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- .gitattributes +1 -0
- A000D/project.json +191 -0
- A000D/records.jsonl +3 -0
- A000J/project.json +196 -0
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.gitattributes
CHANGED
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@@ -57,3 +57,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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all_records.jsonl filter=lfs diff=lfs merge=lfs -text
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A000D/project.json
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| 1 |
+
{
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"accession": "A000D",
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| 3 |
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"published": true,
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| 4 |
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"metadata": {
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"NAME": "Dynarepo 1AY7",
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| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
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| 7 |
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"AUTHORS": [
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"Omid Mokhtari",
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"Hamed Khakzad",
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"Yasaman Karami"
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],
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"GROUPS": [
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"Delta team, Inria center at the University of Lorraine"
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],
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"CONTACT": "yasaman.karami@inria.fr",
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"PROGRAM": "GROMACS",
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"VERSION": "2024.2",
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"TYPE": "trajectory",
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| 19 |
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"METHOD": "Classical MD",
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"LICENSE": "Apache License 2.0",
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| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
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| 24 |
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"LINKS": null,
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| 25 |
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"PDBIDS": [
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| 26 |
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"1AY7"
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| 27 |
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],
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"FORCED_REFERENCES": null,
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| 29 |
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"REFERENCES": [
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| 30 |
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"P05798",
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| 31 |
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"P11540"
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| 32 |
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],
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"INPUT_LIGANDS": null,
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"LIGANDS": [],
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| 35 |
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"LIGANDNAMES": null,
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| 36 |
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"PROTSEQ": [
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"DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC",
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| 38 |
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"KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS"
|
| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Guanyl-specific ribonuclease Sa",
|
| 43 |
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"Barstar"
|
| 44 |
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],
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| 45 |
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"FRAMESTEP": 0.1,
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| 46 |
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"TIMESTEP": 2,
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| 47 |
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"TEMP": 310,
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| 48 |
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"ENSEMBLE": "NPT",
|
| 49 |
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"FF": [
|
| 50 |
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"CHARMM36m"
|
| 51 |
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],
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| 52 |
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"WAT": "TIP3P",
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| 53 |
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"BOXTYPE": "Dodecahedron",
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| 54 |
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"SYSTATS": 2875,
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"SYSTRES": 185,
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"PROTATS": 2875,
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"PROTRES": 185,
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"NUCLATS": 0,
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"NUCLRES": 0,
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"LIPIATS": 0,
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"LIPIRES": 0,
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"CARBATS": 0,
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"CARBRES": 0,
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"SOLVATS": 0,
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"SOLVRES": 0,
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"COUNCAT": 0,
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"COUNANI": 0,
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"COUNION": 0,
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| 69 |
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"INTERACTIONS": [
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| 70 |
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{
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| 71 |
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"name": "protein-protein interaction B-A",
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| 72 |
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"agent_1": "protein B",
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| 73 |
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"agent_2": "protein A",
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| 74 |
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"selection_1": "chain A",
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| 75 |
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"selection_2": "chain B",
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| 76 |
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"type": "protein-protein"
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| 77 |
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}
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| 78 |
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],
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"PBC_SELECTION": null,
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| 80 |
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"CHAINNAMES": null,
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"MEMBRANES": null,
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"CUSTOMS": null,
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"ORIENTATION": null,
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"PTM": [],
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"MULTIMERIC": null,
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"COLLECTIONS": "dynarepo",
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| 87 |
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"WARNINGS": [],
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"BOXSIZEX": 8.14692,
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"BOXSIZEY": 8.14692,
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"BOXSIZEZ": 5.75583,
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"mdName": "replica 1",
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"mdAtoms": 2875,
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"mdFrames": 5001
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},
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"mds": [
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"replica 1",
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| 97 |
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"replica 2",
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| 98 |
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"replica 3"
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| 99 |
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],
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| 100 |
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"mdref": 0,
|
| 101 |
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"files": [
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| 102 |
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"topology.tpr",
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"screenshot.jpg",
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| 104 |
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"trajectory.bin",
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| 105 |
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"pca_trajectory_01.bin",
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| 106 |
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"pca_trajectory_02.bin",
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| 107 |
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"pca_trajectory_03.bin",
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| 108 |
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"pca_trajectory_04.bin",
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| 109 |
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"pca_trajectory_05.bin",
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| 110 |
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"pca_trajectory_06.bin",
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| 111 |
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"pca_trajectory_07.bin",
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| 112 |
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"pca_trajectory_08.bin",
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| 113 |
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"pca_trajectory_09.bin",
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"pca_trajectory_10.bin",
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| 115 |
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"pca_trajectory_11.bin",
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| 116 |
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"pca_trajectory_12.bin",
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"pca_trajectory_13.bin",
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"pca_trajectory_14.bin",
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| 119 |
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"pca_trajectory_15.bin",
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"pca_trajectory_16.bin",
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"pca_trajectory_17.bin",
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| 122 |
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"structure.pdb",
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| 123 |
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"trajectory.xtc",
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| 124 |
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"clusters_00_screenshot_00.jpg",
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| 125 |
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"clusters_00_screenshot_01.jpg",
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"clusters_00_screenshot_02.jpg",
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"clusters_00_screenshot_04.jpg",
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"clusters_00_screenshot_07.jpg",
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| 132 |
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"clusters_00_screenshot_09.jpg",
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| 134 |
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"clusters_00_screenshot_10.jpg",
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| 135 |
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"clusters_00_screenshot_11.jpg",
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| 136 |
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"clusters_00_screenshot_12.jpg",
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| 137 |
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"clusters_00_screenshot_13.jpg",
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| 138 |
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"clusters_00_screenshot_14.jpg",
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| 139 |
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"clusters_00_screenshot_15.jpg",
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| 140 |
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"clusters_00_screenshot_16.jpg",
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| 141 |
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"clusters_00_screenshot_17.jpg",
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| 142 |
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"clusters_00_screenshot_18.jpg",
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| 143 |
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"clusters_00_screenshot_19.jpg",
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| 144 |
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"clusters_01_screenshot_00.jpg",
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| 145 |
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"clusters_01_screenshot_01.jpg",
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| 146 |
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"clusters_01_screenshot_02.jpg",
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| 147 |
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"clusters_01_screenshot_03.jpg",
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| 148 |
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"clusters_01_screenshot_04.jpg",
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| 149 |
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"clusters_01_screenshot_05.jpg",
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| 150 |
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"clusters_01_screenshot_06.jpg",
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| 151 |
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"clusters_01_screenshot_07.jpg",
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| 152 |
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"clusters_01_screenshot_08.jpg",
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"clusters_01_screenshot_09.jpg",
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| 154 |
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"clusters_01_screenshot_10.jpg",
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| 155 |
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"clusters_01_screenshot_11.jpg",
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"clusters_01_screenshot_12.jpg",
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| 157 |
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"clusters_01_screenshot_13.jpg",
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| 158 |
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"clusters_01_screenshot_14.jpg",
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| 159 |
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"clusters_01_screenshot_15.jpg",
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| 160 |
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"clusters_01_screenshot_16.jpg",
|
| 161 |
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"pocket_01.pdb",
|
| 162 |
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"pocket_02.pdb",
|
| 163 |
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"pocket_03.pdb",
|
| 164 |
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"pocket_04.pdb",
|
| 165 |
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"pocket_05.pdb"
|
| 166 |
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],
|
| 167 |
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"analyses": [
|
| 168 |
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"clusters",
|
| 169 |
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"clusters-00",
|
| 170 |
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"clusters-01",
|
| 171 |
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"dist-perres",
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| 172 |
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"energies",
|
| 173 |
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"fluctuation",
|
| 174 |
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"hbonds",
|
| 175 |
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"interactions",
|
| 176 |
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"pca",
|
| 177 |
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"pockets",
|
| 178 |
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"rgyr",
|
| 179 |
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"rmsd-pairwise",
|
| 180 |
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"rmsd-perres",
|
| 181 |
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"rmsds",
|
| 182 |
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"sasa",
|
| 183 |
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"tmscores"
|
| 184 |
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],
|
| 185 |
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"mdIndex": 0,
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| 186 |
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"mdNumber": 1,
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| 187 |
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"refframe": 0,
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"internalId": "683f0058acc0a79ac6ea66e7",
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| 189 |
