |
+
"clusters_01_screenshot_16.jpg",
|
| 162 |
+
"clusters_01_screenshot_17.jpg",
|
| 163 |
+
"pocket_01.pdb"
|
| 164 |
+
],
|
| 165 |
+
"analyses": [
|
| 166 |
+
"clusters",
|
| 167 |
+
"clusters-00",
|
| 168 |
+
"clusters-01",
|
| 169 |
+
"dist-perres",
|
| 170 |
+
"energies",
|
| 171 |
+
"fluctuation",
|
| 172 |
+
"hbonds",
|
| 173 |
+
"interactions",
|
| 174 |
+
"pca",
|
| 175 |
+
"pockets",
|
| 176 |
+
"rgyr",
|
| 177 |
+
"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
+
"rmsds",
|
| 180 |
+
"sasa",
|
| 181 |
+
"tmscores"
|
| 182 |
+
],
|
| 183 |
+
"mdIndex": 0,
|
| 184 |
+
"mdNumber": 1,
|
| 185 |
+
"refframe": 0,
|
| 186 |
+
"internalId": "683f923f4ea13e3b8852da80",
|
| 187 |
+
"creationDate": "2025-06-04T00:24:31.000Z",
|
| 188 |
+
"identifier": "A002I"
|
| 189 |
+
}
|
data/files/A002I/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002I", "accession": "A002I", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1YD8", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1YD8"], "FORCED_REFERENCES": null, "REFERENCES": ["P0CH28", "Q9NZ52"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["IQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL"], "NUCLSEQ": [], "DOMAINS": ["Ubiquitin", "Ubiquitin-like 2", "ADP-ribosylation factor-binding protein GGA3", "GAT", "Binds to ARF1 (in long isoform)", "Unstructured hinge"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2675, "SYSTRES": 165, "PROTATS": 2675, "PROTRES": 165, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.29306, "BOXSIZEY": 8.29306, "BOXSIZEZ": 5.84923, "mdName": "replica 1", "mdAtoms": 2675, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002I/files/topology.tpr", "length": 1017160, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002I/files/screenshot.jpg", "length": 18900, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002I/files/trajectory.bin", "length": 160532100, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 5001, "atoms": 2675}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_01.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_02.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_03.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_04.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_05.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_06.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_07.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_08.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_09.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_10.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_11.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_12.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002I/files/structure.pdb", "length": 216710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002I/files/trajectory.xtc", "length": 51154960, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_00.jpg", "length": 18485, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_01.jpg", "length": 18212, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_02.jpg", "length": 18004, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_03.jpg", "length": 18315, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_04.jpg", "length": 17456, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_05.jpg", "length": 17781, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_06.jpg", "length": 17716, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_07.jpg", "length": 18109, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_08.jpg", "length": 17848, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_09.jpg", "length": 18079, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_10.jpg", "length": 18117, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_11.jpg", "length": 18431, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_12.jpg", "length": 18016, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_13.jpg", "length": 17756, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_14.jpg", "length": 18657, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_15.jpg", "length": 19077, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_16.jpg", "length": 18154, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_17.jpg", "length": 18005, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_18.jpg", "length": 18017, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_19.jpg", "length": 17656, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_20.jpg", "length": 18293, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_21.jpg", "length": 18299, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_00.jpg", "length": 18302, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_01.jpg", "length": 17579, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_02.jpg", "length": 17902, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_03.jpg", "length": 17506, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_04.jpg", "length": 17396, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_05.jpg", "length": 17821, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_06.jpg", "length": 17810, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_07.jpg", "length": 17877, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_08.jpg", "length": 17362, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_09.jpg", "length": 17377, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_10.jpg", "length": 17796, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_11.jpg", "length": 17521, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_12.jpg", "length": 17927, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_13.jpg", "length": 17872, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_14.jpg", "length": 17907, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_15.jpg", "length": 17989, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_16.jpg", "length": 17502, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_17.jpg", "length": 17333, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002I/files/pocket_01.pdb", "length": 8576, "contentType": "chemical/x-pdb", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002I", "accession": "A002I", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1YD8", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1YD8"], "FORCED_REFERENCES": null, "REFERENCES": ["P0CH28", "Q9NZ52"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["IQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL"], "NUCLSEQ": [], "DOMAINS": ["Ubiquitin", "Ubiquitin-like 2", "ADP-ribosylation factor-binding protein GGA3", "GAT", "Binds to ARF1 (in long isoform)", "Unstructured hinge"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2675, "SYSTRES": 165, "PROTATS": 2675, "PROTRES": 165, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.29306, "BOXSIZEY": 8.29306, "BOXSIZEZ": 5.84923, "mdName": "replica 1", "mdAtoms": 2675, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002I/files/topology.tpr", "length": 1017160, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002I/files/screenshot.jpg", "length": 18900, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002I/files/trajectory.bin", "length": 160532100, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 5001, "atoms": 2675}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_01.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_02.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_03.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_04.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_05.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_06.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_07.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_08.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_09.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_10.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_11.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_12.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002I/files/structure.pdb", "length": 216710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002I/files/trajectory.xtc", "length": 51154960, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_00.jpg", "length": 18485, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_01.jpg", "length": 18212, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_02.jpg", "length": 18004, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_03.jpg", "length": 18315, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_04.jpg", "length": 17456, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_05.jpg", "length": 17781, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_06.jpg", "length": 17716, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_07.jpg", "length": 18109, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_08.jpg", "length": 17848, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_09.jpg", "length": 18079, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_10.jpg", "length": 18117, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_11.jpg", "length": 18431, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_12.jpg", "length": 18016, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_13.jpg", "length": 17756, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_14.jpg", "length": 18657, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_15.jpg", "length": 19077, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_16.jpg", "length": 18154, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_17.jpg", "length": 18005, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_18.jpg", "length": 18017, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_19.jpg", "length": 17656, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_20.jpg", "length": 18293, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_21.jpg", "length": 18299, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_00.jpg", "length": 18302, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_01.jpg", "length": 17579, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_02.jpg", "length": 17902, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_03.jpg", "length": 17506, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_04.jpg", "length": 17396, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_05.jpg", "length": 17821, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_06.jpg", "length": 17810, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_07.jpg", "length": 17877, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_08.jpg", "length": 17362, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_09.jpg", "length": 17377, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_10.jpg", "length": 17796, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_11.jpg", "length": 17521, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_12.jpg", "length": 17927, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_13.jpg", "length": 17872, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_14.jpg", "length": 17907, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_15.jpg", "length": 17989, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_16.jpg", "length": 17502, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_17.jpg", "length": 17333, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002I/files/pocket_01.pdb", "length": 8576, "contentType": "chemical/x-pdb", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002I", "accession": "A002I", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1YD8", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1YD8"], "FORCED_REFERENCES": null, "REFERENCES": ["P0CH28", "Q9NZ52"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["IQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLFKLASETEDNDNSLGDILQASDNLSRVINSYKTIIEG", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL"], "NUCLSEQ": [], "DOMAINS": ["Ubiquitin", "Ubiquitin-like 2", "ADP-ribosylation factor-binding protein GGA3", "GAT", "Binds to ARF1 (in long isoform)", "Unstructured hinge"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2675, "SYSTRES": 165, "PROTATS": 2675, "PROTRES": 165, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.29306, "BOXSIZEY": 8.29306, "BOXSIZEZ": 5.84923, "mdName": "replica 1", "mdAtoms": 2675, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002I/files/topology.tpr", "length": 1017160, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002I/files/screenshot.jpg", "length": 18900, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002I/files/trajectory.bin", "length": 160532100, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 5001, "atoms": 2675}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_01.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_02.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_03.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_04.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_05.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_06.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_07.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_08.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_09.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_10.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_11.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002I/files/pca_trajectory_12.bin", "length": 118800, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0, "frames": 20, "atoms": 495}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002I/files/structure.pdb", "length": 216710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002I/files/trajectory.xtc", "length": 51154960, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_00.jpg", "length": 18485, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_01.jpg", "length": 18212, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_02.jpg", "length": 18004, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_03.jpg", "length": 18315, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_04.jpg", "length": 17456, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_05.jpg", "length": 17781, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_06.jpg", "length": 17716, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_07.jpg", "length": 18109, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_08.jpg", "length": 17848, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_09.jpg", "length": 18079, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_10.jpg", "length": 18117, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_11.jpg", "length": 18431, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_12.jpg", "length": 18016, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_13.jpg", "length": 17756, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_14.jpg", "length": 18657, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_15.jpg", "length": 19077, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_16.jpg", "length": 18154, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_17.jpg", "length": 18005, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_18.jpg", "length": 18017, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_19.jpg", "length": 17656, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_20.jpg", "length": 18293, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A002I/files/clusters_00_screenshot_21.jpg", "length": 18299, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_00.jpg", "length": 18302, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_01.jpg", "length": 17579, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_02.jpg", "length": 17902, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_03.jpg", "length": 17506, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_04.jpg", "length": 17396, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_05.jpg", "length": 17821, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_06.jpg", "length": 17810, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_07.jpg", "length": 17877, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_08.jpg", "length": 17362, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_09.jpg", "length": 17377, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_10.jpg", "length": 17796, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_11.jpg", "length": 17521, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_12.jpg", "length": 17927, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_13.jpg", "length": 17872, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_14.jpg", "length": 17907, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_15.jpg", "length": 17989, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_16.jpg", "length": 17502, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002I/files/clusters_01_screenshot_17.jpg", "length": 17333, "contentType": "application/octet-stream", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002I/files/pocket_01.pdb", "length": 8576, "contentType": "chemical/x-pdb", "metadata": {"project": "683f923f4ea13e3b8852da80", "md": 0}}]}
|
data/files/A002J/project.json
ADDED
|
@@ -0,0 +1,265 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002J",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2AEQ",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2AEQ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q80DL0",
|
| 31 |
+
"P84750",
|
| 32 |
+
"P84751"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELK",
|
| 39 |
+
"AEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKILFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI",
|
| 40 |
+
"EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTMEYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTL"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Head of neuraminidase",
|
| 45 |
+
"Ig kappa chain V region Mem5",
|
| 46 |
+
"Ig-like V-type",
|
| 47 |
+
"Framework-1",
|
| 48 |
+
"Complementarity-determining-1",
|
| 49 |
+
"Framework-2",
|
| 50 |
+
"Complementarity-determining-2",
|
| 51 |
+
"Framework-3",
|
| 52 |
+
"Complementarity-determining-3",
|
| 53 |
+
"Framework-4",
|
| 54 |
+
"Ig heavy chain Mem5",
|
| 55 |
+
"Ig-like 1",
|
| 56 |
+
"D segment",
|
| 57 |
+
"JH2 segment"
|
| 58 |
+
],
|
| 59 |
+
"FRAMESTEP": 0.1,
|
| 60 |
+
"TIMESTEP": 2,
|
| 61 |
+
"TEMP": 310,
|
| 62 |
+
"ENSEMBLE": "NPT",
|
| 63 |
+
"FF": [
|
| 64 |
+
"CHARMM36m"
|
| 65 |
+
],
|
| 66 |
+
"WAT": "TIP3P",
|
| 67 |
+
"BOXTYPE": "Dodecahedron",
|
| 68 |
+
"SYSTATS": 9300,
|
| 69 |
+
"SYSTRES": 611,
|
| 70 |
+
"PROTATS": 9300,
|
| 71 |
+
"PROTRES": 611,
|
| 72 |
+
"NUCLATS": 0,
|
| 73 |
+
"NUCLRES": 0,
|
| 74 |
+
"LIPIATS": 0,
|
| 75 |
+
"LIPIRES": 0,
|
| 76 |
+
"CARBATS": 0,
|
| 77 |
+
"CARBRES": 0,
|
| 78 |
+
"SOLVATS": 0,
|
| 79 |
+
"SOLVRES": 0,
|
| 80 |
+
"COUNCAT": 0,
|
| 81 |
+
"COUNANI": 0,
|
| 82 |
+
"COUNION": 0,
|
| 83 |
+
"INTERACTIONS": [
|
| 84 |
+
{
|
| 85 |
+
"name": "chain A-chain B interaction",
|
| 86 |
+
"agent_1": "chain A",
|
| 87 |
+
"agent_2": "chain B",
|
| 88 |
+
"selection_1": "chain A",
|
| 89 |
+
"selection_2": "chain B",
|
| 90 |
+
"type": "protein-protein"
|
| 91 |
+
},
|
| 92 |
+
{
|
| 93 |
+
"name": "chain A-chain C interaction",
|
| 94 |
+
"agent_1": "chain A",
|
| 95 |
+
"agent_2": "chain C",
|
| 96 |
+
"selection_1": "chain A",
|
| 97 |
+
"selection_2": "chain C",
|
| 98 |
+
"type": "protein-protein"
|
| 99 |
+
},
|
| 100 |
+
{
|
| 101 |
+
"name": "chain B-chain C interaction",
|
| 102 |
+
"agent_1": "chain B",
|
| 103 |
+
"agent_2": "chain C",
|
| 104 |
+
"selection_1": "chain B",
|
| 105 |
+
"selection_2": "chain C",
|
| 106 |
+
"type": "protein-protein"
|
| 107 |
+
}
|
| 108 |
+
],
|
| 109 |
+
"PBC_SELECTION": null,
|
| 110 |
+
"CHAINNAMES": null,
|
| 111 |
+
"MEMBRANES": null,
|
| 112 |
+
"CUSTOMS": null,
|
| 113 |
+
"ORIENTATION": null,
|
| 114 |
+
"PTM": [],
|
| 115 |
+
"MULTIMERIC": null,
|
| 116 |
+
"COLLECTIONS": "dynarepo",
|
| 117 |
+
"WARNINGS": [],
|
| 118 |
+
"BOXSIZEX": 11.559,
|
| 119 |
+
"BOXSIZEY": 11.559,
|
| 120 |
+
"BOXSIZEZ": 8.19652,
|
| 121 |
+
"mdName": "replica 1",
|
| 122 |
+
"mdAtoms": 9300,
|
| 123 |
+
"mdFrames": 5001
|
| 124 |
+
},
|
| 125 |
+
"mds": [
|
| 126 |
+
"replica 1",
|
| 127 |
+
"replica 2",
|
| 128 |
+
"replica 3"
|
| 129 |
+
],
|
| 130 |
+
"mdref": 0,
|
| 131 |
+
"files": [
|
| 132 |
+
"topology.tpr",
|
| 133 |
+
"screenshot.jpg",
|
| 134 |
+
"trajectory.bin",
|
| 135 |
+
"pca_trajectory_01.bin",
|
| 136 |
+
"pca_trajectory_02.bin",
|
| 137 |
+
"pca_trajectory_03.bin",
|
| 138 |
+
"pca_trajectory_04.bin",
|
| 139 |
+
"pca_trajectory_05.bin",
|
| 140 |
+
"pca_trajectory_06.bin",
|
| 141 |
+
"pca_trajectory_07.bin",
|
| 142 |
+
"pca_trajectory_08.bin",
|
| 143 |
+
"pca_trajectory_09.bin",
|
| 144 |
+
"pca_trajectory_10.bin",
|
| 145 |
+
"pca_trajectory_11.bin",
|
| 146 |
+
"pca_trajectory_12.bin",
|
| 147 |
+
"pca_trajectory_13.bin",
|
| 148 |
+
"structure.pdb",
|
| 149 |
+
"trajectory.xtc",
|
| 150 |
+
"clusters_00_screenshot_00.jpg",
|
| 151 |
+
"clusters_00_screenshot_01.jpg",
|
| 152 |
+
"clusters_00_screenshot_02.jpg",
|
| 153 |
+
"clusters_00_screenshot_03.jpg",
|
| 154 |
+
"clusters_00_screenshot_04.jpg",
|
| 155 |
+
"clusters_00_screenshot_05.jpg",
|
| 156 |
+
"clusters_00_screenshot_06.jpg",
|
| 157 |
+
"clusters_00_screenshot_07.jpg",
|
| 158 |
+
"clusters_00_screenshot_08.jpg",
|
| 159 |
+
"clusters_00_screenshot_09.jpg",
|
| 160 |
+
"clusters_00_screenshot_10.jpg",
|
| 161 |
+
"clusters_00_screenshot_11.jpg",
|
| 162 |
+
"clusters_00_screenshot_12.jpg",
|
| 163 |
+
"clusters_00_screenshot_13.jpg",
|
| 164 |
+
"clusters_00_screenshot_14.jpg",
|
| 165 |
+
"clusters_00_screenshot_15.jpg",
|
| 166 |
+
"clusters_00_screenshot_16.jpg",
|
| 167 |
+
"clusters_00_screenshot_17.jpg",
|
| 168 |
+
"clusters_00_screenshot_18.jpg",
|
| 169 |
+
"clusters_00_screenshot_19.jpg",
|
| 170 |
+
"clusters_01_screenshot_00.jpg",
|
| 171 |
+
"clusters_01_screenshot_01.jpg",
|
| 172 |
+
"clusters_01_screenshot_02.jpg",
|
| 173 |
+
"clusters_01_screenshot_03.jpg",
|
| 174 |
+
"clusters_01_screenshot_04.jpg",
|
| 175 |
+
"clusters_01_screenshot_05.jpg",
|
| 176 |
+
"clusters_01_screenshot_06.jpg",
|
| 177 |
+
"clusters_01_screenshot_07.jpg",
|
| 178 |
+
"clusters_01_screenshot_08.jpg",
|
| 179 |
+
"clusters_01_screenshot_09.jpg",
|
| 180 |
+
"clusters_01_screenshot_10.jpg",
|
| 181 |
+
"clusters_01_screenshot_11.jpg",
|
| 182 |
+
"clusters_01_screenshot_12.jpg",
|
| 183 |
+
"clusters_01_screenshot_13.jpg",
|
| 184 |
+
"clusters_01_screenshot_14.jpg",
|
| 185 |
+
"clusters_01_screenshot_15.jpg",
|
| 186 |
+
"clusters_01_screenshot_16.jpg",
|
| 187 |
+
"clusters_01_screenshot_17.jpg",
|
| 188 |
+
"clusters_01_screenshot_18.jpg",
|
| 189 |
+
"clusters_01_screenshot_19.jpg",
|
| 190 |
+
"clusters_02_screenshot_00.jpg",
|
| 191 |
+
"clusters_02_screenshot_01.jpg",
|
| 192 |
+
"clusters_02_screenshot_02.jpg",
|
| 193 |
+
"clusters_02_screenshot_03.jpg",
|
| 194 |
+
"clusters_02_screenshot_04.jpg",
|
| 195 |
+
"clusters_02_screenshot_05.jpg",
|
| 196 |
+
"clusters_02_screenshot_06.jpg",
|
| 197 |
+
"clusters_02_screenshot_07.jpg",
|
| 198 |
+
"clusters_02_screenshot_08.jpg",
|
| 199 |
+
"clusters_02_screenshot_09.jpg",
|
| 200 |
+
"clusters_02_screenshot_10.jpg",
|
| 201 |
+
"clusters_02_screenshot_11.jpg",
|
| 202 |
+
"clusters_02_screenshot_12.jpg",
|
| 203 |
+
"clusters_02_screenshot_13.jpg",
|
| 204 |
+
"clusters_02_screenshot_14.jpg",
|
| 205 |
+
"clusters_02_screenshot_15.jpg",
|
| 206 |
+
"clusters_02_screenshot_16.jpg",
|
| 207 |
+
"clusters_02_screenshot_17.jpg",
|
| 208 |
+
"clusters_02_screenshot_18.jpg",
|
| 209 |
+
"clusters_02_screenshot_19.jpg",
|
| 210 |
+
"clusters_03_screenshot_00.jpg",
|
| 211 |
+
"clusters_03_screenshot_01.jpg",
|
| 212 |
+
"clusters_03_screenshot_02.jpg",
|
| 213 |
+
"clusters_03_screenshot_03.jpg",
|
| 214 |
+
"clusters_03_screenshot_04.jpg",
|
| 215 |
+
"clusters_03_screenshot_05.jpg",
|
| 216 |
+
"clusters_03_screenshot_06.jpg",
|
| 217 |
+
"clusters_03_screenshot_07.jpg",
|
| 218 |
+
"clusters_03_screenshot_08.jpg",
|
| 219 |
+
"clusters_03_screenshot_09.jpg",
|
| 220 |
+
"clusters_03_screenshot_10.jpg",
|
| 221 |
+
"clusters_03_screenshot_11.jpg",
|
| 222 |
+
"clusters_03_screenshot_12.jpg",
|
| 223 |
+
"clusters_03_screenshot_13.jpg",
|
| 224 |
+
"clusters_03_screenshot_14.jpg",
|
| 225 |
+
"clusters_03_screenshot_15.jpg",
|
| 226 |
+
"clusters_03_screenshot_16.jpg",
|
| 227 |
+
"clusters_03_screenshot_17.jpg",
|
| 228 |
+
"pocket_01.pdb",
|
| 229 |
+
"pocket_02.pdb",
|
| 230 |
+
"pocket_03.pdb",
|
| 231 |
+
"pocket_04.pdb",
