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  1. A000A/project.json +189 -0
  2. A000A/records.jsonl +3 -0
  3. A000H/project.json +194 -0
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  40. A002R/project.json +184 -0
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  44. A0033/project.json +188 -0
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A000A/project.json ADDED
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1
+ {
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+ "accession": "A000A",
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+ "published": true,
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+ "metadata": {
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+ "NAME": "Dynarepo 1AK4",
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+ "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
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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": "[email protected]",
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+ "PROGRAM": "GROMACS",
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+ "VERSION": "2024.2",
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+ "TYPE": "trajectory",
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+ "METHOD": "Classical MD",
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+ "LICENSE": "Apache License 2.0",
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+ "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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+ "CITATION": "DynaRepo citation",
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+ "THANKS": "DynaRepo Acknowledgements",
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+ "LINKS": null,
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+ "PDBIDS": [
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+ "1AK4"
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+ ],
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+ "FORCED_REFERENCES": null,
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+ "REFERENCES": [
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+ "P62937",
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+ ],
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+ "NUCLSEQ": [],
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+ "DOMAINS": [
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+ "Peptidyl-prolyl cis-trans isomerase A",
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+ "Peptidyl-prolyl cis-trans isomerase A, N-terminally processed",
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+ "PPIase cyclophilin-type",
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+ "Gag-Pol polyprotein",
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+ "Capsid protein p24",
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+ "Interaction with human PPIA/CYPA and NUP153",
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+ "Dimerization/Multimerization of capsid protein p24",
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+ "Cleavage; by viral protease",
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+ "Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA"
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+ ],
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+ "TIMESTEP": 2,
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+ "TEMP": 310,
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+ "ENSEMBLE": "NPT",
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+ "FF": [
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+ "CHARMM36m"
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+ "name": "protein-protein interaction B-A",
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+ "agent_1": "protein B",
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+ "selection_1": "chain A",
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+ "type": "protein-protein"
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+ "pocket_01.pdb"
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+ ],
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+ "clusters-01",
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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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+ "identifier": "A000A"
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+ }
A000A/records.jsonl ADDED
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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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+ "Delta team, Inria center at the University of Lorraine"
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+ ],
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+ "CONTACT": "[email protected]",
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+ "METHOD": "Classical MD",
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+ "LICENSE": "Apache License 2.0",
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+ "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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+ "CITATION": "DynaRepo citation",
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+ "THANKS": "DynaRepo Acknowledgements",
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+ "LINKS": null,
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+ "PDBIDS": [
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+ "1GO4"
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1
+ {
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+ "accession": "A002P",
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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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+ "PROGRAM": "GROMACS",
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+ "2BP7"
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+ "rmsd-pairwise",
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+ "rmsd-perres",
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+ "rmsds",
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