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"creationDate": "2025-06-03T14:02:00.000Z",
|
| 190 |
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"identifier": "A000D"
|
| 191 |
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}
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A000D/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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|
A000J/project.json
ADDED
|
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| 1 |
+
{
|
| 2 |
+
"accession": "A000J",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1E3U",
|
| 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 |
+
"1E3U"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P14489"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII",
|
| 37 |
+
"ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"
|
| 38 |
+
],
|
| 39 |
+
"NUCLSEQ": [],
|
| 40 |
+
"DOMAINS": [
|
| 41 |
+
"Beta-lactamase OXA-10"
|
| 42 |
+
],
|
| 43 |
+
"FRAMESTEP": 0.1,
|
| 44 |
+
"TIMESTEP": 2,
|
| 45 |
+
"TEMP": 310,
|
| 46 |
+
"ENSEMBLE": "NPT",
|
| 47 |
+
"FF": [
|
| 48 |
+
"CHARMM36m"
|
| 49 |
+
],
|
| 50 |
+
"WAT": "TIP3P",
|
| 51 |
+
"BOXTYPE": "Dodecahedron",
|
| 52 |
+
"SYSTATS": 7716,
|
| 53 |
+
"SYSTRES": 488,
|
| 54 |
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| 55 |
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| 56 |
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|
| 66 |
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| 67 |
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|
| 68 |
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{
|
| 69 |
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|
| 70 |
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|
| 71 |
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|
| 72 |
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"selection_1": "chain A",
|
| 73 |
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"selection_2": "chain B",
|
| 74 |
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"type": "protein-protein"
|
| 75 |
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|
| 76 |
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|
| 77 |
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|
| 78 |
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|
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| 80 |
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|
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|
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|
| 83 |
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|
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| 90 |
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|
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|
| 92 |
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|
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|
| 94 |
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|
| 95 |
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|
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|
| 97 |
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|
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|
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|
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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| 108 |
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| 109 |
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|
| 110 |
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| 111 |
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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| 119 |
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| 131 |
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| 132 |
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| 135 |
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| 136 |
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| 137 |
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| 138 |
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| 139 |
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| 140 |
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| 141 |
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| 142 |
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|
| 143 |
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| 144 |
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|
| 145 |
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|
| 146 |
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| 147 |
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| 148 |
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| 149 |
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|
| 150 |
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"clusters_01_screenshot_09.jpg",
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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"clusters_01_screenshot_13.jpg",
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| 155 |
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"clusters_01_screenshot_14.jpg",
|
| 156 |
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"clusters_01_screenshot_15.jpg",
|
| 157 |
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"clusters_01_screenshot_16.jpg",
|
| 158 |
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"clusters_01_screenshot_17.jpg",
|
| 159 |
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"clusters_01_screenshot_18.jpg",
|
| 160 |
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"clusters_01_screenshot_19.jpg",
|
| 161 |
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"pocket_01.pdb",
|
| 162 |
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"pocket_02.pdb",
|
| 163 |
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"pocket_03.pdb",
|
| 164 |
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"pocket_04.pdb",
|
| 165 |
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"pocket_05.pdb",
|
| 166 |
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"pocket_06.pdb",
|
| 167 |
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"pocket_07.pdb",
|
| 168 |
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"pocket_08.pdb",
|
| 169 |
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"pocket_09.pdb",
|
| 170 |
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"pocket_10.pdb"
|
| 171 |
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],
|
| 172 |
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"analyses": [
|
| 173 |
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"clusters",
|
| 174 |
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"clusters-00",
|
| 175 |
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"clusters-01",
|
| 176 |
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"dist-perres",
|
| 177 |
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"energies",
|
| 178 |
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"fluctuation",
|
| 179 |
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"hbonds",
|
| 180 |
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"interactions",
|
| 181 |
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"pca",
|
| 182 |
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"pockets",
|
| 183 |
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"rgyr",
|
| 184 |
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"rmsd-pairwise",
|
| 185 |
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"rmsd-perres",
|
| 186 |
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"rmsds",
|
| 187 |
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"sasa",
|
| 188 |
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"tmscores"
|
| 189 |
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],
|
| 190 |
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"mdIndex": 0,
|
| 191 |
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|
| 192 |
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|
| 193 |
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|
| 194 |
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"creationDate": "2025-06-03T16:15:54.000Z",
|
| 195 |
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"identifier": "A000J"
|
| 196 |
+
}
|
A000Z/project.json
ADDED
|
@@ -0,0 +1,344 @@
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|
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|
|
|
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|
|
|
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|
|
|
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|
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|
|
|
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|
|
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|
|
|
|
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|
|
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|
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|
|
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|
|
|
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|
|
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|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000Z",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1I5K",
|
| 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 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
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"1I5K"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00747",
|
| 31 |
+
"P49054"
|
| 32 |
+
],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
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"EKLTADAELQRLKNERHEEAELERLK",
|
| 38 |
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"EECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRC",
|
| 39 |
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"ECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRC"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Plasminogen",
|
| 44 |
+
"Plasmin heavy chain A",
|
| 45 |
+
"Angiostatin",
|
| 46 |
+
"Plasmin heavy chain A, short form",
|
| 47 |
+
"Kringle 2",
|
| 48 |
+
"Plasminogen-binding group A streptococcal M-like protein PAM",
|
| 49 |
+
"Able to bind plasminogen",
|
| 50 |
+
"2 X approximate tandem repeats, type a",
|
| 51 |
+
"Disordered"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
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"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 3391,
|
| 63 |
+
"SYSTRES": 211,
|
| 64 |
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"PROTATS": 3391,
|
| 65 |
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"PROTRES": 211,
|
| 66 |
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"NUCLATS": 0,
|
| 67 |
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"NUCLRES": 0,
|
| 68 |
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"LIPIATS": 0,
|
| 69 |
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"LIPIRES": 0,
|
| 70 |
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"CARBATS": 0,
|
| 71 |
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"CARBRES": 0,
|
| 72 |
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"SOLVATS": 0,
|
| 73 |
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"SOLVRES": 0,
|
| 74 |
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"COUNCAT": 0,
|
| 75 |
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"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
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{
|
| 79 |
+
"name": "protein-protein interaction C-B",
|
| 80 |
+
"agent_1": "protein C",
|
| 81 |
+
"agent_2": "protein B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
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|
| 93 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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"analyses": [
|
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|
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|
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|
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|
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|
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|
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|
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}
|
A000Z/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A0016/project.json
ADDED
|
@@ -0,0 +1,318 @@
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| 1 |
+
{
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| 2 |
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| 3 |
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| 4 |
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"metadata": {
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 9 |
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"Hamed Khakzad",
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| 10 |
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| 11 |
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],
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| 12 |
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| 13 |
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 24 |
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| 27 |
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| 109 |
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| 281 |
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"pocket_03.pdb",
|
| 282 |
+
"pocket_04.pdb",
|
| 283 |
+
"pocket_05.pdb",
|
| 284 |
+
"pocket_06.pdb",
|
| 285 |
+
"pocket_07.pdb",
|
| 286 |
+
"pocket_08.pdb",
|
| 287 |
+
"pocket_09.pdb",
|
| 288 |
+
"pocket_10.pdb"
|
| 289 |
+
],
|
| 290 |
+
"analyses": [
|
| 291 |
+
"clusters",
|
| 292 |
+
"clusters-00",
|
| 293 |
+
"clusters-01",
|
| 294 |
+
"clusters-02",
|
| 295 |
+
"clusters-03",
|
| 296 |
+
"clusters-04",
|
| 297 |
+
"clusters-05",
|
| 298 |
+
"dist-perres",
|
| 299 |
+
"energies",
|
| 300 |
+
"fluctuation",
|
| 301 |
+
"hbonds",
|
| 302 |
+
"interactions",
|
| 303 |
+
"pca",
|
| 304 |
+
"pockets",
|
| 305 |
+
"rgyr",
|
| 306 |
+
"rmsd-pairwise",
|
| 307 |
+
"rmsd-perres",
|
| 308 |
+
"rmsds",
|
| 309 |
+
"sasa",
|
| 310 |
+
"tmscores"
|
| 311 |
+
],
|
| 312 |
+
"mdIndex": 0,
|
| 313 |
+
"mdNumber": 1,
|
| 314 |
+
"refframe": 2,
|
| 315 |
+
"internalId": "683f3fd4e82f4ec7d5ececad",
|
| 316 |
+
"creationDate": "2025-06-03T18:32:52.000Z",
|
| 317 |
+
"identifier": "A0016"
|
| 318 |
+
}
|
A0016/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A001D/project.json
ADDED
|
@@ -0,0 +1,306 @@
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|
|
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|
|
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|
|
|
|
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|
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|
|
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|
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|
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|
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|
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|
|
|
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|
|
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|
|
|
|
|
|
|
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|
|
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|
|
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|
|
|
|
|
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|
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|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A001D",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1LJ2",
|
| 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 |
+
"1LJ2"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P03536",
|
| 31 |
+
"Q04637"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"KTIRIRDPNQGGKDITEEIMSG",
|
| 38 |
+
"PKRERKTIRIRDPNQGGKDITEEIMSG",
|
| 39 |
+
"HSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSF",
|
| 40 |
+
"MHSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSFGSE"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Non-structural protein 3",
|
| 45 |
+
"Dimerization",
|
| 46 |
+
"Interaction with host ZC3H7B",
|
| 47 |
+
"Interaction with host EIF4G1",
|
| 48 |
+
"Eukaryotic translation initiation factor 4 gamma 1",
|
| 49 |
+
"Disordered",
|
| 50 |
+
"PABPC1-binding"
|
| 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": 4321,
|
| 62 |
+
"SYSTRES": 265,
|
| 63 |
+
"PROTATS": 4321,
|
| 64 |
+
"PROTRES": 265,
|
| 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 |
+
"name": "chain A-chain C interaction",
|
| 87 |
+
"agent_1": "chain A",
|
| 88 |
+
"agent_2": "chain C",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain C",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "chain A-chain D interaction",
|
| 95 |
+
"agent_1": "chain A",
|
| 96 |
+
"agent_2": "chain D",
|
| 97 |
+
"selection_1": "chain A",
|
| 98 |
+
"selection_2": "chain D",
|
| 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 |
+
"name": "chain B-chain D interaction",
|
| 111 |
+
"agent_1": "chain B",
|
| 112 |
+
"agent_2": "chain D",
|
| 113 |
+
"selection_1": "chain B",
|
| 114 |
+
"selection_2": "chain D",
|
| 115 |
+
"type": "protein-protein"
|
| 116 |
+
}
|
| 117 |
+
],
|
| 118 |
+
"PBC_SELECTION": null,
|
| 119 |
+
"CHAINNAMES": null,
|
| 120 |
+
"MEMBRANES": null,
|
| 121 |
+
"CUSTOMS": null,
|
| 122 |
+
"ORIENTATION": null,
|
| 123 |
+
"PTM": [],
|
| 124 |
+
"MULTIMERIC": null,
|
| 125 |
+
"COLLECTIONS": "dynarepo",
|
| 126 |
+
"WARNINGS": [],
|
| 127 |
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"BOXSIZEX": 12.1659,
|
| 128 |
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"BOXSIZEY": 12.1659,
|
| 129 |
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"BOXSIZEZ": 8.6127,
|
| 130 |
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"mdName": "replica 1",
|
| 131 |
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"mdAtoms": 4321,
|
| 132 |
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"mdFrames": 5001
|
| 133 |
+
},
|
| 134 |
+
"mds": [
|
| 135 |
+
"replica 1",
|
| 136 |
+
"replica 2",
|
| 137 |
+
"replica 3"
|
| 138 |
+
],
|
| 139 |
+
"mdref": 0,
|
| 140 |
+
"files": [
|
| 141 |
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"topology.tpr",
|
| 142 |
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"screenshot.jpg",
|
| 143 |
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"trajectory.bin",
|
| 144 |
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"pca_trajectory_01.bin",
|
| 145 |
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"pca_trajectory_02.bin",
|
| 146 |
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"pca_trajectory_03.bin",
|
| 147 |
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"pca_trajectory_04.bin",
|
| 148 |
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"pca_trajectory_05.bin",
|
| 149 |
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"pca_trajectory_06.bin",
|
| 150 |
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"pca_trajectory_07.bin",
|
| 151 |
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"pca_trajectory_08.bin",
|
| 152 |
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"pca_trajectory_09.bin",
|
| 153 |
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"pca_trajectory_10.bin",
|