|
| 232 |
+
"pocket_05.pdb",
|
| 233 |
+
"pocket_06.pdb",
|
| 234 |
+
"pocket_07.pdb",
|
| 235 |
+
"pocket_08.pdb",
|
| 236 |
+
"pocket_09.pdb",
|
| 237 |
+
"pocket_10.pdb"
|
| 238 |
+
],
|
| 239 |
+
"analyses": [
|
| 240 |
+
"clusters",
|
| 241 |
+
"clusters-00",
|
| 242 |
+
"clusters-01",
|
| 243 |
+
"clusters-02",
|
| 244 |
+
"clusters-03",
|
| 245 |
+
"dist-perres",
|
| 246 |
+
"energies",
|
| 247 |
+
"fluctuation",
|
| 248 |
+
"hbonds",
|
| 249 |
+
"interactions",
|
| 250 |
+
"pca",
|
| 251 |
+
"pockets",
|
| 252 |
+
"rgyr",
|
| 253 |
+
"rmsd-pairwise",
|
| 254 |
+
"rmsd-perres",
|
| 255 |
+
"rmsds",
|
| 256 |
+
"sasa",
|
| 257 |
+
"tmscores"
|
| 258 |
+
],
|
| 259 |
+
"mdIndex": 0,
|
| 260 |
+
"mdNumber": 1,
|
| 261 |
+
"refframe": 0,
|
| 262 |
+
"internalId": "683ff4ea7d2501ff97442b43",
|
| 263 |
+
"creationDate": "2025-06-04T07:25:30.000Z",
|
| 264 |
+
"identifier": "A002J"
|
| 265 |
+
}
|
data/files/A002J/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002J", "accession": "A002J", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2AEQ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2AEQ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q80DL0", "P84750", "P84751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELK", "AEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKILFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI", "EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTMEYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTL"], "NUCLSEQ": [], "DOMAINS": ["Head of neuraminidase", "Ig kappa chain V region Mem5", "Ig-like V-type", "Framework-1", "Complementarity-determining-1", "Framework-2", "Complementarity-determining-2", "Framework-3", "Complementarity-determining-3", "Framework-4", "Ig heavy chain Mem5", "Ig-like 1", "D segment", "JH2 segment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 9300, "SYSTRES": 611, "PROTATS": 9300, "PROTRES": 611, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.559, "BOXSIZEY": 11.559, "BOXSIZEZ": 8.19652, "mdName": "replica 1", "mdAtoms": 9300, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002J/files/topology.tpr", "length": 2848092, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002J/files/screenshot.jpg", "length": 23962, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002J/files/trajectory.bin", "length": 558111600, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 5001, "atoms": 9300}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_01.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_02.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_03.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_04.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_05.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_06.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_07.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_08.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_09.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_10.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_11.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_12.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_13.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002J/files/structure.pdb", "length": 753335, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002J/files/trajectory.xtc", "length": 176313492, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_00.jpg", "length": 23900, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_01.jpg", "length": 25224, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_02.jpg", "length": 24740, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_03.jpg", "length": 24438, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_04.jpg", "length": 24878, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_05.jpg", "length": 25438, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_06.jpg", "length": 24968, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_07.jpg", "length": 24327, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_08.jpg", "length": 25173, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_09.jpg", "length": 24908, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_10.jpg", "length": 25063, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_11.jpg", "length": 24821, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_12.jpg", "length": 24698, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_13.jpg", "length": 25290, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_14.jpg", "length": 24391, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_15.jpg", "length": 25015, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_16.jpg", "length": 25423, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_17.jpg", "length": 24566, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_18.jpg", "length": 24665, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_19.jpg", "length": 24476, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_00.jpg", "length": 24443, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_01.jpg", "length": 24100, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_02.jpg", "length": 24389, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_03.jpg", "length": 24002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_04.jpg", "length": 23890, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_05.jpg", "length": 23790, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_06.jpg", "length": 23914, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_07.jpg", "length": 24120, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_08.jpg", "length": 24238, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_09.jpg", "length": 24651, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_10.jpg", "length": 24118, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_11.jpg", "length": 24085, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_12.jpg", "length": 24551, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_13.jpg", "length": 24372, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_14.jpg", "length": 24343, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_15.jpg", "length": 24323, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_16.jpg", "length": 24679, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_17.jpg", "length": 24667, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_18.jpg", "length": 24460, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_19.jpg", "length": 24472, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_00.jpg", "length": 23889, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_01.jpg", "length": 24992, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_02.jpg", "length": 24634, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_03.jpg", "length": 24990, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_04.jpg", "length": 24312, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_05.jpg", "length": 24643, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_06.jpg", "length": 24863, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_07.jpg", "length": 24810, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_08.jpg", "length": 24605, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_09.jpg", "length": 25160, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_10.jpg", "length": 24938, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_11.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_12.jpg", "length": 24935, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_13.jpg", "length": 24670, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_14.jpg", "length": 24929, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_15.jpg", "length": 25206, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_16.jpg", "length": 24825, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_17.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_18.jpg", "length": 24925, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_19.jpg", "length": 24294, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_00.jpg", "length": 24701, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_01.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_02.jpg", "length": 24898, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_03.jpg", "length": 24613, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_04.jpg", "length": 24903, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_05.jpg", "length": 24744, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_06.jpg", "length": 25272, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_07.jpg", "length": 24727, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_08.jpg", "length": 24791, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_09.jpg", "length": 24854, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_10.jpg", "length": 25016, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_11.jpg", "length": 25064, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_12.jpg", "length": 24793, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_13.jpg", "length": 24927, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_14.jpg", "length": 25257, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_15.jpg", "length": 25326, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_16.jpg", "length": 24992, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_17.jpg", "length": 25249, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002J/files/pocket_01.pdb", "length": 25929, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002J/files/pocket_02.pdb", "length": 14271, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002J/files/pocket_03.pdb", "length": 11122, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002J/files/pocket_04.pdb", "length": 9782, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002J/files/pocket_05.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002J/files/pocket_06.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002J/files/pocket_07.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002J/files/pocket_08.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002J/files/pocket_09.pdb", "length": 7035, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002J/files/pocket_10.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002J", "accession": "A002J", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2AEQ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2AEQ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q80DL0", "P84750", "P84751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELK", "AEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKILFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI", "EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTMEYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTL"], "NUCLSEQ": [], "DOMAINS": ["Head of neuraminidase", "Ig kappa chain V region Mem5", "Ig-like V-type", "Framework-1", "Complementarity-determining-1", "Framework-2", "Complementarity-determining-2", "Framework-3", "Complementarity-determining-3", "Framework-4", "Ig heavy chain Mem5", "Ig-like 1", "D segment", "JH2 segment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 9300, "SYSTRES": 611, "PROTATS": 9300, "PROTRES": 611, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.559, "BOXSIZEY": 11.559, "BOXSIZEZ": 8.19652, "mdName": "replica 1", "mdAtoms": 9300, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002J/files/topology.tpr", "length": 2848092, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002J/files/screenshot.jpg", "length": 23962, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002J/files/trajectory.bin", "length": 558111600, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 5001, "atoms": 9300}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_01.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_02.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_03.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_04.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_05.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_06.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_07.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_08.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_09.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_10.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_11.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_12.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_13.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002J/files/structure.pdb", "length": 753335, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002J/files/trajectory.xtc", "length": 176313492, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_00.jpg", "length": 23900, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_01.jpg", "length": 25224, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_02.jpg", "length": 24740, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_03.jpg", "length": 24438, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_04.jpg", "length": 24878, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_05.jpg", "length": 25438, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_06.jpg", "length": 24968, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_07.jpg", "length": 24327, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_08.jpg", "length": 25173, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_09.jpg", "length": 24908, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_10.jpg", "length": 25063, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_11.jpg", "length": 24821, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_12.jpg", "length": 24698, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_13.jpg", "length": 25290, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_14.jpg", "length": 24391, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_15.jpg", "length": 25015, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_16.jpg", "length": 25423, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_17.jpg", "length": 24566, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_18.jpg", "length": 24665, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_19.jpg", "length": 24476, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_00.jpg", "length": 24443, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_01.jpg", "length": 24100, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_02.jpg", "length": 24389, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_03.jpg", "length": 24002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_04.jpg", "length": 23890, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_05.jpg", "length": 23790, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_06.jpg", "length": 23914, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_07.jpg", "length": 24120, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_08.jpg", "length": 24238, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_09.jpg", "length": 24651, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_10.jpg", "length": 24118, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_11.jpg", "length": 24085, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_12.jpg", "length": 24551, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_13.jpg", "length": 24372, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_14.jpg", "length": 24343, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_15.jpg", "length": 24323, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_16.jpg", "length": 24679, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_17.jpg", "length": 24667, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_18.jpg", "length": 24460, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_19.jpg", "length": 24472, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_00.jpg", "length": 23889, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_01.jpg", "length": 24992, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_02.jpg", "length": 24634, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_03.jpg", "length": 24990, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_04.jpg", "length": 24312, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_05.jpg", "length": 24643, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_06.jpg", "length": 24863, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_07.jpg", "length": 24810, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_08.jpg", "length": 24605, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_09.jpg", "length": 25160, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_10.jpg", "length": 24938, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_11.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_12.jpg", "length": 24935, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_13.jpg", "length": 24670, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_14.jpg", "length": 24929, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_15.jpg", "length": 25206, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_16.jpg", "length": 24825, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_17.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_18.jpg", "length": 24925, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_19.jpg", "length": 24294, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_00.jpg", "length": 24701, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_01.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_02.jpg", "length": 24898, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_03.jpg", "length": 24613, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_04.jpg", "length": 24903, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_05.jpg", "length": 24744, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_06.jpg", "length": 25272, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_07.jpg", "length": 24727, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_08.jpg", "length": 24791, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_09.jpg", "length": 24854, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_10.jpg", "length": 25016, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_11.jpg", "length": 25064, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_12.jpg", "length": 24793, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_13.jpg", "length": 24927, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_14.jpg", "length": 25257, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_15.jpg", "length": 25326, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_16.jpg", "length": 24992, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_17.jpg", "length": 25249, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002J/files/pocket_01.pdb", "length": 25929, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002J/files/pocket_02.pdb", "length": 14271, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002J/files/pocket_03.pdb", "length": 11122, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002J/files/pocket_04.pdb", "length": 9782, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002J/files/pocket_05.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002J/files/pocket_06.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002J/files/pocket_07.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002J/files/pocket_08.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002J/files/pocket_09.pdb", "length": 7035, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002J/files/pocket_10.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002J", "accession": "A002J", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2AEQ", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2AEQ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q80DL0", "P84750", "P84751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DILMTQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQFNRYPLTFGSGTKLELK", "AEYRNWSKPQCKITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNRHSNDTVHDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCVTGHDENATASFIYDGRLVDSIGSWSKKILRTQESECVCINGTCTVVMTDGSASGRADTKILFIEEGKIVHISPLSGSAQHVEECSCYPRYPGVRCVCRDNWKGSNRPIVDINVKDYSIVSSYVCSGLVGDTPRKNDSSSSSHCLNPNNEEGGHGVKGWAFDDGNDVWMGRTISEKFRSGYETFKVIEGWSKPNSKLQINRQVIVDRGNRSGYSGIFSVEGKSCINRCFYVELIRGRKQETEVWWTSNSIVVFCGTSGTYGTGSWPDGADINLMPI", "EVKLVESGGGLVQPGGSLSLSCATSGFTFIDYYMSWFRQPPGKALEWLGLIRNKGNGYTMEYSASLKGRFTISRDNSQSIVYLHMNTLTAEDSATYYCARVDYGTNYDYWGQGTTL"], "NUCLSEQ": [], "DOMAINS": ["Head of neuraminidase", "Ig kappa chain V region Mem5", "Ig-like V-type", "Framework-1", "Complementarity-determining-1", "Framework-2", "Complementarity-determining-2", "Framework-3", "Complementarity-determining-3", "Framework-4", "Ig heavy chain Mem5", "Ig-like 1", "D segment", "JH2 segment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 9300, "SYSTRES": 611, "PROTATS": 9300, "PROTRES": 611, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.559, "BOXSIZEY": 11.559, "BOXSIZEZ": 8.19652, "mdName": "replica 1", "mdAtoms": 9300, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002J/files/topology.tpr", "length": 2848092, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002J/files/screenshot.jpg", "length": 23962, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002J/files/trajectory.bin", "length": 558111600, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 5001, "atoms": 9300}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_01.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_02.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_03.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_04.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_05.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_06.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_07.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_08.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_09.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_10.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_11.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_12.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002J/files/pca_trajectory_13.bin", "length": 439920, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0, "frames": 20, "atoms": 1833}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002J/files/structure.pdb", "length": 753335, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002J/files/trajectory.xtc", "length": 176313492, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_00.jpg", "length": 23900, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_01.jpg", "length": 25224, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_02.jpg", "length": 24740, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_03.jpg", "length": 24438, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_04.jpg", "length": 24878, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_05.jpg", "length": 25438, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_06.jpg", "length": 24968, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_07.jpg", "length": 24327, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_08.jpg", "length": 25173, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_09.jpg", "length": 24908, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_10.jpg", "length": 25063, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_11.jpg", "length": 24821, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_12.jpg", "length": 24698, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_13.jpg", "length": 25290, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_14.jpg", "length": 24391, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_15.jpg", "length": 25015, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_16.jpg", "length": 25423, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_17.jpg", "length": 24566, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_18.jpg", "length": 24665, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_00_screenshot_19.jpg", "length": 24476, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_00.jpg", "length": 24443, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_01.jpg", "length": 24100, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_02.jpg", "length": 24389, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_03.jpg", "length": 24002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_04.jpg", "length": 23890, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_05.jpg", "length": 23790, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_06.jpg", "length": 23914, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_07.jpg", "length": 24120, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_08.jpg", "length": 24238, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_09.jpg", "length": 24651, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_10.jpg", "length": 24118, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_11.jpg", "length": 24085, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_12.jpg", "length": 24551, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_13.jpg", "length": 24372, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_14.jpg", "length": 24343, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_15.jpg", "length": 24323, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_16.jpg", "length": 24679, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_17.jpg", "length": 24667, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_18.jpg", "length": 24460, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_01_screenshot_19.jpg", "length": 24472, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_00.jpg", "length": 23889, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_01.jpg", "length": 24992, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_02.jpg", "length": 24634, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_03.jpg", "length": 24990, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_04.jpg", "length": 24312, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_05.jpg", "length": 24643, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_06.jpg", "length": 24863, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_07.jpg", "length": 24810, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_08.jpg", "length": 24605, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_09.jpg", "length": 25160, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_10.jpg", "length": 24938, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_11.