| { | |
| "accession": "A000A", | |
| "published": true, | |
| "metadata": { | |
| "NAME": "Dynarepo 1AK4", | |
| "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": [ | |
| "1AK4" | |
| ], | |
| "FORCED_REFERENCES": null, | |
| "REFERENCES": [ | |
| "P62937", | |
| "P12497" | |
| ], | |
| "INPUT_LIGANDS": null, | |
| "LIGANDS": [], | |
| "LIGANDNAMES": null, | |
| "PROTSEQ": [ | |
| "PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMY", | |
| "MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE" | |
| ], | |
| "NUCLSEQ": [], | |
| "DOMAINS": [ | |
| "Peptidyl-prolyl cis-trans isomerase A", | |
| "Peptidyl-prolyl cis-trans isomerase A, N-terminally processed", | |
| "PPIase cyclophilin-type", | |
| "Gag-Pol polyprotein", | |
| "Capsid protein p24", | |
| "Interaction with human PPIA/CYPA and NUP153", | |
| "Dimerization/Multimerization of capsid protein p24", | |
| "Cleavage; by viral protease", | |
| "Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA" | |
| ], | |
| "FRAMESTEP": 0.1, | |
| "TIMESTEP": 2, | |
| "TEMP": 310, | |
| "ENSEMBLE": "NPT", | |
| "FF": [ | |
| "CHARMM36m" | |
| ], | |
| "WAT": "TIP3P", | |
| "BOXTYPE": "Dodecahedron", | |
| "SYSTATS": 4763, | |
| "SYSTRES": 310, | |
| "PROTATS": 4763, | |
| "PROTRES": 310, | |
| "NUCLATS": 0, | |
| "NUCLRES": 0, | |
| "LIPIATS": 0, | |
| "LIPIRES": 0, | |
| "CARBATS": 0, | |
| "CARBRES": 0, | |
| "SOLVATS": 0, | |
| "SOLVRES": 0, | |
| "COUNCAT": 0, | |
| "COUNANI": 0, | |
| "COUNION": 0, | |
| "INTERACTIONS": [ | |
| { | |
| "name": "protein-protein interaction B-A", | |
| "agent_1": "protein B", | |
| "agent_2": "protein A", | |
| "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": 10.6979, | |
| "BOXSIZEY": 10.6979, | |
| "BOXSIZEZ": 7.58653, | |
| "mdName": "replica 1", | |
| "mdAtoms": 4763, | |
| "mdFrames": 5001 | |
| }, | |
| "mds": [ | |
| "replica 1", | |
| "replica 2", | |
| "replica 3" | |
| ], | |
| "mdref": 0, | |
| "files": [ | |
| "topology.tpr", | |
| "screenshot.jpg", | |
| "trajectory.bin", | |
| "pca_trajectory_01.bin", | |
| "pca_trajectory_02.bin", | |
| "pca_trajectory_03.bin", | |
| "pca_trajectory_04.bin", | |
| "pca_trajectory_05.bin", | |
| "pca_trajectory_06.bin", | |
| "pca_trajectory_07.bin", | |
| "structure.pdb", | |
| "trajectory.xtc", | |
| "clusters_00_screenshot_00.jpg", | |
| "clusters_00_screenshot_01.jpg", | |
| "clusters_00_screenshot_02.jpg", | |
| "clusters_00_screenshot_03.jpg", | |
| "clusters_00_screenshot_04.jpg", | |
| "clusters_00_screenshot_05.jpg", | |
| "clusters_00_screenshot_06.jpg", | |
| "clusters_00_screenshot_07.jpg", | |
| "clusters_00_screenshot_08.jpg", | |
| "clusters_00_screenshot_09.jpg", | |
| "clusters_00_screenshot_10.jpg", | |
| "clusters_00_screenshot_11.jpg", | |
| "clusters_00_screenshot_12.jpg", | |
| "clusters_00_screenshot_13.jpg", | |
| "clusters_00_screenshot_14.jpg", | |
| "clusters_00_screenshot_15.jpg", | |
| "clusters_00_screenshot_16.jpg", | |
| "clusters_00_screenshot_17.jpg", | |
| "clusters_00_screenshot_18.jpg", | |
| "clusters_00_screenshot_19.jpg", | |
| "clusters_00_screenshot_20.jpg", | |
| "clusters_00_screenshot_21.jpg", | |
| "clusters_01_screenshot_00.jpg", | |
| "clusters_01_screenshot_01.jpg", | |
| "clusters_01_screenshot_02.jpg", | |
| "clusters_01_screenshot_03.jpg", | |
| "clusters_01_screenshot_04.jpg", | |
| "clusters_01_screenshot_05.jpg", | |
| "clusters_01_screenshot_06.jpg", | |
| "clusters_01_screenshot_07.jpg", | |
| "clusters_01_screenshot_08.jpg", | |
| "clusters_01_screenshot_09.jpg", | |
| "clusters_01_screenshot_10.jpg", | |
| "clusters_01_screenshot_11.jpg", | |
| "clusters_01_screenshot_12.jpg", | |
| "clusters_01_screenshot_13.jpg", | |
| "clusters_01_screenshot_14.jpg", | |
| "clusters_01_screenshot_15.jpg", | |
| "clusters_01_screenshot_16.jpg", | |
| "clusters_01_screenshot_17.jpg", | |
| "clusters_01_screenshot_18.jpg", | |
| "clusters_01_screenshot_19.jpg", | |
| "pocket_01.pdb" | |
| ], | |
| "analyses": [ | |
| "clusters", | |
| "clusters-00", | |
| "clusters-01", | |
| "dist-perres", | |
| "energies", | |
| "fluctuation", | |
| "hbonds", | |
| "interactions", | |
| "pca", | |
| "pockets", | |
| "rgyr", | |
| "rmsd-pairwise", | |
| "rmsd-perres", | |
| "rmsds", | |
| "sasa", | |
| "tmscores" | |
| ], | |
| "mdIndex": 0, | |
| "mdNumber": 1, | |
| "refframe": 0, | |
| "internalId": "683efc9b8959c0a482394c98", | |
| "creationDate": "2025-06-03T13:46:03.000Z", | |
| "identifier": "A000A" | |
| } |