| 154 |
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"pca_trajectory_11.bin",
|
| 155 |
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"pca_trajectory_12.bin",
|
| 156 |
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"pca_trajectory_13.bin",
|
| 157 |
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"structure.pdb",
|
| 158 |
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"trajectory.xtc",
|
| 159 |
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"clusters_00_screenshot_00.jpg",
|
| 160 |
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"clusters_00_screenshot_01.jpg",
|
| 161 |
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|
| 162 |
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|
| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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|
| 167 |
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|
| 168 |
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|
| 169 |
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"clusters_00_screenshot_10.jpg",
|
| 170 |
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"clusters_00_screenshot_11.jpg",
|
| 171 |
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|
| 172 |
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|
| 173 |
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|
| 174 |
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|
| 175 |
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|
| 176 |
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"clusters_00_screenshot_17.jpg",
|
| 177 |
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"clusters_00_screenshot_18.jpg",
|
| 178 |
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|
| 179 |
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"clusters_00_screenshot_20.jpg",
|
| 180 |
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"clusters_01_screenshot_00.jpg",
|
| 181 |
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"clusters_01_screenshot_01.jpg",
|
| 182 |
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|
| 183 |
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|
| 184 |
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|
| 185 |
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|
| 186 |
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|
| 187 |
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|
| 188 |
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|
| 189 |
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|
| 190 |
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|
| 191 |
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|
| 192 |
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|
| 193 |
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"clusters_01_screenshot_13.jpg",
|
| 194 |
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"clusters_01_screenshot_14.jpg",
|
| 195 |
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"clusters_01_screenshot_15.jpg",
|
| 196 |
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"clusters_01_screenshot_16.jpg",
|
| 197 |
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"clusters_01_screenshot_17.jpg",
|
| 198 |
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"clusters_01_screenshot_18.jpg",
|
| 199 |
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"clusters_01_screenshot_19.jpg",
|
| 200 |
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"clusters_02_screenshot_00.jpg",
|
| 201 |
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|
| 202 |
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|
| 203 |
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|
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|
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|
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| 220 |
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|
| 221 |
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|
| 222 |
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| 223 |
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| 234 |
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| 248 |
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| 249 |
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| 250 |
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| 251 |
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| 253 |
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| 254 |
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| 255 |
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| 256 |
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| 257 |
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| 258 |
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|
| 259 |
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| 260 |
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| 261 |
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| 262 |
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|
| 263 |
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|
| 264 |
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|
| 265 |
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|
| 266 |
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| 267 |
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| 268 |
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| 269 |
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|
| 270 |
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| 271 |
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| 272 |
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|
| 273 |
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|
| 274 |
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"clusters_05_screenshot_15.jpg",
|
| 275 |
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"clusters_05_screenshot_16.jpg",
|
| 276 |
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"clusters_05_screenshot_17.jpg",
|
| 277 |
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"clusters_05_screenshot_18.jpg"
|
| 278 |
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],
|
| 279 |
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"analyses": [
|
| 280 |
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"clusters",
|
| 281 |
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"clusters-00",
|
| 282 |
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"clusters-01",
|
| 283 |
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"clusters-02",
|
| 284 |
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"clusters-03",
|
| 285 |
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"clusters-04",
|
| 286 |
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"clusters-05",
|
| 287 |
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"dist-perres",
|
| 288 |
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"energies",
|
| 289 |
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"fluctuation",
|
| 290 |
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"hbonds",
|
| 291 |
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"interactions",
|
| 292 |
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"pca",
|
| 293 |
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"rgyr",
|
| 294 |
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"rmsd-pairwise",
|
| 295 |
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"rmsd-perres",
|
| 296 |
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"rmsds",
|
| 297 |
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|
| 298 |
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"tmscores"
|
| 299 |
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|
| 300 |
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"mdIndex": 0,
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"creationDate": "2025-06-03T19:32:05.000Z",
|
| 305 |
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"identifier": "A001D"
|
| 306 |
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}
|
A001D/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A001I/project.json
ADDED
|
@@ -0,0 +1,189 @@
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|
| 1 |
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{
|
| 2 |
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"accession": "A001I",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1MQ8",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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| 25 |
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| 26 |
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"1MQ8"
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| 27 |
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],
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|
| 29 |
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|
| 30 |
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| 31 |
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| 33 |
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| 39 |
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| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Intercellular adhesion molecule 1",
|
| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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|
| 47 |
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"VWFA"
|
| 48 |
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],
|
| 49 |
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|
| 50 |
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|
| 51 |
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"TEMP": 310,
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|
| 53 |
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| 54 |
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"CHARMM36m"
|
| 55 |
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],
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| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
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| 58 |
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| 59 |
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| 60 |
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{
|
| 75 |
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"name": "chain A-chain B interaction",
|
| 76 |
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|
| 77 |
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|
| 78 |
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"selection_1": "chain A",
|
| 79 |
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"selection_2": "chain B",
|
| 80 |
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"type": "protein-protein"
|
| 81 |
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|
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],
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],
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|
| 162 |
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"pocket_01.pdb",
|
| 163 |
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|
| 164 |
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],
|
| 165 |
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"analyses": [
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| 166 |
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"clusters",
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| 167 |
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"clusters-00",
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| 168 |
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"clusters-01",
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| 169 |
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"dist-perres",
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| 170 |
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"energies",
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| 171 |
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"fluctuation",
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| 172 |
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"hbonds",
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| 173 |
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"interactions",
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| 174 |
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"pca",
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| 175 |
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"pockets",
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| 176 |
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f53a1b9e3119e941968bb",
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"creationDate": "2025-06-03T19:57:21.000Z",
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"identifier": "A001I"
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}
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| 1 |
+
{
|
| 2 |
+
"accession": "A001S",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1RLB",
|
| 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 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
|
| 15 |
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|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
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| 24 |
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| 25 |
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|
| 26 |
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"1RLB"
|
| 27 |
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],
|
| 28 |
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|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P02766",
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| 31 |
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"P02753"
|
| 32 |
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],
|
| 33 |
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|
| 34 |
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|
| 35 |
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| 36 |
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|
| 37 |
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| 38 |
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| 39 |
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|
| 40 |
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],
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| 41 |
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|
| 42 |
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"DOMAINS": [
|
| 43 |
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"Transthyretin",
|
| 44 |
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"Retinol-binding protein 4",
|
| 45 |
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"Plasma retinol-binding protein(1-182)",
|
| 46 |
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"Plasma retinol-binding protein(1-181)",
|
| 47 |
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"Plasma retinol-binding protein(1-179)",
|
| 48 |
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"Plasma retinol-binding protein(1-176)"
|
| 49 |
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],
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| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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|
| 54 |
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"FF": [
|
| 55 |
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"CHARMM36m"
|
| 56 |
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],
|
| 57 |
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"WAT": "TIP3P",
|
| 58 |
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"BOXTYPE": "Dodecahedron",
|
| 59 |
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|
| 60 |
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|
| 61 |
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| 62 |
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| 63 |
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|
| 64 |
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|
| 65 |
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| 66 |
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| 67 |
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| 68 |
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|
| 69 |
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| 70 |
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| 71 |
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|
| 72 |
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|
| 73 |
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|
| 74 |
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|
| 75 |
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{
|
| 76 |
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"name": "chain A-chain B interaction",
|
| 77 |
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"agent_1": "chain A",
|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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"type": "protein-protein"
|
| 82 |
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},
|
| 83 |
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{
|
| 84 |
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"name": "chain A-chain C interaction",
|
| 85 |
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|
| 86 |
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|
| 87 |
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| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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{
|
| 92 |
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"name": "chain A-chain D interaction",
|
| 93 |
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| 94 |
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| 95 |
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| 96 |
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| 97 |
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| 98 |
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},
|
| 99 |
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{
|
| 100 |
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"name": "chain A-chain E interaction",
|
| 101 |
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| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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| 106 |
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| 107 |
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{
|
| 108 |
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"name": "chain A-chain F interaction",
|
| 109 |
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|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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"type": "protein-protein"
|
| 114 |
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},
|
| 115 |
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{
|
| 116 |
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"name": "chain B-chain C interaction",
|
| 117 |
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|
| 118 |
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|
| 119 |
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|
| 120 |
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|