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_12.jpg", "length": 24935, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_13.jpg", "length": 24670, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_14.jpg", "length": 24929, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_15.jpg", "length": 25206, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_16.jpg", "length": 24825, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_17.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_18.jpg", "length": 24925, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002J/files/clusters_02_screenshot_19.jpg", "length": 24294, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_00.jpg", "length": 24701, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_01.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_02.jpg", "length": 24898, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_03.jpg", "length": 24613, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_04.jpg", "length": 24903, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_05.jpg", "length": 24744, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_06.jpg", "length": 25272, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_07.jpg", "length": 24727, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_08.jpg", "length": 24791, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_09.jpg", "length": 24854, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_10.jpg", "length": 25016, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_11.jpg", "length": 25064, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_12.jpg", "length": 24793, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_13.jpg", "length": 24927, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_14.jpg", "length": 25257, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_15.jpg", "length": 25326, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_16.jpg", "length": 24992, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002J/files/clusters_03_screenshot_17.jpg", "length": 25249, "contentType": "application/octet-stream", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002J/files/pocket_01.pdb", "length": 25929, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002J/files/pocket_02.pdb", "length": 14271, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002J/files/pocket_03.pdb", "length": 11122, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002J/files/pocket_04.pdb", "length": 9782, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002J/files/pocket_05.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002J/files/pocket_06.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002J/files/pocket_07.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002J/files/pocket_08.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002J/files/pocket_09.pdb", "length": 7035, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002J/files/pocket_10.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff4ea7d2501ff97442b43", "md": 0}}]}
|
data/files/A002K/project.json
ADDED
|
@@ -0,0 +1,191 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002K",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2AW2",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2AW2"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q7Z6A9",
|
| 31 |
+
"Q92956"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"CDVQLYIKRQSEHSILAGDPFELECPVKYCANRPHVTWCKLNGTTCVKLEDRQTSWKEEKNISFFILHFEPVLPNDNGSYRCSANFQSNLIESHSTTLYVTDVKHHHHHH",
|
| 38 |
+
"PSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAY"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"B- and T-lymphocyte attenuator",
|
| 43 |
+
"Ig-like V-type",
|
| 44 |
+
"Tumor necrosis factor receptor superfamily member 14"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 3185,
|
| 56 |
+
"SYSTRES": 212,
|
| 57 |
+
"PROTATS": 3185,
|
| 58 |
+
"PROTRES": 212,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 11.1358,
|
| 90 |
+
"BOXSIZEY": 11.1358,
|
| 91 |
+
"BOXSIZEZ": 7.87326,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 3185,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"structure.pdb",
|
| 119 |
+
"trajectory.xtc",
|
| 120 |
+
"clusters_00_screenshot_00.jpg",
|
| 121 |
+
"clusters_00_screenshot_01.jpg",
|
| 122 |
+
"clusters_00_screenshot_02.jpg",
|
| 123 |
+
"clusters_00_screenshot_03.jpg",
|
| 124 |
+
"clusters_00_screenshot_04.jpg",
|
| 125 |
+
"clusters_00_screenshot_05.jpg",
|
| 126 |
+
"clusters_00_screenshot_06.jpg",
|
| 127 |
+
"clusters_00_screenshot_07.jpg",
|
| 128 |
+
"clusters_00_screenshot_08.jpg",
|
| 129 |
+
"clusters_00_screenshot_09.jpg",
|
| 130 |
+
"clusters_00_screenshot_10.jpg",
|
| 131 |
+
"clusters_00_screenshot_11.jpg",
|
| 132 |
+
"clusters_00_screenshot_12.jpg",
|
| 133 |
+
"clusters_00_screenshot_13.jpg",
|
| 134 |
+
"clusters_00_screenshot_14.jpg",
|
| 135 |
+
"clusters_00_screenshot_15.jpg",
|
| 136 |
+
"clusters_00_screenshot_16.jpg",
|
| 137 |
+
"clusters_00_screenshot_17.jpg",
|
| 138 |
+
"clusters_00_screenshot_18.jpg",
|
| 139 |
+
"clusters_00_screenshot_19.jpg",
|
| 140 |
+
"clusters_01_screenshot_00.jpg",
|
| 141 |
+
"clusters_01_screenshot_01.jpg",
|
| 142 |
+
"clusters_01_screenshot_02.jpg",
|
| 143 |
+
"clusters_01_screenshot_03.jpg",
|
| 144 |
+
"clusters_01_screenshot_04.jpg",
|
| 145 |
+
"clusters_01_screenshot_05.jpg",
|
| 146 |
+
"clusters_01_screenshot_06.jpg",
|
| 147 |
+
"clusters_01_screenshot_07.jpg",
|
| 148 |
+
"clusters_01_screenshot_08.jpg",
|
| 149 |
+
"clusters_01_screenshot_09.jpg",
|
| 150 |
+
"clusters_01_screenshot_10.jpg",
|
| 151 |
+
"clusters_01_screenshot_11.jpg",
|
| 152 |
+
"clusters_01_screenshot_12.jpg",
|
| 153 |
+
"clusters_01_screenshot_13.jpg",
|
| 154 |
+
"clusters_01_screenshot_14.jpg",
|
| 155 |
+
"clusters_01_screenshot_15.jpg",
|
| 156 |
+
"clusters_01_screenshot_16.jpg",
|
| 157 |
+
"clusters_01_screenshot_17.jpg",
|
| 158 |
+
"clusters_01_screenshot_18.jpg",
|
| 159 |
+
"clusters_01_screenshot_19.jpg",
|
| 160 |
+
"clusters_01_screenshot_20.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb",
|
| 165 |
+
"pocket_05.pdb"
|
| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
+
"clusters",
|
| 169 |
+
"clusters-00",
|
| 170 |
+
"clusters-01",
|
| 171 |
+
"dist-perres",
|
| 172 |
+
"energies",
|
| 173 |
+
"fluctuation",
|
| 174 |
+
"hbonds",
|
| 175 |
+
"interactions",
|
| 176 |
+
"pca",
|
| 177 |
+
"pockets",
|
| 178 |
+
"rgyr",
|
| 179 |
+
"rmsd-pairwise",
|
| 180 |
+
"rmsd-perres",
|
| 181 |
+
"rmsds",
|
| 182 |
+
"sasa",
|
| 183 |
+
"tmscores"
|
| 184 |
+
],
|
| 185 |
+
"mdIndex": 0,
|
| 186 |
+
"mdNumber": 1,
|
| 187 |
+
"refframe": 0,
|
| 188 |
+
"internalId": "683ff7415ebe54217d0a33e8",
|
| 189 |
+
"creationDate": "2025-06-04T07:35:29.000Z",
|
| 190 |
+
"identifier": "A002K"
|
| 191 |
+
}
|
data/files/A002K/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002K", "accession": "A002K", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2AW2", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2AW2"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7Z6A9", "Q92956"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["CDVQLYIKRQSEHSILAGDPFELECPVKYCANRPHVTWCKLNGTTCVKLEDRQTSWKEEKNISFFILHFEPVLPNDNGSYRCSANFQSNLIESHSTTLYVTDVKHHHHHH", "PSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAY"], "NUCLSEQ": [], "DOMAINS": ["B- and T-lymphocyte attenuator", "Ig-like V-type", "Tumor necrosis factor receptor superfamily member 14"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3185, "SYSTRES": 212, "PROTATS": 3185, "PROTRES": 212, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.1358, "BOXSIZEY": 11.1358, "BOXSIZEZ": 7.87326, "mdName": "replica 1", "mdAtoms": 3185, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002K/files/topology.tpr", "length": 1270600, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002K/files/screenshot.jpg", "length": 15136, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002K/files/trajectory.bin", "length": 191138220, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 5001, "atoms": 3185}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_01.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_02.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_03.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_04.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_05.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_06.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_07.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_08.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_09.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_10.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_11.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_12.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002K/files/structure.pdb", "length": 258020, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002K/files/trajectory.xtc", "length": 60985288, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_00.jpg", "length": 15782, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_01.jpg", "length": 15676, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_02.jpg", "length": 15547, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_03.jpg", "length": 15527, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_04.jpg", "length": 15498, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_05.jpg", "length": 15674, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_06.jpg", "length": 15997, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_07.jpg", "length": 15522, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_08.jpg", "length": 15628, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_09.jpg", "length": 15653, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_10.jpg", "length": 15763, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_11.jpg", "length": 15123, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_12.jpg", "length": 15740, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_13.jpg", "length": 15606, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_14.jpg", "length": 15426, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_15.jpg", "length": 15412, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_16.jpg", "length": 15474, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_17.jpg", "length": 15223, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_18.jpg", "length": 15398, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_19.jpg", "length": 15442, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_00.jpg", "length": 14778, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_01.jpg", "length": 15156, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_02.jpg", "length": 15143, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_03.jpg", "length": 14292, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_04.jpg", "length": 14637, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_05.jpg", "length": 15242, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_06.jpg", "length": 14734, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_07.jpg", "length": 14847, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_08.jpg", "length": 14962, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_09.jpg", "length": 14940, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_10.jpg", "length": 14349, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_11.jpg", "length": 14947, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_12.jpg", "length": 14292, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_13.jpg", "length": 14557, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_14.jpg", "length": 14991, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_15.jpg", "length": 14848, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_16.jpg", "length": 14783, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_17.jpg", "length": 14954, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_18.jpg", "length": 14593, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_19.jpg", "length": 14734, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_20.jpg", "length": 14879, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002K/files/pocket_01.pdb", "length": 6030, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002K/files/pocket_02.pdb", "length": 5360, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002K/files/pocket_03.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002K/files/pocket_04.pdb", "length": 3551, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002K/files/pocket_05.pdb", "length": 3149, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002K", "accession": "A002K", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2AW2", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2AW2"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7Z6A9", "Q92956"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["CDVQLYIKRQSEHSILAGDPFELECPVKYCANRPHVTWCKLNGTTCVKLEDRQTSWKEEKNISFFILHFEPVLPNDNGSYRCSANFQSNLIESHSTTLYVTDVKHHHHHH", "PSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAY"], "NUCLSEQ": [], "DOMAINS": ["B- and T-lymphocyte attenuator", "Ig-like V-type", "Tumor necrosis factor receptor superfamily member 14"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3185, "SYSTRES": 212, "PROTATS": 3185, "PROTRES": 212, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.1358, "BOXSIZEY": 11.1358, "BOXSIZEZ": 7.87326, "mdName": "replica 1", "mdAtoms": 3185, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002K/files/topology.tpr", "length": 1270600, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002K/files/screenshot.jpg", "length": 15136, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002K/files/trajectory.bin", "length": 191138220, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 5001, "atoms": 3185}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_01.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_02.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_03.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_04.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_05.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_06.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_07.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_08.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_09.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_10.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_11.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_12.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002K/files/structure.pdb", "length": 258020, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002K/files/trajectory.xtc", "length": 60985288, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_00.jpg", "length": 15782, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_01.jpg", "length": 15676, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_02.jpg", "length": 15547, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_03.jpg", "length": 15527, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_04.jpg", "length": 15498, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_05.jpg", "length": 15674, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_06.jpg", "length": 15997, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_07.jpg", "length": 15522, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_08.jpg", "length": 15628, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_09.jpg", "length": 15653, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_10.jpg", "length": 15763, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_11.jpg", "length": 15123, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_12.jpg", "length": 15740, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_13.jpg", "length": 15606, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_14.jpg", "length": 15426, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_15.jpg", "length": 15412, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_16.jpg", "length": 15474, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_17.jpg", "length": 15223, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_18.jpg", "length": 15398, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_19.jpg", "length": 15442, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_00.jpg", "length": 14778, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_01.jpg", "length": 15156, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_02.jpg", "length": 15143, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_03.jpg", "length": 14292, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_04.jpg", "length": 14637, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_05.jpg", "length": 15242, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_06.jpg", "length": 14734, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_07.jpg", "length": 14847, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_08.jpg", "length": 14962, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_09.jpg", "length": 14940, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_10.jpg", "length": 14349, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_11.jpg", "length": 14947, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_12.jpg", "length": 14292, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_13.jpg", "length": 14557, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_14.jpg", "length": 14991, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_15.jpg", "length": 14848, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_16.jpg", "length": 14783, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_17.jpg", "length": 14954, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_18.jpg", "length": 14593, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_19.jpg", "length": 14734, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_20.jpg", "length": 14879, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002K/files/pocket_01.pdb", "length": 6030, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002K/files/pocket_02.pdb", "length": 5360, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002K/files/pocket_03.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002K/files/pocket_04.pdb", "length": 3551, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002K/files/pocket_05.pdb", "length": 3149, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002K", "accession": "A002K", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2AW2", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2AW2"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7Z6A9", "Q92956"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["CDVQLYIKRQSEHSILAGDPFELECPVKYCANRPHVTWCKLNGTTCVKLEDRQTSWKEEKNISFFILHFEPVLPNDNGSYRCSANFQSNLIESHSTTLYVTDVKHHHHHH", "PSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAY"], "NUCLSEQ": [], "DOMAINS": ["B- and T-lymphocyte attenuator", "Ig-like V-type", "Tumor necrosis factor receptor superfamily member 14"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3185, "SYSTRES": 212, "PROTATS": 3185, "PROTRES": 212, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.1358, "BOXSIZEY": 11.1358, "BOXSIZEZ": 7.87326, "mdName": "replica 1", "mdAtoms": 3185, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002K/files/topology.tpr", "length": 1270600, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002K/files/screenshot.jpg", "length": 15136, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002K/files/trajectory.bin", "length": 191138220, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 5001, "atoms": 3185}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_01.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_02.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_03.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_04.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_05.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_06.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_07.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_08.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_09.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_10.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_11.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002K/files/pca_trajectory_12.bin", "length": 152640, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0, "frames": 20, "atoms": 636}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002K/files/structure.pdb", "length": 258020, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002K/files/trajectory.xtc", "length": 60985288, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_00.jpg", "length": 15782, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_01.jpg", "length": 15676, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_02.jpg", "length": 15547, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_03.jpg", "length": 15527, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_04.jpg", "length": 15498, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_05.jpg", "length": 15674, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_06.jpg", "length": 15997, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_07.jpg", "length": 15522, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_08.jpg", "length": 15628, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_09.jpg", "length": 15653, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_10.jpg", "length": 15763, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_11.jpg", "length": 15123, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_12.jpg", "length": 15740, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_13.jpg", "length": 15606, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_14.jpg", "length": 15426, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_15.jpg", "length": 15412, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_16.jpg", "length": 15474, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_17.jpg", "length": 15223, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_18.jpg", "length": 15398, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002K/files/clusters_00_screenshot_19.jpg", "length": 15442, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_00.jpg", "length": 14778, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_01.jpg", "length": 15156, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_02.jpg", "length": 15143, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_03.jpg", "length": 14292, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_04.jpg", "length": 14637, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_05.jpg", "length": 15242, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_06.jpg", "length": 14734, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_07.jpg", "length": 14847, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_08.jpg", "length": 14962, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_09.jpg", "length": 14940, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_10.jpg", "length": 14349, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_11.jpg", "length": 14947, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_12.jpg", "length": 14292, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_13.jpg", "length": 14557, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_14.jpg", "length": 14991, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_15.jpg", "length": 14848, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_16.jpg", "length": 14783, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_17.jpg", "length": 14954, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_18.jpg", "length": 14593, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_19.jpg", "length": 14734, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002K/files/clusters_01_screenshot_20.jpg", "length": 14879, "contentType": "application/octet-stream", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002K/files/pocket_01.pdb", "length": 6030, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002K/files/pocket_02.pdb", "length": 5360, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002K/files/pocket_03.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002K/files/pocket_04.pdb", "length": 3551, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002K/files/pocket_05.pdb", "length": 3149, "contentType": "chemical/x-pdb", "metadata": {"project": "683ff7415ebe54217d0a33e8", "md": 0}}]}
