A000C/project.json

{
  "accession": "A000C",
  "published": true,
  "metadata": {
    "NAME": "Dynarepo 1AVA",
    "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": [
      "1AVA"
    ],
    "FORCED_REFERENCES": null,
    "REFERENCES": [
      "P04063",
      "P07596"
    ],
    "INPUT_LIGANDS": null,
    "LIGANDS": [],
    "LIGANDNAMES": null,
    "PROTSEQ": [
      "QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI",
      "ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA"
    ],
    "NUCLSEQ": [],
    "DOMAINS": [
      "Alpha-amylase type B isozyme",
      "Transition state stabilizer",
      "Alpha-amylase/subtilisin inhibitor",
      "Disordered",
      "Reactive bond"
    ],
    "FRAMESTEP": 0.1,
    "TIMESTEP": 2,
    "TEMP": 310,
    "ENSEMBLE": "NPT",
    "FF": [
      "CHARMM36m"
    ],
    "WAT": "TIP3P",
    "BOXTYPE": "Dodecahedron",
    "SYSTATS": 8969,
    "SYSTRES": 584,
    "PROTATS": 8969,
    "PROTRES": 584,
    "NUCLATS": 0,
    "NUCLRES": 0,
    "LIPIATS": 0,
    "LIPIRES": 0,
    "CARBATS": 0,
    "CARBRES": 0,
    "SOLVATS": 0,
    "SOLVRES": 0,
    "COUNCAT": 0,
    "COUNANI": 0,
    "COUNION": 0,
    "INTERACTIONS": [
      {
        "name": "protein-protein interaction A-B",
        "agent_1": "protein A",
        "agent_2": "protein B",
        "selection_1": "chain A",
        "selection_2": "chain B",
        "type": "protein-protein"
      }
    ],
    "PBC_SELECTION": null,
    "CHAINNAMES": null,
    "MEMBRANES": null,
    "CUSTOMS": null,
    "ORIENTATION": null,
    "PTM": [],
    "MULTIMERIC": null,
    "COLLECTIONS": "dynarepo",
    "WARNINGS": [],
    "BOXSIZEX": 10.5469,
    "BOXSIZEY": 10.5469,
    "BOXSIZEZ": 7.48757,
    "mdName": "replica 1",
    "mdAtoms": 8969,
    "mdFrames": 5001
  },
  "mds": [
    "replica 1",
    "replica 2",
    "replica 3"
  ],
  "mdref": 0,
  "files": [
    "topology.tpr",
    "screenshot.jpg",
    "trajectory.bin",
    "pca_trajectory_01.bin",
    "pca_trajectory_02.bin",
    "pca_trajectory_03.bin",
    "pca_trajectory_04.bin",
    "pca_trajectory_05.bin",
    "pca_trajectory_06.bin",
    "pca_trajectory_07.bin",
    "pca_trajectory_08.bin",
    "pca_trajectory_09.bin",
    "pca_trajectory_10.bin",
    "pca_trajectory_11.bin",
    "pca_trajectory_12.bin",
    "pca_trajectory_13.bin",
    "pca_trajectory_14.bin",
    "structure.pdb",
    "trajectory.xtc",
    "clusters_00_screenshot_00.jpg",
    "clusters_00_screenshot_01.jpg",
    "clusters_00_screenshot_02.jpg",
    "clusters_00_screenshot_03.jpg",
    "clusters_00_screenshot_04.jpg",
    "clusters_00_screenshot_05.jpg",
    "clusters_00_screenshot_06.jpg",
    "clusters_00_screenshot_07.jpg",
    "clusters_00_screenshot_08.jpg",
    "clusters_00_screenshot_09.jpg",
    "clusters_00_screenshot_10.jpg",
    "clusters_00_screenshot_11.jpg",
    "clusters_00_screenshot_12.jpg",
    "clusters_00_screenshot_13.jpg",
    "clusters_00_screenshot_14.jpg",
    "clusters_00_screenshot_15.jpg",
    "clusters_00_screenshot_16.jpg",
    "clusters_00_screenshot_17.jpg",
    "clusters_00_screenshot_18.jpg",
    "clusters_00_screenshot_19.jpg",
    "clusters_00_screenshot_20.jpg",
    "clusters_00_screenshot_21.jpg",
    "clusters_01_screenshot_00.jpg",
    "clusters_01_screenshot_01.jpg",
    "clusters_01_screenshot_02.jpg",
    "clusters_01_screenshot_03.jpg",
    "clusters_01_screenshot_04.jpg",
    "clusters_01_screenshot_05.jpg",
    "clusters_01_screenshot_06.jpg",
    "clusters_01_screenshot_07.jpg",
    "clusters_01_screenshot_08.jpg",
    "clusters_01_screenshot_09.jpg",
    "clusters_01_screenshot_10.jpg",
    "clusters_01_screenshot_11.jpg",
    "clusters_01_screenshot_12.jpg",
    "clusters_01_screenshot_13.jpg",
    "clusters_01_screenshot_14.jpg",
    "clusters_01_screenshot_15.jpg",
    "clusters_01_screenshot_16.jpg",
    "clusters_01_screenshot_17.jpg",
    "clusters_01_screenshot_18.jpg",
    "clusters_01_screenshot_19.jpg",
    "pocket_01.pdb",
    "pocket_02.pdb",
    "pocket_03.pdb",
    "pocket_04.pdb",
    "pocket_05.pdb",
    "pocket_06.pdb",
    "pocket_07.pdb",
    "pocket_08.pdb",
    "pocket_09.pdb",
    "pocket_10.pdb"
  ],
  "analyses": [
    "clusters",
    "clusters-00",
    "clusters-01",
    "dist-perres",
    "energies",
    "fluctuation",
    "hbonds",
    "interactions",
    "pca",
    "pockets",
    "rgyr",
    "rmsd-pairwise",
    "rmsd-perres",
    "rmsds",
    "sasa",
    "tmscores"
  ],
  "mdIndex": 0,
  "mdNumber": 1,
  "refframe": 0,
  "internalId": "683efeec19836add5539898f",
  "creationDate": "2025-06-03T13:55:56.000Z",
  "identifier": "A000C"
}