| 121 |
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"type": "protein-protein"
|
| 122 |
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|
| 123 |
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{
|
| 124 |
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"name": "chain B-chain D interaction",
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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"type": "protein-protein"
|
| 130 |
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| 131 |
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{
|
| 132 |
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"name": "chain B-chain E interaction",
|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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| 137 |
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|
| 138 |
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|
| 139 |
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{
|
| 140 |
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"name": "chain B-chain F interaction",
|
| 141 |
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|
| 142 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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{
|
| 148 |
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"name": "chain C-chain D interaction",
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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{
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| 156 |
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| 157 |
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| 158 |
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| 159 |
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| 161 |
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| 162 |
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| 163 |
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{
|
| 164 |
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| 165 |
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| 166 |
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| 168 |
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| 169 |
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| 170 |
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| 171 |
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{
|
| 172 |
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"name": "chain D-chain F interaction",
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| 173 |
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| 174 |
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| 175 |
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|
| 177 |
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| 178 |
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|
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|
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],
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 410 |
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|
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|
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|
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| 414 |
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| 417 |
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|
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|
| 419 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 457 |
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|
| 458 |
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|
| 459 |
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|
| 460 |
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|
| 461 |
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|
| 462 |
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|
| 463 |
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|
| 464 |
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|
| 465 |
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|
| 466 |
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|
| 467 |
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|
| 468 |
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|
| 469 |
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|
| 470 |
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|
| 471 |
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|
| 472 |
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|
| 473 |
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|
| 474 |
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|
| 475 |
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"clusters_12_screenshot_12.jpg",
|
| 476 |
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|
| 477 |
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"clusters_12_screenshot_14.jpg",
|
| 478 |
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"clusters_12_screenshot_15.jpg",
|
| 479 |
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"clusters_12_screenshot_16.jpg",
|
| 480 |
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"clusters_12_screenshot_17.jpg",
|
| 481 |
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"clusters_12_screenshot_18.jpg",
|
| 482 |
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"clusters_12_screenshot_19.jpg",
|
| 483 |
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|
| 484 |
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|
| 485 |
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|
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|
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|
| 488 |
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|
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|
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|
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|
| 494 |
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|
| 495 |
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|
| 496 |
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|
| 497 |
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|
| 498 |
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|
| 499 |
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|
| 500 |
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|
| 501 |
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|
| 502 |
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|
| 503 |
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|
| 504 |
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|
| 505 |
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|
| 506 |
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"clusters_13_screenshot_23.jpg",
|
| 507 |
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"clusters_13_screenshot_24.jpg",
|
| 508 |
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"pocket_01.pdb",
|
| 509 |
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"pocket_02.pdb",
|
| 510 |
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"pocket_03.pdb",
|
| 511 |
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"pocket_04.pdb",
|
| 512 |
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"pocket_05.pdb",
|
| 513 |
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"pocket_06.pdb",
|
| 514 |
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"pocket_07.pdb",
|
| 515 |
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"pocket_08.pdb",
|
| 516 |
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"pocket_09.pdb",
|
| 517 |
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"pocket_10.pdb"
|
| 518 |
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],
|
| 519 |
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"analyses": [
|
| 520 |
+
"clusters",
|
| 521 |
+
"clusters-00",
|
| 522 |
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"clusters-01",
|
| 523 |
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"clusters-02",
|
| 524 |
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"clusters-03",
|
| 525 |
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"clusters-04",
|
| 526 |
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"clusters-05",
|
| 527 |
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"clusters-06",
|
| 528 |
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"clusters-07",
|
| 529 |
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"clusters-08",
|
| 530 |
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"clusters-09",
|
| 531 |
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"clusters-10",
|
| 532 |
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"clusters-11",
|
| 533 |
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"clusters-12",
|
| 534 |
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"clusters-13",
|
| 535 |
+
"dist-perres",
|
| 536 |
+
"energies",
|
| 537 |
+
"fluctuation",
|
| 538 |
+
"hbonds",
|
| 539 |
+
"interactions",
|
| 540 |
+
"pca",
|
| 541 |
+
"pockets",
|
| 542 |
+
"rgyr",
|
| 543 |
+
"rmsd-pairwise",
|
| 544 |
+
"rmsd-perres",
|
| 545 |
+
"rmsds",
|
| 546 |
+
"sasa",
|
| 547 |
+
"tmscores"
|
| 548 |
+
],
|
| 549 |
+
"mdIndex": 0,
|
| 550 |
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"mdNumber": 1,
|
| 551 |
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"refframe": 0,
|
| 552 |
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"internalId": "683f6396821889b377defe7a",
|
| 553 |
+
"creationDate": "2025-06-03T21:05:26.000Z",
|
| 554 |
+
"identifier": "A001S"
|
| 555 |
+
}
|
A001S/records.jsonl
ADDED
|
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|
|
|
A001V/project.json
ADDED
|
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| 1 |
+
{
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| 2 |
+
"accession": "A001V",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1S1Q",
|
| 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 |
+
"1S1Q"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q99816",
|
| 31 |
+
"P0CG48"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"VSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS",
|
| 38 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tumor susceptibility gene 101 protein",
|
| 43 |
+
"UEV",
|
| 44 |
+
"Ubiquitin",
|
| 45 |
+
"Ubiquitin-like 1",
|
| 46 |
+
"Interacts with activating enzyme",
|
| 47 |
+
"Essential for function"
|
| 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": 3471,
|
| 59 |
+
"SYSTRES": 213,
|
| 60 |
+
"PROTATS": 3471,
|
| 61 |
+
"PROTRES": 213,
|
| 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": 8.11817,
|
| 93 |
+
"BOXSIZEY": 8.11817,
|
| 94 |
+
"BOXSIZEZ": 5.75796,
|
| 95 |
+
"mdName": "replica 1",
|
| 96 |
+
"mdAtoms": 3471,
|
| 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",
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| 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_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 |
+
],
|
| 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": "683f69e5c42215fa3dde639e",
|
| 191 |
+
"creationDate": "2025-06-03T21:32:21.000Z",
|
| 192 |
+
"identifier": "A001V"
|
| 193 |
+
}
|
A001V/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
{"project_identifier": "A001V", "accession": "A001V", "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 1S1Q", "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": ["1S1Q"], "FORCED_REFERENCES": null, "REFERENCES": ["Q99816", "P0CG48"], 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A001X/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A001X",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1SYQ",
|
| 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 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"1SYQ"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P18206",
|
| 31 |
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"Q9Y490"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"PLLQAAKGLAGAVSELLRSAQPASA",
|
| 38 |
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"HMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Vinculin",
|
| 43 |
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"N-terminal globular head",
|
| 44 |
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"Talin-interaction",
|
| 45 |
+
"3 X 112 AA tandem repeats",
|
| 46 |
+
"Talin-1",
|
| 47 |
+
"Helical bundle R1"
|
| 48 |
+
],
|
| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
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"TIMESTEP": 2,
|
| 51 |
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"TEMP": 310,
|
| 52 |
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"ENSEMBLE": "NPT",
|
| 53 |
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"FF": [
|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
|
| 58 |
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"SYSTATS": 4466,
|
| 59 |
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"SYSTRES": 284,
|
| 60 |
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"PROTATS": 4466,
|
| 61 |
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"PROTRES": 284,
|
| 62 |
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"NUCLATS": 0,
|
| 63 |
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"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
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"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
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"SOLVRES": 0,
|
| 70 |
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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
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"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 |
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"type": "protein-protein"
|
| 81 |
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}
|
| 82 |
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],
|
| 83 |
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"PBC_SELECTION": null,
|
| 84 |
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"CHAINNAMES": null,
|
| 85 |
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"MEMBRANES": null,
|
| 86 |
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"CUSTOMS": null,
|
| 87 |
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"ORIENTATION": null,
|
| 88 |
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"PTM": [],
|
| 89 |
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"MULTIMERIC": null,
|
| 90 |
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"COLLECTIONS": "dynarepo",
|
| 91 |
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"WARNINGS": [],
|
| 92 |
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"BOXSIZEX": 12.5935,
|
| 93 |
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"BOXSIZEY": 12.5935,
|
| 94 |
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"BOXSIZEZ": 8.89058,
|
| 95 |
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"mdName": "replica 1",
|
| 96 |
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"mdAtoms": 4466,
|
| 97 |
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"mdFrames": 5001
|
| 98 |
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},
|
| 99 |
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"mds": [
|
| 100 |
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"replica 1",
|
| 101 |
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"replica 2",
|
| 102 |
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"replica 3"
|
| 103 |
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],
|
| 104 |
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"mdref": 0,
|
| 105 |
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"files": [
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| 106 |
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|
| 107 |
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|
| 108 |
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| 109 |
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|
| 110 |
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|
| 111 |
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| 112 |
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|
| 113 |
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|
| 114 |
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|
| 115 |
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| 116 |
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|
| 118 |
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| 119 |
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|
| 120 |
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|
| 121 |
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|
| 122 |
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|
| 123 |
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|
| 124 |
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|
| 125 |
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| 126 |
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| 127 |
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| 128 |
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| 129 |
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| 130 |
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| 131 |
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| 132 |
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| 133 |
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| 134 |
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| 135 |
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| 136 |
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|
| 137 |
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| 138 |
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| 139 |
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| 140 |
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| 141 |
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| 142 |
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|
| 143 |
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| 144 |
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| 145 |
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| 146 |
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|
| 147 |
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|
| 148 |
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| 149 |
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|
| 150 |
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|
| 151 |
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| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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|
| 163 |
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|
| 164 |
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"clusters_01_screenshot_19.jpg",
|
| 165 |
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"pocket_01.pdb",
|
| 166 |
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"pocket_02.pdb",
|
| 167 |
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"pocket_03.pdb",
|
| 168 |
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"pocket_04.pdb",
|
| 169 |
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"pocket_05.pdb"
|
| 170 |
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],
|
| 171 |