|
data/files/A002M/project.json
ADDED
|
@@ -0,0 +1,199 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2B7C",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2B7C"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P02994",
|
| 31 |
+
"P32471"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"PAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQAL",
|
| 38 |
+
"KSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Elongation factor 1-alpha",
|
| 43 |
+
"tr-type G",
|
| 44 |
+
"G1",
|
| 45 |
+
"G2",
|
| 46 |
+
"G3",
|
| 47 |
+
"G4",
|
| 48 |
+
"G5",
|
| 49 |
+
"Not modified",
|
| 50 |
+
"Elongation factor 1-beta"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 8169,
|
| 62 |
+
"SYSTRES": 527,
|
| 63 |
+
"PROTATS": 8169,
|
| 64 |
+
"PROTRES": 527,
|
| 65 |
+
"NUCLATS": 0,
|
| 66 |
+
"NUCLRES": 0,
|
| 67 |
+
"LIPIATS": 0,
|
| 68 |
+
"LIPIRES": 0,
|
| 69 |
+
"CARBATS": 0,
|
| 70 |
+
"CARBRES": 0,
|
| 71 |
+
"SOLVATS": 0,
|
| 72 |
+
"SOLVRES": 0,
|
| 73 |
+
"COUNCAT": 0,
|
| 74 |
+
"COUNANI": 0,
|
| 75 |
+
"COUNION": 0,
|
| 76 |
+
"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
}
|
| 85 |
+
],
|
| 86 |
+
"PBC_SELECTION": null,
|
| 87 |
+
"CHAINNAMES": null,
|
| 88 |
+
"MEMBRANES": null,
|
| 89 |
+
"CUSTOMS": null,
|
| 90 |
+
"ORIENTATION": null,
|
| 91 |
+
"PTM": [],
|
| 92 |
+
"MULTIMERIC": null,
|
| 93 |
+
"COLLECTIONS": "dynarepo",
|
| 94 |
+
"WARNINGS": [],
|
| 95 |
+
"BOXSIZEX": 10.4467,
|
| 96 |
+
"BOXSIZEY": 10.4467,
|
| 97 |
+
"BOXSIZEZ": 7.36216,
|
| 98 |
+
"mdName": "replica 1",
|
| 99 |
+
"mdAtoms": 8169,
|
| 100 |
+
"mdFrames": 5001
|
| 101 |
+
},
|
| 102 |
+
"mds": [
|
| 103 |
+
"replica 1",
|
| 104 |
+
"replica 2",
|
| 105 |
+
"replica 3"
|
| 106 |
+
],
|
| 107 |
+
"mdref": 0,
|
| 108 |
+
"files": [
|
| 109 |
+
"topology.tpr",
|
| 110 |
+
"screenshot.jpg",
|
| 111 |
+
"trajectory.bin",
|
| 112 |
+
"pca_trajectory_01.bin",
|
| 113 |
+
"pca_trajectory_02.bin",
|
| 114 |
+
"pca_trajectory_03.bin",
|
| 115 |
+
"pca_trajectory_04.bin",
|
| 116 |
+
"pca_trajectory_05.bin",
|
| 117 |
+
"pca_trajectory_06.bin",
|
| 118 |
+
"pca_trajectory_07.bin",
|
| 119 |
+
"pca_trajectory_08.bin",
|
| 120 |
+
"pca_trajectory_09.bin",
|
| 121 |
+
"pca_trajectory_10.bin",
|
| 122 |
+
"pca_trajectory_11.bin",
|
| 123 |
+
"pca_trajectory_12.bin",
|
| 124 |
+
"structure.pdb",
|
| 125 |
+
"trajectory.xtc",
|
| 126 |
+
"clusters_00_screenshot_00.jpg",
|
| 127 |
+
"clusters_00_screenshot_01.jpg",
|
| 128 |
+
"clusters_00_screenshot_02.jpg",
|
| 129 |
+
"clusters_00_screenshot_03.jpg",
|
| 130 |
+
"clusters_00_screenshot_04.jpg",
|
| 131 |
+
"clusters_00_screenshot_05.jpg",
|
| 132 |
+
"clusters_00_screenshot_06.jpg",
|
| 133 |
+
"clusters_00_screenshot_07.jpg",
|
| 134 |
+
"clusters_00_screenshot_08.jpg",
|
| 135 |
+
"clusters_00_screenshot_09.jpg",
|
| 136 |
+
"clusters_00_screenshot_10.jpg",
|
| 137 |
+
"clusters_00_screenshot_11.jpg",
|
| 138 |
+
"clusters_00_screenshot_12.jpg",
|
| 139 |
+
"clusters_00_screenshot_13.jpg",
|
| 140 |
+
"clusters_00_screenshot_14.jpg",
|
| 141 |
+
"clusters_00_screenshot_15.jpg",
|
| 142 |
+
"clusters_00_screenshot_16.jpg",
|
| 143 |
+
"clusters_00_screenshot_17.jpg",
|
| 144 |
+
"clusters_00_screenshot_18.jpg",
|
| 145 |
+
"clusters_00_screenshot_19.jpg",
|
| 146 |
+
"clusters_01_screenshot_00.jpg",
|
| 147 |
+
"clusters_01_screenshot_01.jpg",
|
| 148 |
+
"clusters_01_screenshot_02.jpg",
|
| 149 |
+
"clusters_01_screenshot_03.jpg",
|
| 150 |
+
"clusters_01_screenshot_04.jpg",
|
| 151 |
+
"clusters_01_screenshot_05.jpg",
|
| 152 |
+
"clusters_01_screenshot_06.jpg",
|
| 153 |
+
"clusters_01_screenshot_07.jpg",
|
| 154 |
+
"clusters_01_screenshot_08.jpg",
|
| 155 |
+
"clusters_01_screenshot_09.jpg",
|
| 156 |
+
"clusters_01_screenshot_10.jpg",
|
| 157 |
+
"clusters_01_screenshot_11.jpg",
|
| 158 |
+
"clusters_01_screenshot_12.jpg",
|
| 159 |
+
"clusters_01_screenshot_13.jpg",
|
| 160 |
+
"clusters_01_screenshot_14.jpg",
|
| 161 |
+
"clusters_01_screenshot_15.jpg",
|
| 162 |
+
"clusters_01_screenshot_16.jpg",
|
| 163 |
+
"clusters_01_screenshot_17.jpg",
|
| 164 |
+
"pocket_01.pdb",
|
| 165 |
+
"pocket_02.pdb",
|
| 166 |
+
"pocket_03.pdb",
|
| 167 |
+
"pocket_04.pdb",
|
| 168 |
+
"pocket_05.pdb",
|
| 169 |
+
"pocket_06.pdb",
|
| 170 |
+
"pocket_07.pdb",
|
| 171 |
+
"pocket_08.pdb",
|
| 172 |
+
"pocket_09.pdb",
|
| 173 |
+
"pocket_10.pdb"
|
| 174 |
+
],
|
| 175 |
+
"analyses": [
|
| 176 |
+
"clusters",
|
| 177 |
+
"clusters-00",
|
| 178 |
+
"clusters-01",
|
| 179 |
+
"dist-perres",
|
| 180 |
+
"energies",
|
| 181 |
+
"fluctuation",
|
| 182 |
+
"hbonds",
|
| 183 |
+
"interactions",
|
| 184 |
+
"pca",
|
| 185 |
+
"pockets",
|
| 186 |
+
"rgyr",
|
| 187 |
+
"rmsd-pairwise",
|
| 188 |
+
"rmsd-perres",
|
| 189 |
+
"rmsds",
|
| 190 |
+
"sasa",
|
| 191 |
+
"tmscores"
|
| 192 |
+
],
|
| 193 |
+
"mdIndex": 0,
|
| 194 |
+
"mdNumber": 1,
|
| 195 |
+
"refframe": 0,
|
| 196 |
+
"internalId": "6840142f5888b6538abe7db3",
|
| 197 |
+
"creationDate": "2025-06-04T09:38:55.000Z",
|
| 198 |
+
"identifier": "A002M"
|
| 199 |
+
}
|
data/files/A002M/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002M", "accession": "A002M", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2B7C", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2B7C"], "FORCED_REFERENCES": null, "REFERENCES": ["P02994", "P32471"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQAL", "KSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK"], "NUCLSEQ": [], "DOMAINS": ["Elongation factor 1-alpha", "tr-type G", "G1", "G2", "G3", "G4", "G5", "Not modified", "Elongation factor 1-beta"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8169, "SYSTRES": 527, "PROTATS": 8169, "PROTRES": 527, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.4467, "BOXSIZEY": 10.4467, "BOXSIZEZ": 7.36216, "mdName": "replica 1", "mdAtoms": 8169, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002M/files/topology.tpr", "length": 2506964, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002M/files/screenshot.jpg", "length": 24273, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002M/files/trajectory.bin", "length": 490238028, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 5001, "atoms": 8169}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_01.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_02.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_03.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_04.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_05.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_06.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_07.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_08.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_09.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_10.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_11.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_12.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002M/files/structure.pdb", "length": 661724, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002M/files/trajectory.xtc", "length": 155393908, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_00.jpg", "length": 25942, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_01.jpg", "length": 25632, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_02.jpg", "length": 25621, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_03.jpg", "length": 25799, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_04.jpg", "length": 26058, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_05.jpg", "length": 26490, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_06.jpg", "length": 26326, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_07.jpg", "length": 26112, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_08.jpg", "length": 26406, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_09.jpg", "length": 26290, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_10.jpg", "length": 25977, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_11.jpg", "length": 25993, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_12.jpg", "length": 25770, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_13.jpg", "length": 26351, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_14.jpg", "length": 26121, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_15.jpg", "length": 26116, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_16.jpg", "length": 25940, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_17.jpg", "length": 26780, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_18.jpg", "length": 26407, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_19.jpg", "length": 25829, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_00.jpg", "length": 24634, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_01.jpg", "length": 24587, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_02.jpg", "length": 23929, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_03.jpg", "length": 23416, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_04.jpg", "length": 24128, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_05.jpg", "length": 23875, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_06.jpg", "length": 23360, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_07.jpg", "length": 24523, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_08.jpg", "length": 24261, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_09.jpg", "length": 25316, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_10.jpg", "length": 24493, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_11.jpg", "length": 24674, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_12.jpg", "length": 23761, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_13.jpg", "length": 24406, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_14.jpg", "length": 23952, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_15.jpg", "length": 23614, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_16.jpg", "length": 23904, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_17.jpg", "length": 23843, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002M/files/pocket_01.pdb", "length": 75777, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002M/files/pocket_02.pdb", "length": 43550, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002M/files/pocket_03.pdb", "length": 22177, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002M/files/pocket_04.pdb", "length": 18894, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002M/files/pocket_05.pdb", "length": 16750, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002M/files/pocket_06.pdb", "length": 13199, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002M/files/pocket_07.pdb", "length": 11725, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002M/files/pocket_08.pdb", "length": 10318, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002M/files/pocket_09.pdb", "length": 10318, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002M/files/pocket_10.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002M", "accession": "A002M", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2B7C", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2B7C"], "FORCED_REFERENCES": null, "REFERENCES": ["P02994", "P32471"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQAL", "KSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK"], "NUCLSEQ": [], "DOMAINS": ["Elongation factor 1-alpha", "tr-type G", "G1", "G2", "G3", "G4", "G5", "Not modified", "Elongation factor 1-beta"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8169, "SYSTRES": 527, "PROTATS": 8169, "PROTRES": 527, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.4467, "BOXSIZEY": 10.4467, "BOXSIZEZ": 7.36216, "mdName": "replica 1", "mdAtoms": 8169, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002M/files/topology.tpr", "length": 2506964, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002M/files/screenshot.jpg", "length": 24273, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002M/files/trajectory.bin", "length": 490238028, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 5001, "atoms": 8169}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_01.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_02.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_03.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_04.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_05.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_06.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_07.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_08.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_09.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_10.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_11.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_12.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002M/files/structure.pdb", "length": 661724, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002M/files/trajectory.xtc", "length": 155393908, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_00.jpg", "length": 25942, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_01.jpg", "length": 25632, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_02.jpg", "length": 25621, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_03.jpg", "length": 25799, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_04.jpg", "length": 26058, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_05.jpg", "length": 26490, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_06.jpg", "length": 26326, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_07.jpg", "length": 26112, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_08.jpg", "length": 26406, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_09.jpg", "length": 26290, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_10.jpg", "length": 25977, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_11.jpg", "length": 25993, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_12.jpg", "length": 25770, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_13.jpg", "length": 26351, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_14.jpg", "length": 26121, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_15.jpg", "length": 26116, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_16.jpg", "length": 25940, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_17.jpg", "length": 26780, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_18.jpg", "length": 26407, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_19.jpg", "length": 25829, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_00.jpg", "length": 24634, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_01.jpg", "length": 24587, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_02.jpg", "length": 23929, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_03.jpg", "length": 23416, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_04.jpg", "length": 24128, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_05.jpg", "length": 23875, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_06.jpg", "length": 23360, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_07.jpg", "length": 24523, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_08.jpg", "length": 24261, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_09.jpg", "length": 25316, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_10.jpg", "length": 24493, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_11.jpg", "length": 24674, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_12.jpg", "length": 23761, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_13.jpg", "length": 24406, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_14.jpg", "length": 23952, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_15.jpg", "length": 23614, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_16.jpg", "length": 23904, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_17.jpg", "length": 23843, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002M/files/pocket_01.pdb", "length": 75777, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002M/files/pocket_02.pdb", "length": 43550, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002M/files/pocket_03.pdb", "length": 22177, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002M/files/pocket_04.pdb", "length": 18894, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002M/files/pocket_05.pdb", "length": 16750, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002M/files/pocket_06.pdb", "length": 13199, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002M/files/pocket_07.pdb", "length": 11725, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002M/files/pocket_08.pdb", "length": 10318, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002M/files/pocket_09.pdb", "length": 10318, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002M/files/pocket_10.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002M", "accession": "A002M", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2B7C", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2B7C"], "FORCED_REFERENCES": null, "REFERENCES": ["P02994", "P32471"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQAL", "KSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK"], "NUCLSEQ": [], "DOMAINS": ["Elongation factor 1-alpha", "tr-type G", "G1", "G2", "G3", "G4", "G5", "Not modified", "Elongation factor 1-beta"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8169, "SYSTRES": 527, "PROTATS": 8169, "PROTRES": 527, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.4467, "BOXSIZEY": 10.4467, "BOXSIZEZ": 7.36216, "mdName": "replica 1", "mdAtoms": 8169, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002M/files/topology.tpr", "length": 2506964, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002M/files/screenshot.jpg", "length": 24273, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002M/files/trajectory.bin", "length": 490238028, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 5001, "atoms": 8169}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_01.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_02.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_03.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_04.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_05.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_06.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_07.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_08.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_09.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_10.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_11.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002M/files/pca_trajectory_12.bin", "length": 379440, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0, "frames": 20, "atoms": 1581}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002M/files/structure.pdb", "length": 661724, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002M/files/trajectory.xtc", "length": 155393908, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_00.jpg", "length": 25942, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_01.jpg", "length": 25632, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_02.jpg", "length": 25621, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_03.jpg", "length": 25799, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_04.jpg", "length": 26058, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_05.jpg", "length": 26490, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_06.jpg", "length": 26326, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_07.jpg", "length": 26112, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_08.jpg", "length": 26406, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_09.jpg", "length": 26290, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_10.jpg", "length": 25977, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_11.jpg", "length": 25993, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_12.jpg", "length": 25770, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_13.jpg", "length": 26351, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_14.jpg", "length": 26121, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_15.jpg", "length": 26116, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_16.jpg", "length": 25940, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_17.jpg", "length": 26780, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_18.jpg", "length": 26407, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002M/files/clusters_00_screenshot_19.jpg", "length": 25829, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_00.jpg", "length": 24634, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_01.jpg", "length": 24587, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_02.jpg", "length": 23929, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_03.jpg", "length": 23416, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_04.jpg", "length": 24128, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_05.jpg", "length": 23875, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_06.jpg", "length": 23360, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_07.jpg", "length": 24523, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_08.jpg", "length": 24261, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_09.jpg", "length": 25316, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_10.jpg", "length": 24493, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_11.jpg", "length": 24674, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_12.jpg", "length": 23761, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_13.jpg", "length": 24406, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_14.jpg", "length": 23952, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_15.jpg", "length": 23614, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_16.jpg", "length": 23904, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002M/files/clusters_01_screenshot_17.jpg", "length": 23843, "contentType": "application/octet-stream", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002M/files/pocket_01.pdb", "length": 75777, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002M/files/pocket_02.pdb", "length": 43550, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002M/files/pocket_03.pdb", "length": 22177, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002M/files/pocket_04.pdb", "length": 18894, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002M/files/pocket_05.pdb", "length": 16750, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002M/files/pocket_06.pdb", "length": 13199, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002M/files/pocket_07.pdb", "length": 11725, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002M/files/pocket_08.pdb", "length": 10318, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002M/files/pocket_09.pdb", "length": 10318, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002M/files/pocket_10.pdb", "length": 9648, "contentType": "chemical/x-pdb", "metadata": {"project": "6840142f5888b6538abe7db3", "md": 0}}]}
