| { |
| "accession": "A0013", |
| "published": true, |
| "metadata": { |
| "NAME": "Dynarepo 1J7D", |
| "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": [ |
| "1J7D" |
| ], |
| "FORCED_REFERENCES": null, |
| "REFERENCES": [ |
| "Q15819", |
| "P61088" |
| ], |
| "INPUT_LIGANDS": null, |
| "LIGANDS": [], |
| "LIGANDNAMES": null, |
| "PROTSEQ": [ |
| "AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN", |
| "GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN" |
| ], |
| "NUCLSEQ": [], |
| "DOMAINS": [ |
| "Ubiquitin-conjugating enzyme E2 variant 2", |
| "UBC core", |
| "Ubiquitin-conjugating enzyme E2 N", |
| "UBC core" |
| ], |
| "FRAMESTEP": 0.1, |
| "TIMESTEP": 2, |
| "TEMP": 310, |
| "ENSEMBLE": "NPT", |
| "FF": [ |
| "CHARMM36m" |
| ], |
| "WAT": "TIP3P", |
| "BOXTYPE": "Dodecahedron", |
| "SYSTATS": 4609, |
| "SYSTRES": 289, |
| "PROTATS": 4609, |
| "PROTRES": 289, |
| "NUCLATS": 0, |
| "NUCLRES": 0, |
| "LIPIATS": 0, |
| "LIPIRES": 0, |
| "CARBATS": 0, |
| "CARBRES": 0, |
| "SOLVATS": 0, |
| "SOLVRES": 0, |
| "COUNCAT": 0, |
| "COUNANI": 0, |
| "COUNION": 0, |
| "INTERACTIONS": [ |
| { |
| "name": "protein-protein interaction B-A", |
| "agent_1": "protein B", |
| "agent_2": "protein A", |
| "selection_1": "chain A", |
| "selection_2": "chain B", |
| "type": "protein-protein" |
| } |
| ], |
| "PBC_SELECTION": null, |
| "CHAINNAMES": null, |
| "MEMBRANES": null, |
| "CUSTOMS": null, |
| "ORIENTATION": null, |
| "PTM": [], |
| "MULTIMERIC": null, |
| "COLLECTIONS": "dynarepo", |
| "WARNINGS": [], |
| "BOXSIZEX": 9.80096, |
| "BOXSIZEY": 9.80096, |
| "BOXSIZEZ": 6.94512, |
| "mdName": "replica 1", |
| "mdAtoms": 4609, |
| "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", |
| "pca_trajectory_15.bin", |
| "pca_trajectory_16.bin", |
| "pca_trajectory_17.bin", |
| "pca_trajectory_18.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_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", |
| "pocket_01.pdb", |
| "pocket_02.pdb", |
| "pocket_03.pdb", |
| "pocket_04.pdb", |
| "pocket_05.pdb", |
| "pocket_06.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": "683f39723fbce78ed0de2e0d", |
| "creationDate": "2025-06-03T18:05:38.000Z", |
| "identifier": "A0013" |
| } |