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"analyses": [
|
| 172 |
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"clusters",
|
| 173 |
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"clusters-00",
|
| 174 |
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"clusters-01",
|
| 175 |
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"dist-perres",
|
| 176 |
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"energies",
|
| 177 |
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"fluctuation",
|
| 178 |
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"hbonds",
|
| 179 |
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"interactions",
|
| 180 |
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"pca",
|
| 181 |
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"pockets",
|
| 182 |
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"rgyr",
|
| 183 |
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"rmsd-pairwise",
|
| 184 |
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"rmsd-perres",
|
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f6be396ae352bdf893b46",
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"creationDate": "2025-06-03T21:40:51.000Z",
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"identifier": "A001X"
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}
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|
A0024/project.json
ADDED
|
@@ -0,0 +1,197 @@
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| 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 |
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"PROTRES": 305,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
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"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
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"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 |
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"BOXSIZEY": 8.47508,
|
| 90 |
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"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 |
+
}
|
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"], 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|
A002A/project.json
ADDED
|
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|
| 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 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"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 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
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"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 |
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"ORIENTATION": null,
|
| 87 |
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"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 8.13965,
|
| 92 |
+
"BOXSIZEY": 8.13965,
|
| 93 |
+
"BOXSIZEZ": 5.73787,
|
| 94 |
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"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 2816,
|
| 96 |
+
"mdFrames": 5001
|
| 97 |
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},
|
| 98 |
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"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
+
"mdref": 0,
|
| 104 |
+
"files": [
|
| 105 |
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"topology.tpr",
|
| 106 |
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"screenshot.jpg",
|
| 107 |
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"trajectory.bin",
|
| 108 |
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"pca_trajectory_01.bin",
|
| 109 |
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"pca_trajectory_02.bin",
|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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"pca_trajectory_06.bin",
|
| 114 |
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|
| 115 |
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|
| 116 |
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|
| 117 |
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|
| 118 |
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|
| 119 |
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|
| 120 |
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"pca_trajectory_13.bin",
|
| 121 |
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"structure.pdb",
|
| 122 |
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"trajectory.xtc",
|
| 123 |
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"clusters_00_screenshot_00.jpg",
|
| 124 |
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"clusters_00_screenshot_01.jpg",
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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"clusters_00_screenshot_06.jpg",
|
| 130 |
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|
| 131 |
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"clusters_00_screenshot_08.jpg",
|
| 132 |
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"clusters_00_screenshot_09.jpg",
|
| 133 |
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"clusters_00_screenshot_10.jpg",
|
| 134 |
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"clusters_00_screenshot_11.jpg",
|
| 135 |
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"clusters_00_screenshot_12.jpg",
|
| 136 |
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"clusters_00_screenshot_13.jpg",
|
| 137 |
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"clusters_00_screenshot_14.jpg",
|
| 138 |
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"clusters_00_screenshot_15.jpg",
|
| 139 |
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"clusters_00_screenshot_16.jpg",
|
| 140 |
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"clusters_00_screenshot_17.jpg",
|
| 141 |
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"clusters_00_screenshot_18.jpg",
|
| 142 |
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"clusters_00_screenshot_19.jpg",
|
| 143 |
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"clusters_01_screenshot_00.jpg",
|
| 144 |
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"clusters_01_screenshot_01.jpg",
|
| 145 |
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"clusters_01_screenshot_02.jpg",
|
| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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"clusters_01_screenshot_08.jpg",
|
| 152 |
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"clusters_01_screenshot_09.jpg",
|
| 153 |
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"clusters_01_screenshot_10.jpg",
|
| 154 |
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"clusters_01_screenshot_11.jpg",
|
| 155 |
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"clusters_01_screenshot_12.jpg",
|
| 156 |
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"clusters_01_screenshot_13.jpg",
|
| 157 |
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"clusters_01_screenshot_14.jpg",
|
| 158 |
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"clusters_01_screenshot_15.jpg",
|
| 159 |
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"clusters_01_screenshot_16.jpg",
|
| 160 |
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"clusters_01_screenshot_17.jpg",
|
| 161 |
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"clusters_01_screenshot_18.jpg",
|
| 162 |
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"clusters_01_screenshot_19.jpg",
|
| 163 |
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"clusters_01_screenshot_20.jpg",
|
| 164 |
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"pocket_01.pdb",
|
| 165 |
+
"pocket_02.pdb"
|
| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
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"clusters",
|
| 169 |
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"clusters-00",
|
| 170 |
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"clusters-01",
|
| 171 |
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"dist-perres",
|
| 172 |
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"energies",
|
| 173 |
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"fluctuation",
|
| 174 |
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"hbonds",
|
| 175 |
+
"interactions",
|
| 176 |
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"pca",
|
| 177 |
+
"pockets",
|
| 178 |
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"rgyr",
|
| 179 |
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"rmsd-pairwise",
|
| 180 |
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"rmsd-perres",
|
| 181 |
+
"rmsds",
|
| 182 |
+
"sasa",
|
| 183 |
+
"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f7e53033ad70f2bcb1da1",
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"creationDate": "2025-06-03T22:59:31.000Z",
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"identifier": "A002A"
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}
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| 1 |
+
{
|
| 2 |
+
"accession": "A0039",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2J8S",
|
| 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 |
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"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
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"2J8S"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"P31224",
|
| 31 |
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"Q00420"
|
| 32 |
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],
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| 33 |
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"INPUT_LIGANDS": null,
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| 34 |
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"LIGANDS": [],
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| 35 |
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| 36 |
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"PROTSEQ": [
|
| 37 |
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| 38 |
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| 39 |
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| 40 |
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| 42 |
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| 43 |
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| 44 |
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| 45 |
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| 46 |
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| 51 |
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| 52 |
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| 53 |
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| 54 |
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| 55 |
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| 56 |
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|
| 122 |
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| 262 |
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| 263 |
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| 264 |
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| 265 |
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| 266 |
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|
| 267 |
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|
| 268 |
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|
| 269 |
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|
| 270 |
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|
| 271 |
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|
| 272 |
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|
| 273 |
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|
| 274 |
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"clusters_05_screenshot_08.jpg",
|
| 275 |
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"clusters_05_screenshot_09.jpg",
|
| 276 |
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"clusters_05_screenshot_10.jpg",
|
| 277 |
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"clusters_05_screenshot_11.jpg",
|
| 278 |
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"clusters_05_screenshot_12.jpg",
|
| 279 |
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"clusters_05_screenshot_13.jpg",
|
| 280 |
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"clusters_05_screenshot_14.jpg",
|
| 281 |
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|
| 282 |
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"clusters_05_screenshot_16.jpg",
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| 283 |
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| 284 |
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"clusters_06_screenshot_00.jpg",
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| 285 |
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| 286 |
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| 287 |
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|
| 288 |
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|
| 289 |
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|
| 290 |
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|
| 291 |
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| 292 |
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| 293 |
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| 294 |
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| 295 |
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| 297 |
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| 298 |
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| 299 |
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|
| 300 |
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| 301 |
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| 302 |
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|
| 303 |
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| 304 |
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"clusters_07_screenshot_00.jpg",
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| 305 |
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| 306 |
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| 307 |
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| 308 |
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"clusters_07_screenshot_04.jpg",
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| 309 |
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| 310 |
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| 311 |
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"clusters_07_screenshot_07.jpg",
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| 312 |
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"clusters_07_screenshot_08.jpg",
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| 313 |
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|
| 314 |
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"clusters_07_screenshot_10.jpg",
|
| 315 |
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"clusters_07_screenshot_11.jpg",
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| 316 |
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"clusters_07_screenshot_12.jpg",
|
| 317 |
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"clusters_07_screenshot_13.jpg",
|
| 318 |
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"clusters_07_screenshot_14.jpg",
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| 319 |
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"clusters_07_screenshot_15.jpg",
|
| 320 |
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"clusters_07_screenshot_16.jpg",
|
| 321 |
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"clusters_07_screenshot_17.jpg",
|
| 322 |
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"pocket_01.pdb",
|
| 323 |
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"pocket_02.pdb",
|
| 324 |
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"pocket_03.pdb",
|
| 325 |
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"pocket_04.pdb",
|
| 326 |
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"pocket_05.pdb",
|
| 327 |
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"pocket_06.pdb",
|
| 328 |
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"pocket_07.pdb",
|
| 329 |
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"pocket_08.pdb",
|
| 330 |
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"pocket_09.pdb",
|
| 331 |
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"pocket_10.pdb"
|
| 332 |
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],
|
| 333 |
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"analyses": [
|
| 334 |
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"clusters",
|
| 335 |
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"clusters-00",
|
| 336 |
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"clusters-01",
|
| 337 |
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"clusters-02",
|
| 338 |
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|
| 339 |
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|
| 340 |
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"clusters-05",
|
| 341 |
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"clusters-06",
|
| 342 |
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"clusters-07",
|
| 343 |
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"dist-perres",
|
| 344 |
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"energies",
|
| 345 |
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"fluctuation",
|
| 346 |
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"hbonds",
|
| 347 |
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"interactions",
|
| 348 |
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"pca",
|
| 349 |
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"pockets",
|
| 350 |
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"rgyr",
|
| 351 |
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"rmsd-pairwise",
|
| 352 |
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"rmsd-perres",
|
| 353 |
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"rmsds",
|
| 354 |
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"sasa",
|
| 355 |
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"tmscores"
|
| 356 |
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|
| 357 |
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|
| 358 |
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|
| 360 |
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| 361 |
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"creationDate": "2025-06-04T14:00:47.000Z",
|
| 362 |
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"identifier": "A0039"
|
| 363 |
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}
|
A0039/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A003E/project.json
ADDED
|
@@ -0,0 +1,200 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003E",
|
| 3 |
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"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2NQD",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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|
| 26 |
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"2NQD"
|
| 27 |
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],