|
data/files/A002N/project.json
ADDED
|
@@ -0,0 +1,270 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002N",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2BDN",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2BDN"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P13500",
|
| 31 |
+
"P0DOX7",
|
| 32 |
+
"P84751"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"EVQLQQSGAELVKAGASVKLSCPASGLNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKFDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARGVFGFFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPR",
|
| 39 |
+
"AINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSMDHLDKQT",
|
| 40 |
+
"DIQMTQSSSSFSVSLGDRVTITCKATEDIYNRLAWYQQKPGSAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTEDVATYYCQQFWSAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"C-C motif chemokine 2",
|
| 45 |
+
"Involved in dimerization",
|
| 46 |
+
"Involved in dimerization, receptor binding and signaling",
|
| 47 |
+
"Involved in GAG binding",
|
| 48 |
+
"Involved in GAG binding and receptor binding",
|
| 49 |
+
"Immunoglobulin kappa light chain",
|
| 50 |
+
"Ig-like 1",
|
| 51 |
+
"Ig-like 2",
|
| 52 |
+
"Variable (V) domain, involved in antigen recognition",
|
| 53 |
+
"Constant (C) domain",
|
| 54 |
+
"Ig heavy chain Mem5",
|
| 55 |
+
"Ig-like 1",
|
| 56 |
+
"Ig-like 2",
|
| 57 |
+
"D segment",
|
| 58 |
+
"JH2 segment"
|
| 59 |
+
],
|
| 60 |
+
"FRAMESTEP": 0.1,
|
| 61 |
+
"TIMESTEP": 2,
|
| 62 |
+
"TEMP": 310,
|
| 63 |
+
"ENSEMBLE": "NPT",
|
| 64 |
+
"FF": [
|
| 65 |
+
"CHARMM36m"
|
| 66 |
+
],
|
| 67 |
+
"WAT": "TIP3P",
|
| 68 |
+
"BOXTYPE": "Dodecahedron",
|
| 69 |
+
"SYSTATS": 7575,
|
| 70 |
+
"SYSTRES": 499,
|
| 71 |
+
"PROTATS": 7575,
|
| 72 |
+
"PROTRES": 499,
|
| 73 |
+
"NUCLATS": 0,
|
| 74 |
+
"NUCLRES": 0,
|
| 75 |
+
"LIPIATS": 0,
|
| 76 |
+
"LIPIRES": 0,
|
| 77 |
+
"CARBATS": 0,
|
| 78 |
+
"CARBRES": 0,
|
| 79 |
+
"SOLVATS": 0,
|
| 80 |
+
"SOLVRES": 0,
|
| 81 |
+
"COUNCAT": 0,
|
| 82 |
+
"COUNANI": 0,
|
| 83 |
+
"COUNION": 0,
|
| 84 |
+
"INTERACTIONS": [
|
| 85 |
+
{
|
| 86 |
+
"name": "chain A-chain B interaction",
|
| 87 |
+
"agent_1": "chain A",
|
| 88 |
+
"agent_2": "chain B",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain B",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "chain A-chain C interaction",
|
| 95 |
+
"agent_1": "chain A",
|
| 96 |
+
"agent_2": "chain C",
|
| 97 |
+
"selection_1": "chain A",
|
| 98 |
+
"selection_2": "chain C",
|
| 99 |
+
"type": "protein-protein"
|
| 100 |
+
},
|
| 101 |
+
{
|
| 102 |
+
"name": "chain B-chain C interaction",
|
| 103 |
+
"agent_1": "chain B",
|
| 104 |
+
"agent_2": "chain C",
|
| 105 |
+
"selection_1": "chain B",
|
| 106 |
+
"selection_2": "chain C",
|
| 107 |
+
"type": "protein-protein"
|
| 108 |
+
}
|
| 109 |
+
],
|
| 110 |
+
"PBC_SELECTION": null,
|
| 111 |
+
"CHAINNAMES": null,
|
| 112 |
+
"MEMBRANES": null,
|
| 113 |
+
"CUSTOMS": null,
|
| 114 |
+
"ORIENTATION": null,
|
| 115 |
+
"PTM": [],
|
| 116 |
+
"MULTIMERIC": null,
|
| 117 |
+
"COLLECTIONS": "dynarepo",
|
| 118 |
+
"WARNINGS": [],
|
| 119 |
+
"BOXSIZEX": 12.0931,
|
| 120 |
+
"BOXSIZEY": 12.0931,
|
| 121 |
+
"BOXSIZEZ": 8.55536,
|
| 122 |
+
"mdName": "replica 1",
|
| 123 |
+
"mdAtoms": 7575,
|
| 124 |
+
"mdFrames": 5001
|
| 125 |
+
},
|
| 126 |
+
"mds": [
|
| 127 |
+
"replica 1",
|
| 128 |
+
"replica 2",
|
| 129 |
+
"replica 3"
|
| 130 |
+
],
|
| 131 |
+
"mdref": 0,
|
| 132 |
+
"files": [
|
| 133 |
+
"topology.tpr",
|
| 134 |
+
"screenshot.jpg",
|
| 135 |
+
"trajectory.bin",
|
| 136 |
+
"pca_trajectory_01.bin",
|
| 137 |
+
"pca_trajectory_02.bin",
|
| 138 |
+
"pca_trajectory_03.bin",
|
| 139 |
+
"pca_trajectory_04.bin",
|
| 140 |
+
"pca_trajectory_05.bin",
|
| 141 |
+
"pca_trajectory_06.bin",
|
| 142 |
+
"pca_trajectory_07.bin",
|
| 143 |
+
"pca_trajectory_08.bin",
|
| 144 |
+
"pca_trajectory_09.bin",
|
| 145 |
+
"pca_trajectory_10.bin",
|
| 146 |
+
"pca_trajectory_11.bin",
|
| 147 |
+
"pca_trajectory_12.bin",
|
| 148 |
+
"pca_trajectory_13.bin",
|
| 149 |
+
"structure.pdb",
|
| 150 |
+
"trajectory.xtc",
|
| 151 |
+
"clusters_00_screenshot_00.jpg",
|
| 152 |
+
"clusters_00_screenshot_01.jpg",
|
| 153 |
+
"clusters_00_screenshot_02.jpg",
|
| 154 |
+
"clusters_00_screenshot_03.jpg",
|
| 155 |
+
"clusters_00_screenshot_04.jpg",
|
| 156 |
+
"clusters_00_screenshot_05.jpg",
|
| 157 |
+
"clusters_00_screenshot_06.jpg",
|
| 158 |
+
"clusters_00_screenshot_07.jpg",
|
| 159 |
+
"clusters_00_screenshot_08.jpg",
|
| 160 |
+
"clusters_00_screenshot_09.jpg",
|
| 161 |
+
"clusters_00_screenshot_10.jpg",
|
| 162 |
+
"clusters_00_screenshot_11.jpg",
|
| 163 |
+
"clusters_00_screenshot_12.jpg",
|
| 164 |
+
"clusters_00_screenshot_13.jpg",
|
| 165 |
+
"clusters_00_screenshot_14.jpg",
|
| 166 |
+
"clusters_00_screenshot_15.jpg",
|
| 167 |
+
"clusters_00_screenshot_16.jpg",
|
| 168 |
+
"clusters_00_screenshot_17.jpg",
|
| 169 |
+
"clusters_00_screenshot_18.jpg",
|
| 170 |
+
"clusters_00_screenshot_19.jpg",
|
| 171 |
+
"clusters_00_screenshot_20.jpg",
|
| 172 |
+
"clusters_01_screenshot_00.jpg",
|
| 173 |
+
"clusters_01_screenshot_01.jpg",
|
| 174 |
+
"clusters_01_screenshot_02.jpg",
|
| 175 |
+
"clusters_01_screenshot_03.jpg",
|
| 176 |
+
"clusters_01_screenshot_04.jpg",
|
| 177 |
+
"clusters_01_screenshot_05.jpg",
|
| 178 |
+
"clusters_01_screenshot_06.jpg",
|
| 179 |
+
"clusters_01_screenshot_07.jpg",
|
| 180 |
+
"clusters_01_screenshot_08.jpg",
|
| 181 |
+
"clusters_01_screenshot_09.jpg",
|
| 182 |
+
"clusters_01_screenshot_10.jpg",
|
| 183 |
+
"clusters_01_screenshot_11.jpg",
|
| 184 |
+
"clusters_01_screenshot_12.jpg",
|
| 185 |
+
"clusters_01_screenshot_13.jpg",
|
| 186 |
+
"clusters_01_screenshot_14.jpg",
|
| 187 |
+
"clusters_01_screenshot_15.jpg",
|
| 188 |
+
"clusters_01_screenshot_16.jpg",
|
| 189 |
+
"clusters_01_screenshot_17.jpg",
|
| 190 |
+
"clusters_01_screenshot_18.jpg",
|
| 191 |
+
"clusters_01_screenshot_19.jpg",
|
| 192 |
+
"clusters_01_screenshot_20.jpg",
|
| 193 |
+
"clusters_02_screenshot_00.jpg",
|
| 194 |
+
"clusters_02_screenshot_01.jpg",
|
| 195 |
+
"clusters_02_screenshot_02.jpg",
|
| 196 |
+
"clusters_02_screenshot_03.jpg",
|
| 197 |
+
"clusters_02_screenshot_04.jpg",
|
| 198 |
+
"clusters_02_screenshot_05.jpg",
|
| 199 |
+
"clusters_02_screenshot_06.jpg",
|
| 200 |
+
"clusters_02_screenshot_07.jpg",
|
| 201 |
+
"clusters_02_screenshot_08.jpg",
|
| 202 |
+
"clusters_02_screenshot_09.jpg",
|
| 203 |
+
"clusters_02_screenshot_10.jpg",
|
| 204 |
+
"clusters_02_screenshot_11.jpg",
|
| 205 |
+
"clusters_02_screenshot_12.jpg",
|
| 206 |
+
"clusters_02_screenshot_13.jpg",
|
| 207 |
+
"clusters_02_screenshot_14.jpg",
|
| 208 |
+
"clusters_02_screenshot_15.jpg",
|
| 209 |
+
"clusters_02_screenshot_16.jpg",
|
| 210 |
+
"clusters_02_screenshot_17.jpg",
|
| 211 |
+
"clusters_02_screenshot_18.jpg",
|
| 212 |
+
"clusters_02_screenshot_19.jpg",
|
| 213 |
+
"clusters_03_screenshot_00.jpg",
|
| 214 |
+
"clusters_03_screenshot_01.jpg",
|
| 215 |
+
"clusters_03_screenshot_02.jpg",
|
| 216 |
+
"clusters_03_screenshot_03.jpg",
|
| 217 |
+
"clusters_03_screenshot_04.jpg",
|
| 218 |
+
"clusters_03_screenshot_05.jpg",
|
| 219 |
+
"clusters_03_screenshot_06.jpg",
|
| 220 |
+
"clusters_03_screenshot_07.jpg",
|
| 221 |
+
"clusters_03_screenshot_08.jpg",
|
| 222 |
+
"clusters_03_screenshot_09.jpg",
|
| 223 |
+
"clusters_03_screenshot_10.jpg",
|
| 224 |
+
"clusters_03_screenshot_11.jpg",
|
| 225 |
+
"clusters_03_screenshot_12.jpg",
|
| 226 |
+
"clusters_03_screenshot_13.jpg",
|
| 227 |
+
"clusters_03_screenshot_14.jpg",
|
| 228 |
+
"clusters_03_screenshot_15.jpg",
|
| 229 |
+
"clusters_03_screenshot_16.jpg",
|
| 230 |
+
"clusters_03_screenshot_17.jpg",
|
| 231 |
+
"clusters_03_screenshot_18.jpg",
|
| 232 |
+
"clusters_03_screenshot_19.jpg",
|
| 233 |
+
"pocket_01.pdb",
|
| 234 |
+
"pocket_02.pdb",
|
| 235 |
+
"pocket_03.pdb",
|
| 236 |
+
"pocket_04.pdb",
|
| 237 |
+
"pocket_05.pdb",
|
| 238 |
+
"pocket_06.pdb",
|
| 239 |
+
"pocket_07.pdb",
|
| 240 |
+
"pocket_08.pdb",
|
| 241 |
+
"pocket_09.pdb",
|
| 242 |
+
"pocket_10.pdb"
|
| 243 |
+
],
|
| 244 |
+
"analyses": [
|
| 245 |
+
"clusters",
|
| 246 |
+
"clusters-00",
|
| 247 |
+
"clusters-01",
|
| 248 |
+
"clusters-02",
|
| 249 |
+
"clusters-03",
|
| 250 |
+
"dist-perres",
|
| 251 |
+
"energies",
|
| 252 |
+
"fluctuation",
|
| 253 |
+
"hbonds",
|
| 254 |
+
"interactions",
|
| 255 |
+
"pca",
|
| 256 |
+
"pockets",
|
| 257 |
+
"rgyr",
|
| 258 |
+
"rmsd-pairwise",
|
| 259 |
+
"rmsd-perres",
|
| 260 |
+
"rmsds",
|
| 261 |
+
"sasa",
|
| 262 |
+
"tmscores"
|
| 263 |
+
],
|
| 264 |
+
"mdIndex": 0,
|
| 265 |
+
"mdNumber": 1,
|
| 266 |
+
"refframe": 0,
|
| 267 |
+
"internalId": "68401761d94df07e4f4f5569",
|
| 268 |
+
"creationDate": "2025-06-04T09:52:33.000Z",
|
| 269 |
+
"identifier": "A002N"
|
| 270 |
+
}
|
data/files/A002N/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002N", "accession": "A002N", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2BDN", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2BDN"], "FORCED_REFERENCES": null, "REFERENCES": ["P13500", "P0DOX7", "P84751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EVQLQQSGAELVKAGASVKLSCPASGLNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKFDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARGVFGFFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPR", "AINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSMDHLDKQT", "DIQMTQSSSSFSVSLGDRVTITCKATEDIYNRLAWYQQKPGSAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTEDVATYYCQQFWSAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC"], "NUCLSEQ": [], "DOMAINS": ["C-C motif chemokine 2", "Involved in dimerization", "Involved in dimerization, receptor binding and signaling", "Involved in GAG binding", "Involved in GAG binding and receptor binding", "Immunoglobulin kappa light chain", "Ig-like 1", "Ig-like 2", "Variable (V) domain, involved in antigen recognition", "Constant (C) domain", "Ig heavy chain Mem5", "Ig-like 1", "Ig-like 2", "D segment", "JH2 segment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7575, "SYSTRES": 499, "PROTATS": 7575, "PROTRES": 499, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.0931, "BOXSIZEY": 12.0931, "BOXSIZEZ": 8.55536, "mdName": "replica 1", "mdAtoms": 7575, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002N/files/topology.tpr", "length": 2453492, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002N/files/screenshot.jpg", "length": 20366, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002N/files/trajectory.bin", "length": 454590900, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 5001, "atoms": 7575}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_01.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_02.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_03.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_04.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_05.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_06.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_07.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_08.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_09.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_10.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_11.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_12.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_13.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002N/files/structure.pdb", "length": 613610, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002N/files/trajectory.xtc", "length": 143686856, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_00.jpg", "length": 20664, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_01.jpg", "length": 20796, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_02.jpg", "length": 20133, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_03.jpg", "length": 20378, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_04.jpg", "length": 20724, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_05.jpg", "length": 20489, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_06.jpg", "length": 20368, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_07.jpg", "length": 20527, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_08.jpg", "length": 20578, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_09.jpg", "length": 20180, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_10.jpg", "length": 20693, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_11.jpg", "length": 20680, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_12.jpg", "length": 20570, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_13.jpg", "length": 20815, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_14.jpg", "length": 21194, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_15.jpg", "length": 20260, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_16.jpg", "length": 20916, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_17.jpg", "length": 20759, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_18.jpg", "length": 20612, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_19.jpg", "length": 20464, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_20.jpg", "length": 20079, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_00.jpg", "length": 19999, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_01.jpg", "length": 20705, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_02.jpg", "length": 20563, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_03.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_04.jpg", "length": 20827, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_05.jpg", "length": 20266, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_06.jpg", "length": 20460, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_07.jpg", "length": 20489, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_08.jpg", "length": 20825, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_09.jpg", "length": 20328, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_10.jpg", "length": 20964, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_11.jpg", "length": 20334, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_12.jpg", "length": 20609, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_13.jpg", "length": 20746, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_14.jpg", "length": 20434, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_15.jpg", "length": 20861, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_16.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_17.jpg", "length": 20916, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_18.jpg", "length": 20940, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_19.jpg", "length": 20915, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_20.jpg", "length": 20298, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_00.jpg", "length": 21332, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_01.jpg", "length": 21552, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_02.jpg", "length": 21254, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_03.jpg", "length": 21510, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_04.jpg", "length": 21200, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_05.jpg", "length": 21602, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_06.jpg", "length": 21192, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_07.jpg", "length": 20824, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_08.jpg", "length": 21185, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_09.jpg", "length": 20873, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_10.jpg", "length": 21407, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_11.jpg", "length": 21688, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_12.jpg", "length": 21745, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_13.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_14.jpg", "length": 21121, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_15.jpg", "length": 21147, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_16.jpg", "length": 20965, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_17.jpg", "length": 21399, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_18.jpg", "length": 21568, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_19.jpg", "length": 21221, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_00.jpg", "length": 19993, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_01.jpg", "length": 20766, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_02.jpg", "length": 20680, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_03.jpg", "length": 20178, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_04.jpg", "length": 20398, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_05.jpg", "length": 20177, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_06.jpg", "length": 20379, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_07.jpg", "length": 20453, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_08.jpg", "length": 20738, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_09.jpg", "length": 20409, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_10.jpg", "length": 20685, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_11.jpg", "length": 20702, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_12.jpg", "length": 20999, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_13.jpg", "length": 20941, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_14.jpg", "length": 20624, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_15.jpg", "length": 20499, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_16.jpg", "length": 20104, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_17.jpg", "length": 20847, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_18.jpg", "length": 20246, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_19.jpg", "length": 20496, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002N/files/pocket_01.pdb", "length": 28810, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002N/files/pocket_02.pdb", "length": 28408, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002N/files/pocket_03.pdb", "length": 16951, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002N/files/pocket_04.pdb", "length": 14941, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002N/files/pocket_05.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002N/files/pocket_06.pdb", "length": 10586, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002N/files/pocket_07.pdb", "length": 8777, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002N/files/pocket_08.pdb", "length": 8509, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002N/files/pocket_09.pdb", "length": 6767, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002N/files/pocket_10.pdb", "length": 2948, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002N", "accession": "A002N", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2BDN", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2BDN"], "FORCED_REFERENCES": null, "REFERENCES": ["P13500", "P0DOX7", "P84751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EVQLQQSGAELVKAGASVKLSCPASGLNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKFDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARGVFGFFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPR", "AINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSMDHLDKQT", "DIQMTQSSSSFSVSLGDRVTITCKATEDIYNRLAWYQQKPGSAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTEDVATYYCQQFWSAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC"], "NUCLSEQ": [], "DOMAINS": ["C-C motif chemokine 2", "Involved in dimerization", "Involved in dimerization, receptor binding and signaling", "Involved in GAG binding", "Involved in GAG binding and receptor binding", "Immunoglobulin kappa light chain", "Ig-like 1", "Ig-like 2", "Variable (V) domain, involved in antigen recognition", "Constant (C) domain", "Ig heavy chain Mem5", "Ig-like 1", "Ig-like 2", "D segment", "JH2 segment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7575, "SYSTRES": 499, "PROTATS": 7575, "PROTRES": 499, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.0931, "BOXSIZEY": 12.0931, "BOXSIZEZ": 8.55536, "mdName": "replica 1", "mdAtoms": 7575, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002N/files/topology.tpr", "length": 2453492, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002N/files/screenshot.jpg", "length": 20366, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002N/files/trajectory.bin", "length": 454590900, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 5001, "atoms": 7575}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_01.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_02.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_03.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_04.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_05.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_06.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_07.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_08.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_09.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_10.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_11.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_12.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_13.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002N/files/structure.pdb", "length": 613610, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002N/files/trajectory.xtc", "length": 143686856, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_00.jpg", "length": 20664, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_01.jpg", "length": 20796, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_02.jpg", "length": 20133, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_03.jpg", "length": 20378, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_04.jpg", "length": 20724, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_05.jpg", "length": 20489, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_06.jpg", "length": 20368, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_07.jpg", "length": 20527, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_08.jpg", "length": 20578, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_09.jpg", "length": 20180, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_10.jpg", "length": 20693, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_11.jpg", "length": 20680, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_12.jpg", "length": 20570, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_13.jpg", "length": 20815, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_14.jpg", "length": 21194, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_15.jpg", "length": 20260, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_16.jpg", "length": 20916, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_17.jpg", "length": 20759, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_18.jpg", "length": 20612, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_19.jpg", "length": 20464, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_20.jpg", "length": 20079, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_00.jpg", "length": 19999, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_01.jpg", "length": 20705, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_02.jpg", "length": 20563, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_03.