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  1. A000C/project.json +201 -0
  2. A000C/records.jsonl +3 -0
  3. A000E/project.json +184 -0
  4. A000E/records.jsonl +3 -0
  5. A000F/project.json +202 -0
  6. A000F/records.jsonl +3 -0
  7. A000K/project.json +198 -0
  8. A000K/records.jsonl +3 -0
  9. A000L/project.json +183 -0
  10. A000L/records.jsonl +3 -0
  11. A000P/project.json +188 -0
  12. A000P/records.jsonl +3 -0
  13. A000R/project.json +190 -0
  14. A000R/records.jsonl +3 -0
  15. A000S/project.json +304 -0
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  17. A001B/project.json +254 -0
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  19. A001G/project.json +194 -0
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  21. A001Q/project.json +191 -0
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  27. A002C/project.json +340 -0
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  29. A002J/project.json +265 -0
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  35. A002Z/project.json +198 -0
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  39. A0037/project.json +193 -0
  40. A0037/records.jsonl +3 -0
  41. A003R/project.json +183 -0
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  43. A003U/project.json +197 -0
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  45. A0043/project.json +256 -0
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  50. A004A/records.jsonl +3 -0
A000C/project.json ADDED
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1
+ {
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+ "accession": "A000C",
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+ "published": true,
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+ "metadata": {
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+ "NAME": "Dynarepo 1AVA",
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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": "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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+ "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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+ "1AVA"
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+ ],
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+ "REFERENCES": [
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+ "P04063",
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+ "P07596"
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+ ],
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+ "NUCLSEQ": [],
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+ "DOMAINS": [
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+ "Alpha-amylase type B isozyme",
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+ "Transition state stabilizer",
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+ "Alpha-amylase/subtilisin inhibitor",
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+ "Disordered",
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+ "Reactive bond"
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+ ],
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+ "FRAMESTEP": 0.1,
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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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+ ],
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+ "WAT": "TIP3P",
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+ "BOXTYPE": "Dodecahedron",
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+ "SYSTATS": 8969,
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+ {
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+ "name": "protein-protein interaction A-B",
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+ "agent_1": "protein A",
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+ "agent_2": "protein B",
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+ "selection_1": "chain A",
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+ "selection_2": "chain B",
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+ "type": "protein-protein"
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+ }
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+ ],
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+ "replica 2",
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+ "pocket_01.pdb",
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+ "pocket_08.pdb",
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+ "pocket_09.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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+ "creationDate": "2025-06-03T13:55:56.000Z",
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+ "identifier": "A000C"
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+ }
A000C/records.jsonl ADDED
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A0023/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
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