|
| 28 |
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|
| 29 |
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"REFERENCES": [
|
| 30 |
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|
| 31 |
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"P07711"
|
| 32 |
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],
|
| 33 |
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|
| 34 |
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|
| 35 |
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|
| 36 |
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| 37 |
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| 38 |
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| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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|
| 42 |
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"Chagasin",
|
| 43 |
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"BC loop",
|
| 44 |
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"DE loop",
|
| 45 |
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"FG loop",
|
| 46 |
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"Cathepsin L",
|
| 47 |
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"Cathepsin L heavy chain",
|
| 48 |
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"Cathepsin L light chain",
|
| 49 |
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"Cleavage; by autolysis"
|
| 50 |
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],
|
| 51 |
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|
| 52 |
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"TIMESTEP": 2,
|
| 53 |
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"TEMP": 310,
|
| 54 |
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|
| 55 |
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|
| 56 |
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"CHARMM36m"
|
| 57 |
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],
|
| 58 |
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"WAT": "TIP3P",
|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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"PROTRES": 330,
|
| 64 |
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| 66 |
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| 68 |
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|
| 70 |
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|
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| 73 |
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|
| 74 |
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|
| 75 |
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"INTERACTIONS": [
|
| 76 |
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{
|
| 77 |
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"name": "chain A-chain B interaction",
|
| 78 |
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"agent_1": "chain A",
|
| 79 |
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"agent_2": "chain B",
|
| 80 |
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"selection_1": "chain A",
|
| 81 |
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"selection_2": "chain B",
|
| 82 |
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"type": "protein-protein"
|
| 83 |
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}
|
| 84 |
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],
|
| 85 |
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"PBC_SELECTION": null,
|
| 86 |
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|
| 87 |
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|
| 88 |
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| 89 |
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| 91 |
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| 92 |
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| 93 |
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},
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|
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|
| 104 |
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|
| 105 |
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],
|
| 106 |
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|
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|
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|
| 111 |
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|
| 112 |
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|
| 113 |
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|
| 114 |
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|
| 115 |
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|
| 116 |
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|
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|
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|
| 121 |
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|
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|
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|
| 124 |
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|
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|
| 163 |
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|
| 164 |
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|
| 165 |
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"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb",
|
| 173 |
+
"pocket_09.pdb",
|
| 174 |
+
"pocket_10.pdb"
|
| 175 |
+
],
|
| 176 |
+
"analyses": [
|
| 177 |
+
"clusters",
|
| 178 |
+
"clusters-00",
|
| 179 |
+
"clusters-01",
|
| 180 |
+
"dist-perres",
|
| 181 |
+
"energies",
|
| 182 |
+
"fluctuation",
|
| 183 |
+
"hbonds",
|
| 184 |
+
"interactions",
|
| 185 |
+
"pca",
|
| 186 |
+
"pockets",
|
| 187 |
+
"rgyr",
|
| 188 |
+
"rmsd-pairwise",
|
| 189 |
+
"rmsd-perres",
|
| 190 |
+
"rmsds",
|
| 191 |
+
"sasa",
|
| 192 |
+
"tmscores"
|
| 193 |
+
],
|
| 194 |
+
"mdIndex": 0,
|
| 195 |
+
"mdNumber": 1,
|
| 196 |
+
"refframe": 0,
|
| 197 |
+
"internalId": "6840630af49fd4972b4ea47e",
|
| 198 |
+
"creationDate": "2025-06-04T15:15:22.000Z",
|
| 199 |
+
"identifier": "A003E"
|
| 200 |
+
}
|
A003E/records.jsonl
ADDED
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| 1 |
+
{
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| 2 |
+
"accession": "A003L",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2PCB",
|
| 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 |
+
"2PCB"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00431",
|
| 31 |
+
"P00004"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL",
|
| 38 |
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"GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Cytochrome c peroxidase, mitochondrial",
|
| 43 |
+
"Transition state stabilizer",
|
| 44 |
+
"Cytochrome c"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 6295,
|
| 56 |
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"SYSTRES": 398,
|
| 57 |
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"PROTATS": 6295,
|
| 58 |
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"PROTRES": 398,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
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{
|
| 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 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 10.2184,
|
| 90 |
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"BOXSIZEY": 10.2184,
|
| 91 |
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"BOXSIZEZ": 7.22271,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 6295,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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"pca_trajectory_01.bin",
|
| 107 |
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"pca_trajectory_02.bin",
|
| 108 |
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"pca_trajectory_03.bin",
|
| 109 |
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"pca_trajectory_04.bin",
|
| 110 |
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"pca_trajectory_05.bin",
|
| 111 |
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"pca_trajectory_06.bin",
|
| 112 |
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"pca_trajectory_07.bin",
|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
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"pca_trajectory_09.bin",
|
| 115 |
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"pca_trajectory_10.bin",
|
| 116 |
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"pca_trajectory_11.bin",
|
| 117 |
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"structure.pdb",
|
| 118 |
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"trajectory.xtc",
|
| 119 |
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"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
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"clusters_00_screenshot_02.jpg",
|
| 122 |
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"clusters_00_screenshot_03.jpg",
|
| 123 |
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"clusters_00_screenshot_04.jpg",
|
| 124 |
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"clusters_00_screenshot_05.jpg",
|
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"clusters_00_screenshot_06.jpg",
|
| 126 |
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"clusters_00_screenshot_07.jpg",
|
| 127 |
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"clusters_00_screenshot_08.jpg",
|
| 128 |
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"clusters_00_screenshot_09.jpg",
|
| 129 |
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"clusters_00_screenshot_10.jpg",
|
| 130 |
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"clusters_00_screenshot_11.jpg",
|
| 131 |
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"clusters_00_screenshot_12.jpg",
|
| 132 |
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"clusters_00_screenshot_13.jpg",
|
| 133 |
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"clusters_00_screenshot_14.jpg",
|
| 134 |
+
"clusters_00_screenshot_15.jpg",
|
| 135 |
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"clusters_00_screenshot_16.jpg",
|
| 136 |
+
"clusters_00_screenshot_17.jpg",
|
| 137 |
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"clusters_00_screenshot_18.jpg",
|
| 138 |
+
"clusters_00_screenshot_19.jpg",
|
| 139 |
+
"clusters_01_screenshot_00.jpg",
|
| 140 |
+
"clusters_01_screenshot_01.jpg",
|
| 141 |
+
"clusters_01_screenshot_02.jpg",
|
| 142 |
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"clusters_01_screenshot_03.jpg",
|
| 143 |
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"clusters_01_screenshot_04.jpg",
|
| 144 |
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"clusters_01_screenshot_05.jpg",
|
| 145 |
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"clusters_01_screenshot_06.jpg",
|
| 146 |
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"clusters_01_screenshot_07.jpg",
|
| 147 |
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"clusters_01_screenshot_08.jpg",
|
| 148 |
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"clusters_01_screenshot_09.jpg",
|
| 149 |
+
"clusters_01_screenshot_10.jpg",
|
| 150 |
+
"clusters_01_screenshot_11.jpg",
|
| 151 |
+
"clusters_01_screenshot_12.jpg",
|
| 152 |
+
"clusters_01_screenshot_13.jpg",
|
| 153 |
+
"clusters_01_screenshot_14.jpg",
|
| 154 |
+
"clusters_01_screenshot_15.jpg",
|
| 155 |
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"clusters_01_screenshot_16.jpg",
|
| 156 |
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"clusters_01_screenshot_17.jpg",
|
| 157 |
+
"clusters_01_screenshot_18.jpg",
|
| 158 |
+
"clusters_01_screenshot_19.jpg",
|
| 159 |
+
"clusters_01_screenshot_20.jpg",
|
| 160 |
+
"pocket_01.pdb",
|
| 161 |
+
"pocket_02.pdb",
|
| 162 |
+
"pocket_03.pdb",
|
| 163 |
+
"pocket_04.pdb",
|
| 164 |
+
"pocket_05.pdb",
|
| 165 |
+
"pocket_06.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 |
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"mdIndex": 0,
|
| 186 |
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"mdNumber": 1,
|
| 187 |
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"refframe": 0,
|
| 188 |
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"internalId": "68407531c16de68ddf4d4a74",
|
| 189 |
+
"creationDate": "2025-06-04T16:32:49.000Z",
|
| 190 |
+
"identifier": "A003L"
|
| 191 |
+
}
|
A003L/records.jsonl
ADDED
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{"project_identifier": "A003L", "accession": "A003L", "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 2PCB", "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": ["2PCB"], "FORCED_REFERENCES": null, "REFERENCES": ["P00431", "P00004"], 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ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2PJY",
|
| 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 |
+
"2PJY"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P10600",
|
| 31 |
+
"P37173",
|
| 32 |
+
"P36897"
|
| 33 |
+
],
|
| 34 |
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"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
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"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS",
|
| 39 |
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"AGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIF",
|
| 40 |
+
"ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIEL"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Transforming growth factor beta-3",
|
| 45 |
+
"TGF-beta receptor type-2",
|
| 46 |
+
"TGF-beta receptor type-1"
|
| 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": 4573,
|
| 58 |
+
"SYSTRES": 299,
|
| 59 |
+
"PROTATS": 4573,
|
| 60 |
+
"PROTRES": 299,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
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"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 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain B-chain C interaction",
|
| 91 |
+
"agent_1": "chain B",
|
| 92 |
+
"agent_2": "chain C",
|
| 93 |
+
"selection_1": "chain B",
|
| 94 |
+
"selection_2": "chain C",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
}
|
| 97 |
+
],
|
| 98 |
+
"PBC_SELECTION": null,
|
| 99 |
+
"CHAINNAMES": null,
|
| 100 |
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"MEMBRANES": null,
|
| 101 |
+
"CUSTOMS": null,
|
| 102 |
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"ORIENTATION": null,
|
| 103 |
+
"PTM": [],
|
| 104 |
+
"MULTIMERIC": null,
|
| 105 |
+
"COLLECTIONS": "dynarepo",
|
| 106 |
+
"WARNINGS": [],
|
| 107 |
+
"BOXSIZEX": 11.6362,
|
| 108 |
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"BOXSIZEY": 11.6362,
|
| 109 |
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"BOXSIZEZ": 8.22071,
|
| 110 |
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"mdName": "replica 1",
|
| 111 |
+
"mdAtoms": 4573,
|
| 112 |
+
"mdFrames": 5001
|
| 113 |
+
},
|
| 114 |
+
"mds": [
|
| 115 |
+
"replica 1",
|
| 116 |
+
"replica 2",
|
| 117 |
+
"replica 3"
|
| 118 |
+
],
|
| 119 |
+
"mdref": 0,
|
| 120 |
+
"files": [
|
| 121 |
+
"topology.tpr",
|
| 122 |
+
"screenshot.jpg",
|
| 123 |
+
"trajectory.bin",
|
| 124 |
+
"pca_trajectory_01.bin",
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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|
| 134 |
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"pca_trajectory_11.bin",
|
| 135 |
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"pca_trajectory_12.bin",
|
| 136 |
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"structure.pdb",
|
| 137 |
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"trajectory.xtc",
|
| 138 |
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|
| 139 |
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|
| 140 |
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| 141 |
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|
| 142 |
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|
| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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| 150 |
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| 151 |
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| 152 |
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| 154 |
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| 159 |
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|
| 160 |
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb"
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+
],
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+
"analyses": [
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"clusters",
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| 221 |
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"clusters-00",
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+
"clusters-01",
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| 223 |
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"clusters-02",
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"clusters-03",
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| 225 |
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"dist-perres",
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"energies",
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"fluctuation",
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| 228 |
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"hbonds",
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"interactions",
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"pca",
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| 231 |
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "684077693a7982f1ea8aa72e",
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"creationDate": "2025-06-04T16:42:17.000Z",
|
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"identifier": "A003M"
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+
}
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A003M/records.jsonl
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A003O/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A003O",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2PTT",
|
| 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 |
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"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"2PTT"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P18181",
|
| 31 |
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"Q07763"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
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| 37 |
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"DCPDSSEEVVGVSGKPVQLRPSNIQTKDVSVQWKKTEQGSHRKIEILNWYNDGPSWSNVSFSDIYGFDYGDFALSIKSAKLQDSGHYLLEITNTGGKVCNKNFQLLIL",
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| 38 |
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|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"CD48 antigen",
|
| 43 |
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"Ig-like C2-type 1",
|
| 44 |
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"Natural killer cell receptor 2B4",
|
| 45 |
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"Ig-like 1"
|
| 46 |
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],
|
| 47 |