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_04.jpg", "length": 20827, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_05.jpg", "length": 20266, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_06.jpg", "length": 20460, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_07.jpg", "length": 20489, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_08.jpg", "length": 20825, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_09.jpg", "length": 20328, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_10.jpg", "length": 20964, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_11.jpg", "length": 20334, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_12.jpg", "length": 20609, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_13.jpg", "length": 20746, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_14.jpg", "length": 20434, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_15.jpg", "length": 20861, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_16.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_17.jpg", "length": 20916, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_18.jpg", "length": 20940, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_19.jpg", "length": 20915, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_20.jpg", "length": 20298, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_00.jpg", "length": 21332, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_01.jpg", "length": 21552, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_02.jpg", "length": 21254, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_03.jpg", "length": 21510, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_04.jpg", "length": 21200, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_05.jpg", "length": 21602, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_06.jpg", "length": 21192, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_07.jpg", "length": 20824, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_08.jpg", "length": 21185, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_09.jpg", "length": 20873, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_10.jpg", "length": 21407, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_11.jpg", "length": 21688, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_12.jpg", "length": 21745, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_13.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_14.jpg", "length": 21121, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_15.jpg", "length": 21147, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_16.jpg", "length": 20965, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_17.jpg", "length": 21399, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_18.jpg", "length": 21568, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_19.jpg", "length": 21221, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_00.jpg", "length": 19993, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_01.jpg", "length": 20766, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_02.jpg", "length": 20680, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_03.jpg", "length": 20178, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_04.jpg", "length": 20398, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_05.jpg", "length": 20177, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_06.jpg", "length": 20379, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_07.jpg", "length": 20453, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_08.jpg", "length": 20738, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_09.jpg", "length": 20409, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_10.jpg", "length": 20685, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_11.jpg", "length": 20702, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_12.jpg", "length": 20999, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_13.jpg", "length": 20941, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_14.jpg", "length": 20624, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_15.jpg", "length": 20499, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_16.jpg", "length": 20104, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_17.jpg", "length": 20847, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_18.jpg", "length": 20246, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_19.jpg", "length": 20496, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002N/files/pocket_01.pdb", "length": 28810, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002N/files/pocket_02.pdb", "length": 28408, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002N/files/pocket_03.pdb", "length": 16951, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002N/files/pocket_04.pdb", "length": 14941, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002N/files/pocket_05.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002N/files/pocket_06.pdb", "length": 10586, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002N/files/pocket_07.pdb", "length": 8777, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002N/files/pocket_08.pdb", "length": 8509, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002N/files/pocket_09.pdb", "length": 6767, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002N/files/pocket_10.pdb", "length": 2948, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002N", "accession": "A002N", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2BDN", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2BDN"], "FORCED_REFERENCES": null, "REFERENCES": ["P13500", "P0DOX7", "P84751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EVQLQQSGAELVKAGASVKLSCPASGLNIKDTYMHWVKQRPEQGLEWIGRIDPANGNTKFDPKFQGKATITADTSSNTAYLQLSSLTSEDTAVYYCARGVFGFFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPR", "AINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSMDHLDKQT", "DIQMTQSSSSFSVSLGDRVTITCKATEDIYNRLAWYQQKPGSAPRLLISGATSLETGVPSRFSGSGSGKDYTLSITSLQTEDVATYYCQQFWSAPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC"], "NUCLSEQ": [], "DOMAINS": ["C-C motif chemokine 2", "Involved in dimerization", "Involved in dimerization, receptor binding and signaling", "Involved in GAG binding", "Involved in GAG binding and receptor binding", "Immunoglobulin kappa light chain", "Ig-like 1", "Ig-like 2", "Variable (V) domain, involved in antigen recognition", "Constant (C) domain", "Ig heavy chain Mem5", "Ig-like 1", "Ig-like 2", "D segment", "JH2 segment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7575, "SYSTRES": 499, "PROTATS": 7575, "PROTRES": 499, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.0931, "BOXSIZEY": 12.0931, "BOXSIZEZ": 8.55536, "mdName": "replica 1", "mdAtoms": 7575, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002N/files/topology.tpr", "length": 2453492, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002N/files/screenshot.jpg", "length": 20366, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002N/files/trajectory.bin", "length": 454590900, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 5001, "atoms": 7575}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_01.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_02.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_03.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_04.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_05.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_06.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_07.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_08.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_09.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_10.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_11.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_12.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002N/files/pca_trajectory_13.bin", "length": 359280, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0, "frames": 20, "atoms": 1497}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002N/files/structure.pdb", "length": 613610, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002N/files/trajectory.xtc", "length": 143686856, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_00.jpg", "length": 20664, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_01.jpg", "length": 20796, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_02.jpg", "length": 20133, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_03.jpg", "length": 20378, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_04.jpg", "length": 20724, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_05.jpg", "length": 20489, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_06.jpg", "length": 20368, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_07.jpg", "length": 20527, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_08.jpg", "length": 20578, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_09.jpg", "length": 20180, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_10.jpg", "length": 20693, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_11.jpg", "length": 20680, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_12.jpg", "length": 20570, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_13.jpg", "length": 20815, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_14.jpg", "length": 21194, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_15.jpg", "length": 20260, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_16.jpg", "length": 20916, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_17.jpg", "length": 20759, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_18.jpg", "length": 20612, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_19.jpg", "length": 20464, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A002N/files/clusters_00_screenshot_20.jpg", "length": 20079, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_00.jpg", "length": 19999, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_01.jpg", "length": 20705, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_02.jpg", "length": 20563, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_03.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_04.jpg", "length": 20827, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_05.jpg", "length": 20266, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_06.jpg", "length": 20460, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_07.jpg", "length": 20489, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_08.jpg", "length": 20825, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_09.jpg", "length": 20328, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_10.jpg", "length": 20964, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_11.jpg", "length": 20334, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_12.jpg", "length": 20609, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_13.jpg", "length": 20746, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_14.jpg", "length": 20434, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_15.jpg", "length": 20861, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_16.jpg", "length": 20483, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_17.jpg", "length": 20916, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_18.jpg", "length": 20940, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_19.jpg", "length": 20915, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002N/files/clusters_01_screenshot_20.jpg", "length": 20298, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_00.jpg", "length": 21332, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_01.jpg", "length": 21552, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_02.jpg", "length": 21254, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_03.jpg", "length": 21510, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_04.jpg", "length": 21200, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_05.jpg", "length": 21602, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_06.jpg", "length": 21192, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_07.jpg", "length": 20824, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_08.jpg", "length": 21185, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_09.jpg", "length": 20873, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_10.jpg", "length": 21407, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_11.jpg", "length": 21688, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_12.jpg", "length": 21745, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_13.jpg", "length": 21357, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_14.jpg", "length": 21121, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_15.jpg", "length": 21147, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_16.jpg", "length": 20965, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_17.jpg", "length": 21399, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_18.jpg", "length": 21568, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_02_screenshot_19.jpg", "length": 21221, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_00.jpg", "length": 19993, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_01.jpg", "length": 20766, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_02.jpg", "length": 20680, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_03.jpg", "length": 20178, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_04.jpg", "length": 20398, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_05.jpg", "length": 20177, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_06.jpg", "length": 20379, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_07.jpg", "length": 20453, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_08.jpg", "length": 20738, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_09.jpg", "length": 20409, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_10.jpg", "length": 20685, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_11.jpg", "length": 20702, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_12.jpg", "length": 20999, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_13.jpg", "length": 20941, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_14.jpg", "length": 20624, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_15.jpg", "length": 20499, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_16.jpg", "length": 20104, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_17.jpg", "length": 20847, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_18.jpg", "length": 20246, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002N/files/clusters_03_screenshot_19.jpg", "length": 20496, "contentType": "application/octet-stream", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002N/files/pocket_01.pdb", "length": 28810, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002N/files/pocket_02.pdb", "length": 28408, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002N/files/pocket_03.pdb", "length": 16951, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002N/files/pocket_04.pdb", "length": 14941, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002N/files/pocket_05.pdb", "length": 10720, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002N/files/pocket_06.pdb", "length": 10586, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002N/files/pocket_07.pdb", "length": 8777, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002N/files/pocket_08.pdb", "length": 8509, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002N/files/pocket_09.pdb", "length": 6767, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002N/files/pocket_10.pdb", "length": 2948, "contentType": "chemical/x-pdb", "metadata": {"project": "68401761d94df07e4f4f5569", "md": 0}}]}
|
data/files/A002O/project.json
ADDED
|
@@ -0,0 +1,279 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002O",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2BO9",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2BO9"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9UI42",
|
| 31 |
+
"Q9BS40"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SSNNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL",
|
| 38 |
+
"MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNCTAEVLYPSTGQETAPEVNFTFEGETGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPEMTLVLHLAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIELDYTILLHNIASQEIIPWQMQVLWHPQYGTKVKHNSRLPK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Carboxypeptidase A4",
|
| 43 |
+
"Peptidase M14",
|
| 44 |
+
"Latexin",
|
| 45 |
+
"Cystatin LXN-type 1",
|
| 46 |
+
"Cystatin LXN-type 2",
|
| 47 |
+
"Alpha-helical linker"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 16572,
|
| 59 |
+
"SYSTRES": 1048,
|
| 60 |
+
"PROTATS": 16572,
|
| 61 |
+
"PROTRES": 1048,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"name": "chain A-chain C interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain C",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "chain A-chain D interaction",
|
| 92 |
+
"agent_1": "chain A",
|
| 93 |
+
"agent_2": "chain D",
|
| 94 |
+
"selection_1": "chain A",
|
| 95 |
+
"selection_2": "chain D",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
},
|
| 98 |
+
{
|
| 99 |
+
"name": "chain C-chain D interaction",
|
| 100 |
+
"agent_1": "chain C",
|
| 101 |
+
"agent_2": "chain D",
|
| 102 |
+
"selection_1": "chain B",
|
| 103 |
+
"selection_2": "chain C",
|
| 104 |
+
"type": "protein-protein"
|
| 105 |
+
}
|
| 106 |
+
],
|
| 107 |
+
"PBC_SELECTION": null,
|
| 108 |
+
"CHAINNAMES": null,
|
| 109 |
+
"MEMBRANES": null,
|
| 110 |
+
"CUSTOMS": null,
|
| 111 |
+
"ORIENTATION": null,
|
| 112 |
+
"PTM": [],
|
| 113 |
+
"MULTIMERIC": null,
|
| 114 |
+
"COLLECTIONS": "dynarepo",
|
| 115 |
+
"WARNINGS": [],
|
| 116 |
+
"BOXSIZEX": 14.7124,
|
| 117 |
+
"BOXSIZEY": 14.7124,
|
| 118 |
+
"BOXSIZEZ": 10.4197,
|
| 119 |
+
"mdName": "replica 1",
|
| 120 |
+
"mdAtoms": 16572,
|
| 121 |
+
"mdFrames": 5001
|
| 122 |
+
},
|
| 123 |
+
"mds": [
|
| 124 |
+
"replica 1",
|
| 125 |
+
"replica 2",
|
| 126 |
+
"replica 3"
|
| 127 |
+
],
|
| 128 |
+
"mdref": 0,
|
| 129 |
+
"files": [
|
| 130 |
+
"topology.tpr",
|
| 131 |
+
"screenshot.jpg",
|
| 132 |
+
"trajectory.bin",
|
| 133 |
+
"pca_trajectory_01.bin",
|
| 134 |
+
"pca_trajectory_02.bin",
|
| 135 |
+
"pca_trajectory_03.bin",
|
| 136 |
+
"pca_trajectory_04.bin",
|
| 137 |
+
"structure.pdb",
|
| 138 |
+
"trajectory.xtc",
|
| 139 |
+
"clusters_00_screenshot_00.jpg",
|
| 140 |
+
"clusters_00_screenshot_01.jpg",
|
| 141 |
+
"clusters_00_screenshot_02.jpg",
|
| 142 |
+
"clusters_00_screenshot_03.jpg",
|
| 143 |
+
"clusters_00_screenshot_04.jpg",
|
| 144 |
+
"clusters_00_screenshot_05.jpg",
|
| 145 |
+
"clusters_00_screenshot_06.jpg",
|
| 146 |
+
"clusters_00_screenshot_07.jpg",
|
| 147 |
+
"clusters_00_screenshot_08.jpg",
|
| 148 |
+
"clusters_00_screenshot_09.jpg",
|
| 149 |
+
"clusters_00_screenshot_10.jpg",
|
| 150 |
+
"clusters_00_screenshot_11.jpg",
|
| 151 |
+
"clusters_00_screenshot_12.jpg",
|
| 152 |
+
"clusters_00_screenshot_13.jpg",
|
| 153 |
+
"clusters_00_screenshot_14.jpg",
|
| 154 |
+
"clusters_00_screenshot_15.jpg",
|
| 155 |
+
"clusters_00_screenshot_16.jpg",
|
| 156 |
+
"clusters_00_screenshot_17.jpg",
|
| 157 |
+
"clusters_00_screenshot_18.jpg",
|
| 158 |
+
"clusters_00_screenshot_19.jpg",
|
| 159 |
+
"clusters_01_screenshot_00.jpg",
|
| 160 |
+
"clusters_01_screenshot_01.jpg",
|
| 161 |
+
"clusters_01_screenshot_02.jpg",
|
| 162 |
+
"clusters_01_screenshot_03.jpg",
|
| 163 |
+
"clusters_01_screenshot_04.jpg",
|
| 164 |
+
"clusters_01_screenshot_05.jpg",
|
| 165 |
+
"clusters_01_screenshot_06.jpg",
|
| 166 |
+
"clusters_01_screenshot_07.jpg",
|
| 167 |
+
"clusters_01_screenshot_08.jpg",
|
| 168 |
+
"clusters_01_screenshot_09.jpg",
|
| 169 |
+
"clusters_01_screenshot_10.jpg",
|
| 170 |
+
"clusters_01_screenshot_11.jpg",
|
| 171 |
+
"clusters_01_screenshot_12.jpg",
|
| 172 |
+
"clusters_01_screenshot_13.jpg",
|
| 173 |
+
"clusters_01_screenshot_14.jpg",
|
| 174 |
+
"clusters_01_screenshot_15.jpg",
|
| 175 |
+
"clusters_01_screenshot_16.jpg",
|
| 176 |
+
"clusters_01_screenshot_17.jpg",
|
| 177 |
+
"clusters_01_screenshot_18.jpg",
|
| 178 |
+
"clusters_02_screenshot_00.jpg",
|
| 179 |
+
"clusters_02_screenshot_01.jpg",
|
| 180 |
+
"clusters_02_screenshot_02.jpg",
|
| 181 |
+
"clusters_02_screenshot_03.jpg",
|
| 182 |
+
"clusters_02_screenshot_04.jpg",
|
| 183 |
+
"clusters_02_screenshot_05.jpg",
|
| 184 |
+
"clusters_02_screenshot_06.jpg",
|
| 185 |
+
"clusters_02_screenshot_07.jpg",
|
| 186 |
+
"clusters_02_screenshot_08.jpg",
|
| 187 |
+
"clusters_02_screenshot_09.jpg",
|
| 188 |
+
"clusters_02_screenshot_10.jpg",
|
| 189 |
+
"clusters_02_screenshot_11.jpg",
|
| 190 |
+
"clusters_02_screenshot_12.jpg",
|
| 191 |
+
"clusters_02_screenshot_13.jpg",
|
| 192 |
+
"clusters_02_screenshot_14.jpg",
|
| 193 |
+
"clusters_02_screenshot_15.jpg",
|
| 194 |
+
"clusters_02_screenshot_16.jpg",
|
| 195 |
+
"clusters_02_screenshot_17.jpg",
|
| 196 |
+
"clusters_02_screenshot_18.jpg",
|
| 197 |
+
"clusters_02_screenshot_19.jpg",
|
| 198 |
+
"clusters_03_screenshot_00.jpg",
|
| 199 |
+
"clusters_03_screenshot_01.jpg",
|
| 200 |
+
"clusters_03_screenshot_02.jpg",
|
| 201 |
+
"clusters_03_screenshot_03.jpg",
|
| 202 |
+
"clusters_03_screenshot_04.jpg",
|
| 203 |
+
"clusters_03_screenshot_05.jpg",
|
| 204 |
+
"clusters_03_screenshot_06.jpg",
|
| 205 |
+
"clusters_03_screenshot_07.jpg",
|
| 206 |
+
"clusters_03_screenshot_08.jpg",
|
| 207 |
+
"clusters_03_screenshot_09.jpg",
|
| 208 |
+
"clusters_03_screenshot_10.jpg",
|
| 209 |
+
"clusters_03_screenshot_11.jpg",
|
| 210 |
+
"clusters_03_screenshot_12.jpg",
|
| 211 |
+
"clusters_03_screenshot_13.jpg",
|
| 212 |
+
"clusters_03_screenshot_14.jpg",
|
| 213 |
+
"clusters_03_screenshot_15.jpg",
|
| 214 |
+
"clusters_03_screenshot_16.jpg",
|
| 215 |
+
"clusters_03_screenshot_17.jpg",
|
| 216 |
+
"clusters_03_screenshot_18.jpg",
|
| 217 |
+
"clusters_03_screenshot_19.jpg",
|
| 218 |
+
"clusters_03_screenshot_20.jpg",
|
| 219 |
+
"clusters_03_screenshot_21.jpg",
|
| 220 |
+
"clusters_03_screenshot_22.jpg",
|
| 221 |
+
"clusters_04_screenshot_00.jpg",
|
| 222 |
+
"clusters_04_screenshot_01.jpg",
|
| 223 |
+
"clusters_04_screenshot_02.jpg",
|
| 224 |
+
"clusters_04_screenshot_03.jpg",
|
| 225 |
+
"clusters_04_screenshot_04.jpg",
|
| 226 |
+
"clusters_04_screenshot_05.jpg",
|
| 227 |
+
"clusters_04_screenshot_06.jpg",
|
| 228 |
+
"clusters_04_screenshot_07.jpg",
|
| 229 |
+
"clusters_04_screenshot_08.jpg",
|
| 230 |
+
"clusters_04_screenshot_09.jpg",
|
| 231 |
+
"clusters_04_screenshot_10.jpg",
|
| 232 |
+
"clusters_04_screenshot_11.jpg",
|
| 233 |
+
"clusters_04_screenshot_12.jpg",
|
| 234 |
+
"clusters_04_screenshot_13.jpg",
|
| 235 |
+
"clusters_04_screenshot_14.jpg",
|
| 236 |
+
"clusters_04_screenshot_15.jpg",
|
| 237 |
+
"clusters_04_screenshot_16.jpg",
|
| 238 |
+
"clusters_04_screenshot_17.jpg",
|
| 239 |
+
"clusters_04_screenshot_18.jpg",
|
| 240 |
+
"clusters_04_screenshot_19.jpg",
|
| 241 |
+
"pocket_01.pdb",
|
| 242 |
+
"pocket_02.pdb",
|
| 243 |
+
"pocket_03.pdb",
|
| 244 |
+
"pocket_04.pdb",
|
| 245 |
+
"pocket_05.pdb",
|
| 246 |
+
"pocket_06.pdb",
|
| 247 |
+
"pocket_07.pdb",
|
| 248 |
+
"pocket_08.pdb",
|
| 249 |
+
"pocket_09.pdb",
|
| 250 |
+
"pocket_10.pdb"
|
| 251 |
+
],
|
| 252 |
+
"analyses": [
|
| 253 |
+
"clusters",
|
| 254 |
+
"clusters-00",
|
| 255 |
+
"clusters-01",
|
| 256 |
+
"clusters-02",
|
| 257 |
+
"clusters-03",
|
| 258 |
+
"clusters-04",
|
| 259 |
+
"dist-perres",
|
| 260 |
+
"energies",
|
| 261 |
+
"fluctuation",
|
| 262 |
+
"hbonds",
|
| 263 |
+
"interactions",
|
| 264 |
+
"pca",
|
| 265 |
+
"pockets",
|
| 266 |
+
"rgyr",
|
| 267 |
+
"rmsd-pairwise",
|
| 268 |
+
"rmsd-perres",
|
| 269 |
+
"rmsds",
|
| 270 |
+
"sasa",
|
| 271 |
+
"tmscores"
|
| 272 |
+
],
|
| 273 |
+
"mdIndex": 0,
|
| 274 |
+
"mdNumber": 1,
|
| 275 |
+
"refframe": 0,
|
| 276 |
+
"internalId": "68401b5a1557d42c1cfebb0b",
|
| 277 |
+
"creationDate": "2025-06-04T10:09:30.000Z",
|
| 278 |
+
"identifier": "A002O"
|
| 279 |
+
}
|
data/files/A002O/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A002O", "accession": "A002O", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "clusters-04", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2BO9", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2BO9"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9UI42", "Q9BS40"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["SSNNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL", "MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNCTAEVLYPSTGQETAPEVNFTFEGETGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPEMTLVLHLAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIELDYTILLHNIASQEIIPWQMQVLWHPQYGTKVKHNSRLPK"], "NUCLSEQ": [], "DOMAINS": ["Carboxypeptidase A4", "Peptidase M14", "Latexin", "Cystatin LXN-type 1", "Cystatin LXN-type 2", "Alpha-helical linker"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 16572, "SYSTRES": 1048, "PROTATS": 16572, "PROTRES": 1048, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain A-chain D interaction", "agent_1": "chain A", "agent_2": "chain D", "selection_1": "chain A", "selection_2": "chain D", "type": "protein-protein"}, {"name": "chain C-chain D interaction", "agent_1": "chain C", "agent_2": "chain D", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 14.7124, "BOXSIZEY": 14.7124, "BOXSIZEZ": 10.4197, "mdName": "replica 1", "mdAtoms": 16572, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002O/files/topology.tpr", "length": 4957880, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002O/files/screenshot.jpg", "length": 23479, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002O/files/trajectory.bin", "length": 994518864, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 5001, "atoms": 16572}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_01.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_02.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_03.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_04.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002O/files/structure.pdb", "length": 1342367, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002O/files/trajectory.xtc", "length": 314509644, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_00.jpg", "length": 23802, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_01.jpg", "length": 23888, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_02.jpg", "length": 23613, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_03.jpg", "length": 24126, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_04.jpg", "length": 23973, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_05.jpg", "length": 23972, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_06.jpg", "length": 24120, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_07.jpg", "length": 24234, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_08.jpg", "length": 23879, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_09.jpg", "length": 23970, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_10.jpg", "length": 23572, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_11.jpg", "length": 23155, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_12.jpg", "length": 22711, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_13.jpg", "length": 23597, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_14.jpg", "length": 23651, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_15.jpg", "length": 22972, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_16.jpg", "length": 23497, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_17.jpg", "length": 24111, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_18.jpg", "length": 24430, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_19.jpg", "length": 24515, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_00.jpg", "length": 26067, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_01.jpg", "length": 25161, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_02.jpg", "length": 26524, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_03.jpg", "length": 25420, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_04.jpg", "length": 25435, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_05.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_06.jpg", "length": 25232, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_07.jpg", "length": 25559, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_08.jpg", "length": 25412, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_09.jpg", "length": 25471, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_10.jpg", "length": 25691, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_11.jpg", "length": 25438, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_12.jpg", "length": 25385, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_13.jpg", "length": 25484, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_14.jpg", "length": 25470, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_15.jpg", "length": 25824, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_16.jpg", "length": 25633, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_17.jpg", "length": 25798, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_18.jpg", "length": 25836, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_00.jpg", "length": 23732, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_01.jpg", "length": 23821, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_02.jpg", "length": 23979, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_03.jpg", "length": 23568, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_04.jpg", "length": 24072, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_05.jpg", "length": 23976, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_06.jpg", "length": 24035, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_07.jpg", "length": 24283, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_08.jpg", "length": 23982, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_09.jpg", "length": 23602, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_10.jpg", "length": 22991, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_11.jpg", "length": 22723, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_12.jpg", "length": 23628, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_13.jpg", "length": 23677, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_14.jpg", "length": 23450, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_15.jpg", "length": 22910, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_16.jpg", "length": 23490, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_17.jpg", "length": 24094, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_18.jpg", "length": 24284, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_19.jpg", "length": 24356, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_00.jpg", "length": 24682, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_01.jpg", "length": 24740, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_02.jpg", "length": 25076, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_03.jpg", "length": 24988, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_04.jpg", "length": 25297, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_05.jpg", "length": 25233, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_06.jpg", "length": 25255, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_07.jpg", "length": 25421, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_08.jpg", "length": 25116, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_09.jpg", "length": 25229, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_10.jpg", "length": 25120, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_11.jpg", "length": 24256, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_12.jpg", "length": 24449, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_13.jpg", "length": 24032, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_14.jpg", "length": 24376, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_15.jpg", "length": 24446, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_16.jpg", "length": 23866, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_17.jpg", "length": 24538, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_18.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_19.jpg", "length": 24777, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_20.jpg", "length": 25321, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_21.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_21.jpg", "length": 24894, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_22.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_22.jpg", "length": 25132, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_00.jpg", "length": 25471, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_01.jpg", "length": 25580, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_02.jpg", "length": 26201, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_03.jpg", "length": 26394, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_04.jpg", "length": 25754, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_05.jpg", "length": 25708, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_06.jpg", "length": 25845, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_07.jpg", "length": 25563, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_08.jpg", "length": 25445, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_09.jpg", "length": 25698, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_10.jpg", "length": 25810, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_11.jpg", "length": 25967, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_12.jpg", "length": 25613, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_13.jpg", "length": 25588, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_14.jpg", "length": 25822, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_15.jpg", "length": 25875, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_16.jpg", "length": 25693, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_17.jpg", "length": 26106, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_18.jpg", "length": 25873, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_19.jpg", "length": 26153, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002O/files/pocket_01.pdb", "length": 35041, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002O/files/pocket_02.pdb", "length": 22981, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002O/files/pocket_03.pdb", "length": 21909, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002O/files/pocket_04.pdb", "length": 12261, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002O/files/pocket_05.pdb", "length": 11390, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002O/files/pocket_06.pdb", "length": 9246, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002O/files/pocket_07.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002O/files/pocket_08.pdb", "length": 7437, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002O/files/pocket_09.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002O/files/pocket_10.pdb", "length": 7169, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}]}
|
| 2 |
+
{"project_identifier": "A002O", "accession": "A002O", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "clusters-04", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2BO9", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2BO9"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9UI42", "Q9BS40"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["SSNNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL", "MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNCTAEVLYPSTGQETAPEVNFTFEGETGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPEMTLVLHLAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIELDYTILLHNIASQEIIPWQMQVLWHPQYGTKVKHNSRLPK"], "NUCLSEQ": [], "DOMAINS": ["Carboxypeptidase A4", "Peptidase M14", "Latexin", "Cystatin LXN-type 1", "Cystatin LXN-type 2", "Alpha-helical linker"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 16572, "SYSTRES": 1048, "PROTATS": 16572, "PROTRES": 1048, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain A-chain D interaction", "agent_1": "chain A", "agent_2": "chain D", "selection_1": "chain A", "selection_2": "chain D", "type": "protein-protein"}, {"name": "chain C-chain D interaction", "agent_1": "chain C", "agent_2": "chain D", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 14.7124, "BOXSIZEY": 14.7124, "BOXSIZEZ": 10.4197, "mdName": "replica 1", "mdAtoms": 16572, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002O/files/topology.tpr", "length": 4957880, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002O/files/screenshot.jpg", "length": 23479, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002O/files/trajectory.bin", "length": 994518864, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 5001, "atoms": 16572}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_01.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_02.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_03.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_04.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002O/files/structure.pdb", "length": 1342367, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002O/files/trajectory.xtc", "length": 314509644, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_00.jpg", "length": 23802, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_01.jpg", "length": 23888, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_02.jpg", "length": 23613, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_03.jpg", "length": 24126, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_04.jpg", "length": 23973, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_05.jpg", "length": 23972, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_06.jpg", "length": 24120, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_07.jpg", "length": 24234, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_08.jpg", "length": 23879, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_09.jpg", "length": 23970, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_10.jpg", "length": 23572, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_11.jpg", "length": 23155, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_12.jpg", "length": 22711, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_13.jpg", "length": 23597, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_14.jpg", "length": 23651, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_15.jpg", "length": 22972, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_16.jpg", "length": 23497, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_17.jpg", "length": 24111, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_18.jpg", "length": 24430, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_19.jpg", "length": 24515, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_00.jpg", "length": 26067, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_01.jpg", "length": 25161, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_02.jpg", "length": 26524, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_03.jpg", "length": 25420, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_04.jpg", "length": 25435, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_05.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_06.jpg", "length": 25232, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_07.jpg", "length": 25559, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_08.jpg", "length": 25412, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_09.jpg", "length": 25471, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_10.jpg", "length": 25691, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_11.jpg", "length": 25438, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_12.jpg", "length": 25385, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_13.jpg", "length": 25484, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_14.jpg", "length": 25470, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_15.jpg", "length": 25824, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_16.jpg", "length": 25633, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_17.jpg", "length": 25798, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_18.jpg", "length": 25836, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_00.jpg", "length": 23732, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_01.jpg", "length": 23821, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_02.jpg", "length": 23979, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_03.jpg", "length": 23568, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_04.jpg", "length": 24072, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_05.jpg", "length": 23976, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_06.jpg", "length": 24035, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_07.jpg", "length": 24283, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_08.jpg", "length": 23982, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_09.jpg", "length": 23602, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_10.jpg", "length": 22991, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_11.jpg", "length": 22723, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_12.jpg", "length": 23628, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_13.jpg", "length": 23677, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_14.jpg", "length": 23450, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_15.jpg", "length": 22910, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_16.jpg", "length": 23490, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_17.jpg", "length": 24094, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_18.jpg", "length": 24284, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_19.jpg", "length": 24356, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_00.jpg", "length": 24682, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_01.jpg", "length": 24740, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_02.jpg", "length": 25076, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_03.jpg", "length": 24988, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_04.jpg", "length": 25297, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_05.jpg", "length": 25233, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_06.jpg", "length": 25255, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_07.jpg", "length": 25421, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_08.jpg", "length": 25116, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_09.jpg", "length": 25229, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_10.jpg", "length": 25120, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_11.jpg", "length": 24256, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_12.jpg", "length": 24449, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_13.jpg", "length": 24032, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_14.jpg", "length": 24376, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_15.jpg", "length": 24446, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_16.jpg", "length": 23866, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_17.jpg", "length": 24538, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_18.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_19.jpg", "length": 24777, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_20.jpg", "length": 25321, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_21.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_21.jpg", "length": 24894, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_22.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_22.jpg", "length": 25132, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_00.jpg", "length": 25471, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_01.jpg", "length": 25580, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_02.jpg", "length": 26201, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_03.jpg", "length": 26394, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_04.jpg", "length": 25754, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_05.jpg", "length": 25708, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_06.jpg", "length": 25845, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_07.jpg", "length": 25563, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_08.jpg", "length": 25445, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_09.jpg", "length": 25698, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_10.jpg", "length": 25810, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_11.jpg", "length": 25967, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_12.jpg", "length": 25613, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_13.jpg", "length": 25588, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_14.jpg", "length": 25822, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_15.jpg", "length": 25875, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_16.jpg", "length": 25693, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_17.jpg", "length": 26106, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_18.jpg", "length": 25873, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_19.jpg", "length": 26153, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002O/files/pocket_01.pdb", "length": 35041, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002O/files/pocket_02.pdb", "length": 22981, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002O/files/pocket_03.pdb", "length": 21909, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002O/files/pocket_04.pdb", "length": 12261, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002O/files/pocket_05.pdb", "length": 11390, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002O/files/pocket_06.pdb", "length": 9246, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002O/files/pocket_07.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002O/files/pocket_08.pdb", "length": 7437, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002O/files/pocket_09.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002O/files/pocket_10.pdb", "length": 7169, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}]}
|
| 3 |
+