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"FRAMESTEP": 0.1,
|
| 48 |
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"TIMESTEP": 2,
|
| 49 |
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"TEMP": 310,
|
| 50 |
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"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
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"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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"WAT": "TIP3P",
|
| 55 |
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"BOXTYPE": "Dodecahedron",
|
| 56 |
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"SYSTATS": 3383,
|
| 57 |
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"SYSTRES": 211,
|
| 58 |
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"PROTATS": 3383,
|
| 59 |
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"PROTRES": 211,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
|
| 63 |
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"LIPIRES": 0,
|
| 64 |
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"CARBATS": 0,
|
| 65 |
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"CARBRES": 0,
|
| 66 |
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"SOLVATS": 0,
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| 67 |
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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
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"COUNANI": 0,
|
| 70 |
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"COUNION": 0,
|
| 71 |
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"INTERACTIONS": [
|
| 72 |
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{
|
| 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 |
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],
|
| 81 |
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"PBC_SELECTION": null,
|
| 82 |
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"CHAINNAMES": null,
|
| 83 |
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"MEMBRANES": null,
|
| 84 |
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"CUSTOMS": null,
|
| 85 |
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"ORIENTATION": null,
|
| 86 |
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"PTM": [],
|
| 87 |
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"MULTIMERIC": null,
|
| 88 |
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"COLLECTIONS": "dynarepo",
|
| 89 |
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"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 9.60575,
|
| 91 |
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"BOXSIZEY": 9.60575,
|
| 92 |
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"BOXSIZEZ": 6.82951,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 3383,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
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"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
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],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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|
| 105 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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|
| 121 |
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| 122 |
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| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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| 127 |
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|
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| 129 |
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| 130 |
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| 131 |
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| 132 |
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| 133 |
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| 134 |
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| 135 |
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| 136 |
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| 137 |
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| 139 |
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| 163 |
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| 164 |
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"pocket_06.pdb",
|
| 170 |
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"pocket_07.pdb"
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| 171 |
+
],
|
| 172 |
+
"analyses": [
|
| 173 |
+
"clusters",
|
| 174 |
+
"clusters-00",
|
| 175 |
+
"clusters-01",
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| 176 |
+
"dist-perres",
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| 177 |
+
"energies",
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| 178 |
+
"fluctuation",
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| 179 |
+
"hbonds",
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| 180 |
+
"interactions",
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| 181 |
+
"pca",
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| 182 |
+
"pockets",
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| 183 |
+
"rgyr",
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| 184 |
+
"rmsd-pairwise",
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| 185 |
+
"rmsd-perres",
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| 186 |
+
"rmsds",
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| 187 |
+
"sasa",
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| 188 |
+
"tmscores"
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| 189 |
+
],
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| 190 |
+
"mdIndex": 0,
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| 191 |
+
"mdNumber": 1,
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| 192 |
+
"refframe": 0,
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| 193 |
+
"internalId": "68407a6eb314550fea852822",
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| 194 |
+
"creationDate": "2025-06-04T16:55:10.000Z",
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"identifier": "A003O"
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}
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A003O/records.jsonl
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| 1 |
+
{
|
| 2 |
+
"accession": "A003S",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2QXV",
|
| 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 |
+
"2QXV"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q921E6",
|
| 31 |
+
"Q61188"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TMFSSNRQKILERTETLNQEWKQRRIQPV",
|
| 38 |
+
"FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Polycomb protein EED",
|
| 43 |
+
"Interaction with EZH2",
|
| 44 |
+
"Histone-lysine N-methyltransferase EZH2",
|
| 45 |
+
"Interaction with DNMT1, DNMT3A and DNMT3B",
|
| 46 |
+
"Interaction with EED"
|
| 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": 6132,
|
| 58 |
+
"SYSTRES": 381,
|
| 59 |
+
"PROTATS": 6132,
|
| 60 |
+
"PROTRES": 381,
|
| 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": 8.49332,
|
| 92 |
+
"BOXSIZEY": 8.49332,
|
| 93 |
+
"BOXSIZEZ": 6.0081,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 6132,
|
| 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 |
+
"pca_trajectory_14.bin",
|
| 122 |
+
"pca_trajectory_15.bin",
|
| 123 |
+
"pca_trajectory_16.bin",
|
| 124 |
+
"pca_trajectory_17.bin",
|
| 125 |
+
"pca_trajectory_18.bin",
|
| 126 |
+
"pca_trajectory_19.bin",
|
| 127 |
+
"structure.pdb",
|
| 128 |
+
"trajectory.xtc",
|
| 129 |
+
"clusters_00_screenshot_00.jpg",
|
| 130 |
+
"clusters_00_screenshot_01.jpg",
|
| 131 |
+
"clusters_00_screenshot_02.jpg",
|
| 132 |
+
"clusters_00_screenshot_03.jpg",
|
| 133 |
+
"clusters_00_screenshot_04.jpg",
|
| 134 |
+
"clusters_00_screenshot_05.jpg",
|
| 135 |
+
"clusters_00_screenshot_06.jpg",
|
| 136 |
+
"clusters_00_screenshot_07.jpg",
|
| 137 |
+
"clusters_00_screenshot_08.jpg",
|
| 138 |
+
"clusters_00_screenshot_09.jpg",
|
| 139 |
+
"clusters_00_screenshot_10.jpg",
|
| 140 |
+
"clusters_00_screenshot_11.jpg",
|
| 141 |
+
"clusters_00_screenshot_12.jpg",
|
| 142 |
+
"clusters_00_screenshot_13.jpg",
|
| 143 |
+
"clusters_00_screenshot_14.jpg",
|
| 144 |
+
"clusters_00_screenshot_15.jpg",
|
| 145 |
+
"clusters_00_screenshot_16.jpg",
|
| 146 |
+
"clusters_00_screenshot_17.jpg",
|
| 147 |
+
"clusters_00_screenshot_18.jpg",
|
| 148 |
+
"clusters_00_screenshot_19.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 |
+
"pocket_03.pdb",
|
| 172 |
+
"pocket_04.pdb",
|
| 173 |
+
"pocket_05.pdb",
|
| 174 |
+
"pocket_06.pdb",
|
| 175 |
+
"pocket_07.pdb",
|
| 176 |
+
"pocket_08.pdb"
|
| 177 |
+
],
|
| 178 |
+
"analyses": [
|
| 179 |
+
"clusters",
|
| 180 |
+
"clusters-00",
|
| 181 |
+
"clusters-01",
|
| 182 |
+
"dist-perres",
|
| 183 |
+
"energies",
|
| 184 |
+
"fluctuation",
|
| 185 |
+
"hbonds",
|
| 186 |
+
"interactions",
|
| 187 |
+
"pca",
|
| 188 |
+
"pockets",
|
| 189 |
+
"rgyr",
|
| 190 |
+
"rmsd-pairwise",
|
| 191 |
+
"rmsd-perres",
|
| 192 |
+
"rmsds",
|
| 193 |
+
"sasa",
|
| 194 |
+
"tmscores"
|
| 195 |
+
],
|
| 196 |
+
"mdIndex": 0,
|
| 197 |
+
"mdNumber": 1,
|
| 198 |
+
"refframe": 0,
|
| 199 |
+
"internalId": "6840856ec90c3a181a98ed1a",
|
| 200 |
+
"creationDate": "2025-06-04T17:42:06.000Z",
|
| 201 |
+
"identifier": "A003S"
|
| 202 |
+
}
|
A003S/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
| 1 |
+
{"project_identifier": "A003S", "accession": "A003S", "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 2QXV", "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": ["2QXV"], "FORCED_REFERENCES": null, "REFERENCES": ["Q921E6", "Q61188"], 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ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A003T",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2SNI",
|
| 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 |
+
"2SNI"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00782",
|
| 31 |
+
"P01053"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG",
|
| 38 |
+
"AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLQNTTTKLGDSFYYGKGLINVQAAAQ"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Subtilisin BPN'",
|
| 43 |
+
"Peptidase S8",
|
| 44 |
+
"Subtilisin-chymotrypsin inhibitor-2A",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Reactive bond"
|
| 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": 4901,
|
| 58 |
+
"SYSTRES": 339,
|
| 59 |
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"PROTATS": 4901,
|
| 60 |
+
"PROTRES": 339,
|
| 61 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"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": 8.76713,
|
| 92 |
+
"BOXSIZEY": 8.76713,
|
| 93 |
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"BOXSIZEZ": 6.24666,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 4901,
|
| 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 |
+
"pocket_01.pdb",
|
| 164 |
+
"pocket_02.pdb",
|
| 165 |
+
"pocket_03.pdb",
|
| 166 |
+
"pocket_04.pdb",
|
| 167 |
+
"pocket_05.pdb",
|
| 168 |
+
"pocket_06.pdb",
|
| 169 |
+
"pocket_07.pdb"
|
| 170 |
+
],
|
| 171 |
+
"analyses": [
|
| 172 |
+
"clusters",
|
| 173 |
+
"clusters-00",
|
| 174 |
+
"clusters-01",
|
| 175 |
+
"dist-perres",
|
| 176 |
+
"energies",
|
| 177 |
+
"fluctuation",
|
| 178 |
+
"hbonds",
|
| 179 |
+
"interactions",
|
| 180 |
+
"pca",
|
| 181 |
+
"pockets",
|
| 182 |
+
"rgyr",
|
| 183 |
+
"rmsd-pairwise",
|
| 184 |
+
"rmsd-perres",
|
| 185 |
+
"rmsds",
|
| 186 |
+
"sasa",
|
| 187 |
+
"tmscores"
|
| 188 |
+
],
|
| 189 |
+
"mdIndex": 0,
|
| 190 |
+
"mdNumber": 1,
|
| 191 |
+
"refframe": 0,
|
| 192 |
+
"internalId": "6840878bcbe8a3cd5b0dede8",
|
| 193 |
+
"creationDate": "2025-06-04T17:51:07.000Z",
|
| 194 |
+
"identifier": "A003T"
|
| 195 |
+
}
|
A003T/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A003T", "accession": "A003T", "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 2SNI", "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": ["2SNI"], "FORCED_REFERENCES": null, "REFERENCES": ["P00782", "P01053"], 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A0046/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0046",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2X89",
|
| 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 |
+
"2X89"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P61769"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD",
|
| 37 |
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"MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR"
|
| 38 |
+
],
|
| 39 |
+
"NUCLSEQ": [],
|
| 40 |
+
"DOMAINS": [
|
| 41 |
+
"Beta-2-microglobulin",
|
| 42 |
+
"Beta-2-microglobulin form pI 5.3",
|
| 43 |
+
"Ig-like C1-type"
|
| 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": 2978,
|
| 55 |
+
"SYSTRES": 183,
|
| 56 |
+
"PROTATS": 2978,
|
| 57 |
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"PROTRES": 183,
|
| 58 |
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"NUCLATS": 0,
|
| 59 |
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"NUCLRES": 0,
|
| 60 |
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"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
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"CARBATS": 0,
|
| 63 |
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"CARBRES": 0,
|
| 64 |
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"SOLVATS": 0,
|
| 65 |
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"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 |
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"PTM": [],
|
| 85 |
+
"MULTIMERIC": null,
|
| 86 |
+
"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
+
"BOXSIZEX": 9.36749,
|
| 89 |
+
"BOXSIZEY": 9.36749,
|
| 90 |
+
"BOXSIZEZ": 6.57096,
|
| 91 |
+
"mdName": "replica 1",
|
| 92 |
+
"mdAtoms": 2978,
|
| 93 |
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"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
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"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
+
"mdref": 0,
|
| 101 |
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"files": [
|
| 102 |
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"topology.tpr",
|
| 103 |
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"screenshot.jpg",
|
| 104 |
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|
| 105 |
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"pca_trajectory_01.bin",
|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
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"pca_trajectory_07.bin",
|
| 112 |
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"structure.pdb",
|
| 113 |
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"trajectory.xtc",
|
| 114 |
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|
| 115 |
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|
| 116 |
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| 117 |
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| 118 |
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| 119 |
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|
| 120 |
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|
| 121 |
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| 122 |
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|
| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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"clusters_00_screenshot_14.jpg",
|
| 129 |
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"clusters_00_screenshot_15.jpg",
|
| 130 |
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"clusters_00_screenshot_16.jpg",
|
| 131 |
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"clusters_00_screenshot_17.jpg",
|
| 132 |
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"clusters_00_screenshot_18.jpg",
|
| 133 |
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"clusters_00_screenshot_19.jpg",
|
| 134 |
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"clusters_00_screenshot_20.jpg",
|
| 135 |
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"clusters_00_screenshot_21.jpg",
|
| 136 |
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"clusters_01_screenshot_00.jpg",
|
| 137 |
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"clusters_01_screenshot_01.jpg",
|
| 138 |
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"clusters_01_screenshot_02.jpg",
|
| 139 |
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"clusters_01_screenshot_03.jpg",
|
| 140 |
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|
| 141 |
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"clusters_01_screenshot_05.jpg",
|
| 142 |
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"clusters_01_screenshot_06.jpg",
|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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],
|
| 157 |
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"analyses": [
|
| 158 |
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"clusters",
|
| 159 |
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"clusters-00",
|
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"clusters-01",
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "6840aadb3d674274ef7d6e1e",
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"creationDate": "2025-06-04T20:21:47.000Z",
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"identifier": "A0046"
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}
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A0046/records.jsonl
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A0049/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0049",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2XQR",
|
| 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 |
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"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 |
+
"2XQR"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q43866",
|
| 31 |
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"O49908"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL",
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| 38 |
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"NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Beta-fructofuranosidase, insoluble isoenzyme CWINV1",
|
| 43 |
+
"",
|
| 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": 10758,
|
| 56 |
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"SYSTRES": 683,
|
| 57 |
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"PROTATS": 10758,
|
| 58 |
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"PROTRES": 683,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 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 |
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"PBC_SELECTION": null,
|
| 81 |
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"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 11.0762,
|
| 90 |
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"BOXSIZEY": 11.0762,
|
| 91 |
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"BOXSIZEZ": 7.82367,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 10758,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
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"structure.pdb",
|
| 112 |
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"trajectory.xtc",
|
| 113 |
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|
| 114 |
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|
| 115 |
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| 116 |
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| 117 |
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| 118 |
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| 119 |
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| 120 |
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| 121 |
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| 122 |
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| 123 |
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| 124 |
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| 129 |
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"clusters_01_screenshot_19.jpg",
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"pocket_01.pdb"
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],
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"analyses": [
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"clusters",
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"clusters-00",
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"clusters-01",
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "6840b149c79430af3b36cc0d",
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"creationDate": "2025-06-04T20:49:13.000Z",
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"identifier": "A0049"
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}
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A004L/project.json
ADDED
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@@ -0,0 +1,199 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A004L",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3C9A",
|
| 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 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"3C9A"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q00805",
|
| 31 |
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"Q01083"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"DRDVRILYQVGDSEEDLPVCAPNAVCSKIDLYETPWIERQCRCPDGRTCPSSLGVEDGHTIADKTRHYKMCQPVHKLPVCKHFRDYTWTLTTAAELNVTEQIVHCRCPRNSVTYLTKREPIGNDSPGYRYLFACSPLTRLRCQRKQPCKLFTVRKRQEFLDEVNINSLCQCPKGHRCPSHHTQSGVIAGESFLEDNIQTYSGYCMAN",
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| 38 |
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"PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Protein giant-lens",
|
| 43 |
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"Protein spitz",
|
| 44 |
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"EGF-like"
|
| 45 |
+
],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 3991,
|
| 56 |
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"SYSTRES": 255,
|
| 57 |
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"PROTATS": 3991,
|
| 58 |
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"PROTRES": 255,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
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| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
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| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
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{
|
| 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 |
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"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 8.55642,
|
| 90 |
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"BOXSIZEY": 8.55642,
|
| 91 |
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"BOXSIZEZ": 6.04081,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 3991,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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|
| 108 |
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|
| 109 |
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"structure.pdb",
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"trajectory.xtc",
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"clusters_01_screenshot_13.jpg",
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"clusters_01_screenshot_14.jpg",
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"clusters_01_screenshot_18.jpg",
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"clusters_01_screenshot_19.jpg",
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"pocket_01.pdb",
|
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"pocket_02.pdb",
|
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb",
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| 173 |
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"pocket_08.pdb"
|
| 174 |
+
],
|
| 175 |
+
"analyses": [
|
| 176 |
+
"clusters",
|
| 177 |
+
"clusters-00",
|
| 178 |
+
"clusters-01",
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| 179 |
+
"dist-perres",
|
| 180 |
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"energies",
|
| 181 |
+
"fluctuation",
|
| 182 |
+
"hbonds",
|
| 183 |
+
"interactions",
|
| 184 |
+
"pca",
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| 185 |
+
"pockets",
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| 186 |
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "6840cd477aee7e4da27517bb",
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"creationDate": "2025-06-04T22:48:39.000Z",
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"identifier": "A004L"
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}
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A004L/records.jsonl
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|
A004M/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A004M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3CQX",
|
| 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 |
+
"3CQX"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P63017",
|
| 31 |
+
"Q91YN9"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SEESLKHATRIIDEVVSKFLDDLGNAKSHLMSLYSACSSEVPPGPVDQKFQSIVIGCALEDQKKIKRRLETLLRNIDNSDKAIK",
|
| 38 |
+
"PAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS",
|
| 39 |
+
"ESLKHATRIIDEVVSKFLDDLGNAKSHLMSLYSACSSEVPPGPVDQKFQSIVIGCALEDQKKIKRRLETLLRNIDNSDKAI",
|
| 40 |
+
"AVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Heat shock cognate 71 kDa protein",
|
| 45 |
+
"Nucleotide-binding domain (NBD)",
|
| 46 |
+
"Interaction with BAG1",
|
| 47 |
+
"BAG family molecular chaperone regulator 2",
|
| 48 |
+
"BAG"
|
| 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": 14320,
|
| 60 |
+
"SYSTRES": 918,
|
| 61 |
+
"PROTATS": 14320,
|
| 62 |
+
"PROTRES": 918,
|
| 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 C interaction",
|
| 77 |
+
"agent_1": "chain A",
|
| 78 |
+
"agent_2": "chain C",
|
| 79 |
+
"selection_1": "chain A",
|
| 80 |
+
"selection_2": "chain B",
|
| 81 |
+
"type": "protein-protein"
|
| 82 |
+
},
|
| 83 |
+
{
|
| 84 |
+
"name": "chain A-chain D interaction",
|
| 85 |
+
"agent_1": "chain A",
|
| 86 |
+
"agent_2": "chain D",
|
| 87 |
+
"selection_1": "chain A",
|
| 88 |
+
"selection_2": "chain C",
|
| 89 |
+
"type": "protein-protein"
|
| 90 |
+
},
|
| 91 |
+
{
|
| 92 |
+
"name": "chain B-chain C interaction",
|
| 93 |
+
"agent_1": "chain B",
|
| 94 |
+
"agent_2": "chain C",
|
| 95 |
+
"selection_1": "chain A",
|
| 96 |
+
"selection_2": "chain D",
|
| 97 |
+
"type": "protein-protein"
|
| 98 |
+
},
|
| 99 |
+
{
|
| 100 |
+
"name": "chain B-chain D interaction",
|
| 101 |
+
"agent_1": "chain B",
|
| 102 |
+
"agent_2": "chain D",
|
| 103 |
+
"selection_1": "chain B",
|
| 104 |
+
"selection_2": "chain C",
|
| 105 |
+
"type": "protein-protein"
|
| 106 |
+
},
|
| 107 |
+
{
|
| 108 |
+
"name": "chain C-chain D interaction",
|
| 109 |
+
"agent_1": "chain C",
|
| 110 |
+
"agent_2": "chain D",
|
| 111 |
+
"selection_1": "chain B",
|
| 112 |
+
"selection_2": "chain D",
|
| 113 |
+
"type": "protein-protein"
|
| 114 |
+
}
|
| 115 |
+
],
|
| 116 |
+
"PBC_SELECTION": null,
|
| 117 |
+
"CHAINNAMES": null,
|
| 118 |
+
"MEMBRANES": null,
|
| 119 |
+
"CUSTOMS": null,
|
| 120 |
+
"ORIENTATION": null,
|
| 121 |
+
"PTM": [],
|
| 122 |
+
"MULTIMERIC": null,
|
| 123 |
+
"COLLECTIONS": "dynarepo",
|
| 124 |
+
"WARNINGS": [],
|
| 125 |
+
"BOXSIZEX": 14.6656,
|
| 126 |
+
"BOXSIZEY": 14.6656,
|
| 127 |
+
"BOXSIZEZ": 10.3637,
|
| 128 |
+
"mdName": "replica 1",
|
| 129 |
+
"mdAtoms": 14320,
|
| 130 |
+
"mdFrames": 5001
|
| 131 |
+
},
|
| 132 |
+
"mds": [
|
| 133 |
+
"replica 1",
|
| 134 |
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|
A004M/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A004S/project.json
ADDED
|
@@ -0,0 +1,185 @@
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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|
| 6 |
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| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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|
| 10 |
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|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
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| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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| 23 |
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| 24 |
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"3EJH"
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| 27 |
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|
| 29 |
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| 30 |
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| 31 |
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| 32 |
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| 33 |
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| 39 |
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| 40 |
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| 41 |
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| 42 |
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| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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],
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| 50 |
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|
| 53 |
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| 54 |
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"FF": [
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| 55 |
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|
| 56 |
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],
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| 57 |
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"WAT": "TIP3P",
|
| 58 |
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| 59 |
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| 72 |
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| 73 |
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"INTERACTIONS": [
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{
|
| 76 |
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"name": "chain A-chain B interaction",
|
| 77 |
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"agent_1": "chain A",
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| 78 |
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|
| 79 |
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"selection_1": "chain A",
|
| 80 |
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|
| 81 |
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"type": "protein-protein"
|
| 82 |
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}
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| 83 |
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],
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| 85 |
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},
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"mds": [
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|
| 103 |
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|
| 104 |
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"clusters-01",
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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|
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"identifier": "A004S"
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}
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A004S/records.jsonl
ADDED
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|
A0050/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0050",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3GJ8",
|
| 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 |
+
"3GJ8"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P62826",
|
| 31 |
+
"P49791"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTAL",
|
| 38 |
+
"GSWDXEVXLVQNKADSTKXIAXESAKP"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"GTP-binding nuclear protein Ran",
|
| 43 |
+
"Essential for GTP hydrolysis",
|
| 44 |
+
"Nuclear pore complex protein Nup153",
|
| 45 |
+
"29 X 2 AA repeats of F-G"
|
| 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": 3669,
|
| 57 |
+
"SYSTRES": 231,
|
| 58 |
+
"PROTATS": 3669,
|
| 59 |
+
"PROTRES": 231,
|
| 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,
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|
| 83 |
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|
| 84 |
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| 85 |
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| 86 |
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|
| 87 |
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| 89 |
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|
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|
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|
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|
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| 107 |
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"pca_trajectory_01.bin",
|
| 108 |
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|
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| 110 |
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| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
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"pca_trajectory_07.bin",
|
| 114 |
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"structure.pdb",
|
| 115 |
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|
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|
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|
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| 126 |
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|
| 127 |
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|
| 128 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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"clusters_01_screenshot_03.jpg",
|
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|
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|
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|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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"clusters_01_screenshot_10.jpg",
|
| 147 |
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|
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"clusters_01_screenshot_12.jpg",
|
| 149 |
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"clusters_01_screenshot_13.jpg",
|
| 150 |
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"clusters_01_screenshot_14.jpg",
|
| 151 |
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|
| 152 |
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"clusters_01_screenshot_16.jpg",
|
| 153 |
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"clusters_01_screenshot_17.jpg",
|
| 154 |
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"clusters_01_screenshot_18.jpg",
|
| 155 |
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"clusters_01_screenshot_19.jpg",
|
| 156 |
+
"pocket_01.pdb",
|
| 157 |
+
"pocket_02.pdb",
|
| 158 |
+
"pocket_03.pdb",
|
| 159 |
+
"pocket_04.pdb",
|
| 160 |
+
"pocket_05.pdb",
|
| 161 |
+
"pocket_06.pdb",
|
| 162 |
+
"pocket_07.pdb",
|
| 163 |
+
"pocket_08.pdb",
|
| 164 |
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"pocket_09.pdb",
|
| 165 |
+
"pocket_10.pdb"
|
| 166 |
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],
|
| 167 |
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"analyses": [
|
| 168 |
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"clusters",
|
| 169 |
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"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 |
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"tmscores"
|
| 184 |
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|
| 185 |
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|
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|
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"creationDate": "2025-06-05T00:55:21.000Z",
|
| 190 |
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"identifier": "A0050"
|
| 191 |
+
}
|
A0050/records.jsonl
ADDED
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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"Omid Mokhtari",
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| 9 |
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"Hamed Khakzad",
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| 10 |
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| 11 |
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| 12 |
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 24 |
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| 45 |
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| 46 |
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| 47 |
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| 48 |
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| 49 |
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| 53 |
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| 77 |
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| 83 |
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| 84 |
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| 291 |
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"clusters_06_screenshot_09.jpg",
|
| 292 |
+
"clusters_06_screenshot_10.jpg",
|
| 293 |
+
"clusters_06_screenshot_11.jpg",
|
| 294 |
+
"clusters_06_screenshot_12.jpg",
|
| 295 |
+
"clusters_06_screenshot_13.jpg",
|
| 296 |
+
"clusters_06_screenshot_14.jpg",
|
| 297 |
+
"clusters_06_screenshot_15.jpg",
|
| 298 |
+
"clusters_06_screenshot_16.jpg",
|
| 299 |
+
"clusters_06_screenshot_17.jpg",
|
| 300 |
+
"clusters_06_screenshot_18.jpg",
|
| 301 |
+
"clusters_06_screenshot_19.jpg",
|
| 302 |
+
"pocket_01.pdb",
|
| 303 |
+
"pocket_02.pdb",
|
| 304 |
+
"pocket_03.pdb",
|
| 305 |
+
"pocket_04.pdb",
|
| 306 |
+
"pocket_05.pdb",
|
| 307 |
+
"pocket_06.pdb",
|
| 308 |
+
"pocket_07.pdb",
|
| 309 |
+
"pocket_08.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": "6840ecbfd7b6ed7c446d96e7",
|
| 338 |
+
"creationDate": "2025-06-05T01:02:55.000Z",
|
| 339 |
+
"identifier": "A0051"
|
| 340 |
+
}
|
A0051/records.jsonl
ADDED
|
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|
|