{"project_identifier": "A002O", "accession": "A002O", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "clusters-04", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2BO9", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["2BO9"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9UI42", "Q9BS40"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["SSNNFNYGAYHSLEAIYHEMDNIAADFPDLARRVKIGHSFENRPMYVLKFSTGKGVRRPAVWLNAGIHSREWISQATAIWTARKIVSDYQRDPAITSILEKMDIFLLPVANPDGYVYTQTQNRLWRKTRSRNPGSSCIGADPNRNWNASFAGKGASDNPCSEVYHGPHANSEVEVKSVVDFIQKHGNFKGFIDLHSYSQLLMYPYGYSVKKAPDAEELDKVARLAAKALASVSGTEYQVGPTCTTVYPASGSSIDWAYDNGIKFAFTFELRDTGTYGFLLPANQIIPTAEETWLGLKTIMEHVRDNL", "MEIPPTNYPASRAALVAQNYINYQQGTPHRVFEVQKVKQASMEDIPGRGHKYRLKFAVEEIIQKQVKVNCTAEVLYPSTGQETAPEVNFTFEGETGKNPDEEDNTFYQRLKSMKEPLEAQNIPDNFGNVSPEMTLVLHLAWVACGYIIWQNSTEDTWYKMVKIQTVKQVQRNDDFIELDYTILLHNIASQEIIPWQMQVLWHPQYGTKVKHNSRLPK"], "NUCLSEQ": [], "DOMAINS": ["Carboxypeptidase A4", "Peptidase M14", "Latexin", "Cystatin LXN-type 1", "Cystatin LXN-type 2", "Alpha-helical linker"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 16572, "SYSTRES": 1048, "PROTATS": 16572, "PROTRES": 1048, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain A-chain D interaction", "agent_1": "chain A", "agent_2": "chain D", "selection_1": "chain A", "selection_2": "chain D", "type": "protein-protein"}, {"name": "chain C-chain D interaction", "agent_1": "chain C", "agent_2": "chain D", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 14.7124, "BOXSIZEY": 14.7124, "BOXSIZEZ": 10.4197, "mdName": "replica 1", "mdAtoms": 16572, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002O/files/topology.tpr", "length": 4957880, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002O/files/screenshot.jpg", "length": 23479, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002O/files/trajectory.bin", "length": 994518864, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 5001, "atoms": 16572}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_01.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_02.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_03.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002O/files/pca_trajectory_04.bin", "length": 754560, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0, "frames": 20, "atoms": 3144}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002O/files/structure.pdb", "length": 1342367, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002O/files/trajectory.xtc", "length": 314509644, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_00.jpg", "length": 23802, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_01.jpg", "length": 23888, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_02.jpg", "length": 23613, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_03.jpg", "length": 24126, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_04.jpg", "length": 23973, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_05.jpg", "length": 23972, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_06.jpg", "length": 24120, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_07.jpg", "length": 24234, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_08.jpg", "length": 23879, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_09.jpg", "length": 23970, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_10.jpg", "length": 23572, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_11.jpg", "length": 23155, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_12.jpg", "length": 22711, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_13.jpg", "length": 23597, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_14.jpg", "length": 23651, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_15.jpg", "length": 22972, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_16.jpg", "length": 23497, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_17.jpg", "length": 24111, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_18.jpg", "length": 24430, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_00_screenshot_19.jpg", "length": 24515, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_00.jpg", "length": 26067, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_01.jpg", "length": 25161, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_02.jpg", "length": 26524, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_03.jpg", "length": 25420, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_04.jpg", "length": 25435, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_05.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_06.jpg", "length": 25232, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_07.jpg", "length": 25559, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_08.jpg", "length": 25412, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_09.jpg", "length": 25471, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_10.jpg", "length": 25691, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_11.jpg", "length": 25438, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_12.jpg", "length": 25385, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_13.jpg", "length": 25484, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_14.jpg", "length": 25470, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_15.jpg", "length": 25824, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_16.jpg", "length": 25633, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_17.jpg", "length": 25798, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_01_screenshot_18.jpg", "length": 25836, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_00.jpg", "length": 23732, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_01.jpg", "length": 23821, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_02.jpg", "length": 23979, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_03.jpg", "length": 23568, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_04.jpg", "length": 24072, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_05.jpg", "length": 23976, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_06.jpg", "length": 24035, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_07.jpg", "length": 24283, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_08.jpg", "length": 23982, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_09.jpg", "length": 23602, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_10.jpg", "length": 22991, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_11.jpg", "length": 22723, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_12.jpg", "length": 23628, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_13.jpg", "length": 23677, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_14.jpg", "length": 23450, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_15.jpg", "length": 22910, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_16.jpg", "length": 23490, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_17.jpg", "length": 24094, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_18.jpg", "length": 24284, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_02_screenshot_19.jpg", "length": 24356, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_00.jpg", "length": 24682, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_01.jpg", "length": 24740, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_02.jpg", "length": 25076, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_03.jpg", "length": 24988, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_04.jpg", "length": 25297, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_05.jpg", "length": 25233, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_06.jpg", "length": 25255, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_07.jpg", "length": 25421, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_08.jpg", "length": 25116, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_09.jpg", "length": 25229, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_10.jpg", "length": 25120, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_11.jpg", "length": 24256, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_12.jpg", "length": 24449, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_13.jpg", "length": 24032, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_14.jpg", "length": 24376, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_15.jpg", "length": 24446, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_16.jpg", "length": 23866, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_17.jpg", "length": 24538, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_18.jpg", "length": 25002, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_19.jpg", "length": 24777, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_20.jpg", "length": 25321, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_21.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_21.jpg", "length": 24894, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_03_screenshot_22.jpg", "downloadUrl": "/projects/A002O/files/clusters_03_screenshot_22.jpg", "length": 25132, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_00.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_00.jpg", "length": 25471, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_01.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_01.jpg", "length": 25580, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_02.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_02.jpg", "length": 26201, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_03.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_03.jpg", "length": 26394, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_04.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_04.jpg", "length": 25754, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_05.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_05.jpg", "length": 25708, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_06.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_06.jpg", "length": 25845, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_07.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_07.jpg", "length": 25563, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_08.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_08.jpg", "length": 25445, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_09.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_09.jpg", "length": 25698, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_10.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_10.jpg", "length": 25810, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_11.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_11.jpg", "length": 25967, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_12.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_12.jpg", "length": 25613, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_13.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_13.jpg", "length": 25588, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_14.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_14.jpg", "length": 25822, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_15.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_15.jpg", "length": 25875, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_16.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_16.jpg", "length": 25693, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_17.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_17.jpg", "length": 26106, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_18.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_18.jpg", "length": 25873, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "clusters_04_screenshot_19.jpg", "downloadUrl": "/projects/A002O/files/clusters_04_screenshot_19.jpg", "length": 26153, "contentType": "application/octet-stream", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002O/files/pocket_01.pdb", "length": 35041, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002O/files/pocket_02.pdb", "length": 22981, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A002O/files/pocket_03.pdb", "length": 21909, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A002O/files/pocket_04.pdb", "length": 12261, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A002O/files/pocket_05.pdb", "length": 11390, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A002O/files/pocket_06.pdb", "length": 9246, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A002O/files/pocket_07.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A002O/files/pocket_08.pdb", "length": 7437, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A002O/files/pocket_09.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A002O/files/pocket_10.pdb", "length": 7169, "contentType": "chemical/x-pdb", "metadata": {"project": "68401b5a1557d42c1cfebb0b", "md": 0}}]}
|
data/files/A002P/project.json
ADDED
|
@@ -0,0 +1,329 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002P",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2BP7",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2BP7"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P09060",
|
| 31 |
+
"P09061"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ATTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPISESGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSEMARLRYRSAGEFIAPLTLRMPCGGGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAEESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVMEV",
|
| 38 |
+
"NEYAPLRLHVPEPTGRPGCQTDFSYLRLNDAGQARKPPVDVDAADTADLSYSLVRVLDEQGDAQGPWAEDIDPQILRQGMRAMLKTRIFDSRMVVAQRQKKMSFYMQSLGEEAIGSGQALALNRTDMCFPTYRQQSILMARDVSLVEMICQLLSNERDPLKGRQLPIMYSVREAGFFTISGNLATQFVQAVGWAMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVVNNQWAISTFQAIAGGESTTFAGRGVGCGIASLRVDGNDFVAVYAASRWAAERARRGLGPSLIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIGHWSEEEHQATTAEFEAAVIAAQKEAEQYGTLANGHIPSAASMFEDVYKEMPDHLRRQRQEL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"2-oxoisovalerate dehydrogenase subunit alpha",
|
| 43 |
+
"2-oxoisovalerate dehydrogenase subunit beta"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
"SYSTATS": 22762,
|
| 55 |
+
"SYSTRES": 1490,
|
| 56 |
+
"PROTATS": 22762,
|
| 57 |
+
"PROTRES": 1490,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
+
"SOLVRES": 0,
|
| 66 |
+
"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
},
|
| 78 |
+
{
|
| 79 |
+
"name": "chain A-chain C interaction",
|
| 80 |
+
"agent_1": "chain A",
|
| 81 |
+
"agent_2": "chain C",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain C",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
+
"name": "chain A-chain D interaction",
|
| 88 |
+
"agent_1": "chain A",
|
| 89 |
+
"agent_2": "chain D",
|
| 90 |
+
"selection_1": "chain A",
|
| 91 |
+
"selection_2": "chain D",
|
| 92 |
+
"type": "protein-protein"
|
| 93 |
+
},
|
| 94 |
+
{
|
| 95 |
+
"name": "chain B-chain C interaction",
|
| 96 |
+
"agent_1": "chain B",
|
| 97 |
+
"agent_2": "chain C",
|
| 98 |
+
"selection_1": "chain B",
|
| 99 |
+
"selection_2": "chain C",
|
| 100 |
+
"type": "protein-protein"
|
| 101 |
+
},
|
| 102 |
+
{
|
| 103 |
+
"name": "chain B-chain D interaction",
|
| 104 |
+
"agent_1": "chain B",
|
| 105 |
+
"agent_2": "chain D",
|
| 106 |
+
"selection_1": "chain B",
|
| 107 |
+
"selection_2": "chain D",
|
| 108 |
+
"type": "protein-protein"
|
| 109 |
+
},
|
| 110 |
+
{
|
| 111 |
+
"name": "chain C-chain D interaction",
|
| 112 |
+
"agent_1": "chain C",
|
| 113 |
+
"agent_2": "chain D",
|
| 114 |
+
"selection_1": "chain C",
|
| 115 |
+
"selection_2": "chain D",
|
| 116 |
+
"type": "protein-protein"
|
| 117 |
+
}
|
| 118 |
+
],
|
| 119 |
+
"PBC_SELECTION": null,
|
| 120 |
+
"CHAINNAMES": null,
|
| 121 |
+
"MEMBRANES": null,
|
| 122 |
+
"CUSTOMS": null,
|
| 123 |
+
"ORIENTATION": null,
|
| 124 |
+
"PTM": [],
|
| 125 |
+
"MULTIMERIC": null,
|
| 126 |
+
"COLLECTIONS": "dynarepo",
|
| 127 |
+
"WARNINGS": [],
|
| 128 |
+
"BOXSIZEX": 12.5408,
|
| 129 |
+
"BOXSIZEY": 12.5408,
|
| 130 |
+
"BOXSIZEZ": 8.85557,
|
| 131 |
+
"mdName": "replica 1",
|
| 132 |
+
"mdAtoms": 22762,
|
| 133 |
+
"mdFrames": 5001
|
| 134 |
+
},
|
| 135 |
+
"mds": [
|
| 136 |
+
"replica 1",
|
| 137 |
+
"replica 2",
|
| 138 |
+
"replica 3"
|
| 139 |
+
],
|
| 140 |
+
"mdref": 0,
|
| 141 |
+
"files": [
|
| 142 |
+
"topology.tpr",
|
| 143 |
+
"screenshot.jpg",
|
| 144 |
+
"trajectory.bin",
|
| 145 |
+
"pca_trajectory_01.bin",
|
| 146 |
+
"pca_trajectory_02.bin",
|
| 147 |
+
"pca_trajectory_03.bin",
|
| 148 |
+
"pca_trajectory_04.bin",
|
| 149 |
+
"pca_trajectory_05.bin",
|
| 150 |
+
"pca_trajectory_06.bin",
|
| 151 |
+
"pca_trajectory_07.bin",
|
| 152 |
+
"pca_trajectory_08.bin",
|
| 153 |
+
"pca_trajectory_09.bin",
|
| 154 |
+
"pca_trajectory_10.bin",
|
| 155 |
+
"pca_trajectory_11.bin",
|
| 156 |
+
"structure.pdb",
|
| 157 |
+
"trajectory.xtc",
|
| 158 |
+
"clusters_00_screenshot_00.jpg",
|
| 159 |
+
"clusters_00_screenshot_01.jpg",
|
| 160 |
+
"clusters_00_screenshot_02.jpg",
|
| 161 |
+
"clusters_00_screenshot_03.jpg",
|
| 162 |
+
"clusters_00_screenshot_04.jpg",
|
| 163 |
+
"clusters_00_screenshot_05.jpg",
|
| 164 |
+
"clusters_00_screenshot_06.jpg",
|
| 165 |
+
"clusters_00_screenshot_07.jpg",
|
| 166 |
+
"clusters_00_screenshot_08.jpg",
|
| 167 |
+
"clusters_00_screenshot_09.jpg",
|
| 168 |
+
"clusters_00_screenshot_10.jpg",
|
| 169 |
+
"clusters_00_screenshot_11.jpg",
|
| 170 |
+
"clusters_00_screenshot_12.jpg",
|
| 171 |
+
"clusters_00_screenshot_13.jpg",
|
| 172 |
+
"clusters_00_screenshot_14.jpg",
|
| 173 |
+
"clusters_00_screenshot_15.jpg",
|
| 174 |
+
"clusters_00_screenshot_16.jpg",
|
| 175 |
+
"clusters_00_screenshot_17.jpg",
|
| 176 |
+
"clusters_00_screenshot_18.jpg",
|
| 177 |
+
"clusters_00_screenshot_19.jpg",
|
| 178 |
+
"clusters_01_screenshot_00.jpg",
|
| 179 |
+
"clusters_01_screenshot_01.jpg",
|
| 180 |
+
"clusters_01_screenshot_02.jpg",
|
| 181 |
+
"clusters_01_screenshot_03.jpg",
|
| 182 |
+
"clusters_01_screenshot_04.jpg",
|
| 183 |
+
"clusters_01_screenshot_05.jpg",
|
| 184 |
+
"clusters_01_screenshot_06.jpg",
|
| 185 |
+
"clusters_01_screenshot_07.jpg",
|
| 186 |
+
"clusters_01_screenshot_08.jpg",
|
| 187 |
+
"clusters_01_screenshot_09.jpg",
|
| 188 |
+
"clusters_01_screenshot_10.jpg",
|
| 189 |
+
"clusters_01_screenshot_11.jpg",
|
| 190 |
+
"clusters_01_screenshot_12.jpg",
|
| 191 |
+
"clusters_01_screenshot_13.jpg",
|
| 192 |
+
"clusters_01_screenshot_14.jpg",
|
| 193 |
+
"clusters_01_screenshot_15.jpg",
|
| 194 |
+
"clusters_01_screenshot_16.jpg",
|
| 195 |
+
"clusters_01_screenshot_17.jpg",
|
| 196 |
+
"clusters_01_screenshot_18.jpg",
|
| 197 |
+
"clusters_02_screenshot_00.jpg",
|
| 198 |
+
"clusters_02_screenshot_01.jpg",
|
| 199 |
+
"clusters_02_screenshot_02.jpg",
|
| 200 |
+
"clusters_02_screenshot_03.jpg",
|
| 201 |
+
"clusters_02_screenshot_04.jpg",
|
| 202 |
+
"clusters_02_screenshot_05.jpg",
|
| 203 |
+
"clusters_02_screenshot_06.jpg",
|
| 204 |
+
"clusters_02_screenshot_07.jpg",
|
| 205 |
+
"clusters_02_screenshot_08.jpg",
|
| 206 |
+
"clusters_02_screenshot_09.jpg",
|
| 207 |
+
"clusters_02_screenshot_10.jpg",
|
| 208 |
+
"clusters_02_screenshot_11.jpg",
|
| 209 |
+
"clusters_02_screenshot_12.jpg",
|
| 210 |
+
"clusters_02_screenshot_13.jpg",
|
| 211 |
+
"clusters_02_screenshot_14.jpg",
|
| 212 |
+
"clusters_02_screenshot_15.jpg",
|
| 213 |
+
"clusters_02_screenshot_16.jpg",
|
| 214 |
+
"clusters_02_screenshot_17.jpg",
|
| 215 |
+
"clusters_02_screenshot_18.jpg",
|
| 216 |
+
"clusters_03_screenshot_00.jpg",
|
| 217 |
+
"clusters_03_screenshot_01.jpg",
|
| 218 |
+
"clusters_03_screenshot_02.jpg",
|
| 219 |
+
"clusters_03_screenshot_03.jpg",
|
| 220 |
+
"clusters_03_screenshot_04.jpg",
|
| 221 |
+
"clusters_03_screenshot_05.jpg",
|
| 222 |
+
"clusters_03_screenshot_06.jpg",
|
| 223 |
+
"clusters_03_screenshot_07.jpg",
|
| 224 |
+
"clusters_03_screenshot_08.jpg",
|
| 225 |
+
"clusters_03_screenshot_09.jpg",
|
| 226 |
+
"clusters_03_screenshot_10.jpg",
|
| 227 |
+
"clusters_03_screenshot_11.jpg",
|
| 228 |
+
"clusters_03_screenshot_12.jpg",
|
| 229 |
+
"clusters_03_screenshot_13.jpg",
|
| 230 |
+
"clusters_03_screenshot_14.jpg",
|
| 231 |
+
"clusters_03_screenshot_15.jpg",
|
| 232 |
+
"clusters_03_screenshot_16.jpg",
|
| 233 |
+
"clusters_03_screenshot_17.jpg",
|
| 234 |
+
"clusters_04_screenshot_00.jpg",
|
| 235 |
+
"clusters_04_screenshot_01.jpg",
|
| 236 |
+
"clusters_04_screenshot_02.jpg",
|
| 237 |
+
"clusters_04_screenshot_03.jpg",
|
| 238 |
+
"clusters_04_screenshot_04.jpg",
|
| 239 |
+
"clusters_04_screenshot_05.jpg",
|
| 240 |
+
"clusters_04_screenshot_06.jpg",
|
| 241 |
+
"clusters_04_screenshot_07.jpg",
|
| 242 |
+
"clusters_04_screenshot_08.jpg",
|
| 243 |
+
"clusters_04_screenshot_09.jpg",
|
| 244 |
+
"clusters_04_screenshot_10.jpg",
|
| 245 |
+
"clusters_04_screenshot_11.jpg",
|
| 246 |
+
"clusters_04_screenshot_12.jpg",
|
| 247 |
+
"clusters_04_screenshot_13.jpg",
|
| 248 |
+
"clusters_04_screenshot_14.jpg",
|
| 249 |
+
"clusters_04_screenshot_15.jpg",
|
| 250 |
+
"clusters_04_screenshot_16.jpg",
|
| 251 |
+
"clusters_04_screenshot_17.jpg",
|
| 252 |
+
"clusters_04_screenshot_18.jpg",
|
| 253 |
+
"clusters_05_screenshot_00.jpg",
|
| 254 |
+
"clusters_05_screenshot_01.jpg",
|
| 255 |
+
"clusters_05_screenshot_02.jpg",
|
| 256 |
+
"clusters_05_screenshot_03.jpg",
|
| 257 |
+
"clusters_05_screenshot_04.jpg",
|
| 258 |
+
"clusters_05_screenshot_05.jpg",
|
| 259 |
+
"clusters_05_screenshot_06.jpg",
|
| 260 |
+
"clusters_05_screenshot_07.jpg",
|
| 261 |
+
"clusters_05_screenshot_08.jpg",
|
| 262 |
+
"clusters_05_screenshot_09.jpg",
|
| 263 |
+
"clusters_05_screenshot_10.jpg",
|
| 264 |
+
"clusters_05_screenshot_11.jpg",
|
| 265 |
+
"clusters_05_screenshot_12.jpg",
|
| 266 |
+
"clusters_05_screenshot_13.jpg",
|
| 267 |
+
"clusters_05_screenshot_14.jpg",
|
| 268 |
+
"clusters_05_screenshot_15.jpg",
|
| 269 |
+
"clusters_05_screenshot_16.jpg",
|
| 270 |
+
"clusters_06_screenshot_00.jpg",
|
| 271 |
+
"clusters_06_screenshot_01.jpg",
|
| 272 |
+
"clusters_06_screenshot_02.jpg",
|
| 273 |
+
"clusters_06_screenshot_03.jpg",
|
| 274 |
+
"clusters_06_screenshot_04.jpg",
|
| 275 |
+
"clusters_06_screenshot_05.jpg",
|
| 276 |
+
"clusters_06_screenshot_06.jpg",
|
| 277 |
+
"clusters_06_screenshot_07.jpg",
|
| 278 |
+
"clusters_06_screenshot_08.jpg",
|
| 279 |
+
"clusters_06_screenshot_09.jpg",
|
| 280 |
+
"clusters_06_screenshot_10.jpg",
|
| 281 |
+
"clusters_06_screenshot_11.jpg",
|
| 282 |
+
"clusters_06_screenshot_12.jpg",
|
| 283 |
+
"clusters_06_screenshot_13.jpg",
|
| 284 |
+
"clusters_06_screenshot_14.jpg",
|
| 285 |
+
"clusters_06_screenshot_15.jpg",
|
| 286 |
+
"clusters_06_screenshot_16.jpg",
|
| 287 |
+
"clusters_06_screenshot_17.jpg",
|
| 288 |
+
"clusters_06_screenshot_18.jpg",
|
| 289 |
+
"pocket_01.pdb",
|
| 290 |
+
"pocket_02.pdb",
|
| 291 |
+
"pocket_03.pdb",
|
| 292 |
+
"pocket_04.pdb",
|
| 293 |
+
"pocket_05.pdb",
|
| 294 |
+
"pocket_06.pdb",
|
| 295 |
+
"pocket_07.pdb",
|
| 296 |
+
"pocket_08.pdb",
|
| 297 |
+
"pocket_09.pdb",
|
| 298 |
+
"pocket_10.pdb"
|
| 299 |
+
],
|
| 300 |
+
"analyses": [
|
| 301 |
+
"clusters",
|
| 302 |
+
"clusters-00",
|
| 303 |
+
"clusters-01",
|
| 304 |
+
"clusters-02",
|
| 305 |
+
"clusters-03",
|
| 306 |
+
"clusters-04",
|
| 307 |
+
"clusters-05",
|
| 308 |
+
"clusters-06",
|
| 309 |
+
"dist-perres",
|
| 310 |
+
"energies",
|
| 311 |
+
"fluctuation",
|
| 312 |
+
"hbonds",
|
| 313 |
+
"interactions",
|
| 314 |
+
"pca",
|
| 315 |
+
"pockets",
|
| 316 |
+
"rgyr",
|
| 317 |
+
"rmsd-pairwise",
|
| 318 |
+
"rmsd-perres",
|
| 319 |
+
"rmsds",
|
| 320 |
+
"sasa",
|
| 321 |
+
"tmscores"
|
| 322 |
+
],
|
| 323 |
+
"mdIndex": 0,
|
| 324 |
+
"mdNumber": 1,
|
| 325 |
+
"refframe": 2,
|
| 326 |
+
"internalId": "68402169f9c5c39321bf8a6f",
|
| 327 |
+
"creationDate": "2025-06-04T10:35:21.000Z",
|
| 328 |
+
"identifier": "A002P"
|
| 329 |
+
}
|
data/files/A002P/records.jsonl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
data/files/A002Q/project.json
ADDED
|
@@ -0,0 +1,190 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A002Q",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2BYK",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"2BYK"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9V452",
|
| 31 |
+
"Q9V444"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKI",
|
| 38 |
+
"PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Chromatin accessibility complex 16kD protein",
|
| 43 |
+
"DNA polymerase epsilon subunit 3",
|
| 44 |
+
"Disordered"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 2568,
|
| 56 |
+
"SYSTRES": 161,
|
| 57 |
+
"PROTATS": 2568,
|
| 58 |
+
"PROTRES": 161,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 8.95696,
|
| 90 |
+
"BOXSIZEY": 8.95696,
|
| 91 |
+
"BOXSIZEZ": 6.37334,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 2568,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"structure.pdb",
|
| 119 |
+
"trajectory.xtc",
|
| 120 |
+
"clusters_00_screenshot_00.jpg",
|
| 121 |
+
"clusters_00_screenshot_01.jpg",
|
| 122 |
+
"clusters_00_screenshot_02.jpg",
|
| 123 |
+
"clusters_00_screenshot_03.jpg",
|
| 124 |
+
"clusters_00_screenshot_04.jpg",
|
| 125 |
+
"clusters_00_screenshot_05.jpg",
|
| 126 |
+
"clusters_00_screenshot_06.jpg",
|
| 127 |
+
"clusters_00_screenshot_07.jpg",
|
| 128 |
+
"clusters_00_screenshot_08.jpg",
|
| 129 |
+
"clusters_00_screenshot_09.jpg",
|
| 130 |
+
"clusters_00_screenshot_10.jpg",
|
| 131 |
+
"clusters_00_screenshot_11.jpg",
|
| 132 |
+
"clusters_00_screenshot_12.jpg",
|
| 133 |
+
"clusters_00_screenshot_13.jpg",
|
| 134 |
+
"clusters_00_screenshot_14.jpg",
|
| 135 |
+
"clusters_00_screenshot_15.jpg",
|
| 136 |
+
"clusters_00_screenshot_16.jpg",
|
| 137 |
+
"clusters_00_screenshot_17.jpg",
|
| 138 |
+
"clusters_00_screenshot_18.jpg",
|
| 139 |
+
"clusters_00_screenshot_19.jpg",
|
| 140 |
+
"clusters_00_screenshot_20.jpg",
|
| 141 |
+
"clusters_00_screenshot_21.jpg",
|
| 142 |
+
"clusters_00_screenshot_22.jpg",
|
| 143 |
+
"clusters_00_screenshot_23.jpg",
|
| 144 |
+
"clusters_01_screenshot_00.jpg",
|
| 145 |
+
"clusters_01_screenshot_01.jpg",
|
| 146 |
+
"clusters_01_screenshot_02.jpg",
|
| 147 |
+
"clusters_01_screenshot_03.jpg",
|
| 148 |
+
"clusters_01_screenshot_04.jpg",
|
| 149 |
+
"clusters_01_screenshot_05.jpg",
|
| 150 |
+
"clusters_01_screenshot_06.jpg",
|
| 151 |
+
"clusters_01_screenshot_07.jpg",
|
| 152 |
+
"clusters_01_screenshot_08.jpg",
|
| 153 |
+
"clusters_01_screenshot_09.jpg",
|
| 154 |
+
"clusters_01_screenshot_10.jpg",
|
| 155 |
+
"clusters_01_screenshot_11.jpg",
|
| 156 |
+
"clusters_01_screenshot_12.jpg",
|
| 157 |
+
"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
+
"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"clusters_01_screenshot_17.jpg",
|
| 162 |
+
"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"clusters_01_screenshot_19.jpg",
|
| 164 |
+
"pocket_01.pdb"
|
| 165 |
+
],
|
| 166 |
+
"analyses": [
|
| 167 |
+
"clusters",
|
| 168 |
+
"clusters-00",
|
| 169 |
+
"clusters-01",
|
| 170 |
+
"dist-perres",
|
| 171 |
+
"energies",
|
| 172 |
+
"fluctuation",
|
| 173 |
+
"hbonds",
|
| 174 |
+
"interactions",
|
| 175 |
+
"pca",
|
| 176 |
+
"pockets",
|
| 177 |
+
"rgyr",
|
| 178 |
+
"rmsd-pairwise",
|
| 179 |
+
"rmsd-perres",
|
| 180 |
+
"rmsds",
|
| 181 |
+
"sasa",
|
| 182 |
+
"tmscores"
|
| 183 |
+
],
|
| 184 |
+
"mdIndex": 0,
|
| 185 |
+
"mdNumber": 1,
|
| 186 |
+
"refframe": 0,
|
| 187 |
+
"internalId": "684025f0317ca4e20d47d73f",
|
| 188 |
+
"creationDate": "2025-06-04T10:54:40.000Z",
|
| 189 |
+
"identifier": "A002Q"
|
| 190 |
+
}
|