| { | |
| "accession": "A0017", | |
| "published": true, | |
| "metadata": { | |
| "NAME": "Dynarepo 1K5D", | |
| "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": [ | |
| "1K5D" | |
| ], | |
| "FORCED_REFERENCES": null, | |
| "REFERENCES": [ | |
| "P62826", | |
| "P43487", | |
| "P41391" | |
| ], | |
| "INPUT_LIGANDS": null, | |
| "LIGANDS": [], | |
| "LIGANDNAMES": null, | |
| "PROTSEQ": [ | |
| "NHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDLPEWKERGTGDVKLLKHKEKGAIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADECPKPELLAIRFLNAENAQKFKTKFEECRKEIEEREK", | |
| "QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDED", | |
| "ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEE" | |
| ], | |
| "NUCLSEQ": [], | |
| "DOMAINS": [ | |
| "GTP-binding nuclear protein Ran", | |
| "Interaction with RANBP1", | |
| "Essential for GTP hydrolysis", | |
| "Ran-specific GTPase-activating protein", | |
| "RanBD1", | |
| "Disordered", | |
| "Ran GTPase-activating protein 1", | |
| "Disordered", | |
| "Critical residue for GTP hydrolysis" | |
| ], | |
| "FRAMESTEP": 0.1, | |
| "TIMESTEP": 2, | |
| "TEMP": 310, | |
| "ENSEMBLE": "NPT", | |
| "FF": [ | |
| "CHARMM36m" | |
| ], | |
| "WAT": "TIP3P", | |
| "BOXTYPE": "Dodecahedron", | |
| "SYSTATS": 11179, | |
| "SYSTRES": 696, | |
| "PROTATS": 11179, | |
| "PROTRES": 696, | |
| "NUCLATS": 0, | |
| "NUCLRES": 0, | |
| "LIPIATS": 0, | |
| "LIPIRES": 0, | |
| "CARBATS": 0, | |
| "CARBRES": 0, | |
| "SOLVATS": 0, | |
| "SOLVRES": 0, | |
| "COUNCAT": 0, | |
| "COUNANI": 0, | |
| "COUNION": 0, | |
| "INTERACTIONS": [ | |
| { | |
| "name": "chain A-chain B interaction", | |
| "agent_1": "chain A", | |
| "agent_2": "chain B", | |
| "selection_1": "chain A", | |
| "selection_2": "chain B", | |
| "type": "protein-protein" | |
| }, | |
| { | |
| "name": "chain A-chain C interaction", | |
| "agent_1": "chain A", | |
| "agent_2": "chain C", | |
| "selection_1": "chain A", | |
| "selection_2": "chain C", | |
| "type": "protein-protein" | |
| }, | |
| { | |
| "name": "chain B-chain C interaction", | |
| "agent_1": "chain B", | |
| "agent_2": "chain C", | |
| "selection_1": "chain B", | |
| "selection_2": "chain C", | |
| "type": "protein-protein" | |
| } | |
| ], | |
| "PBC_SELECTION": null, | |
| "CHAINNAMES": null, | |
| "MEMBRANES": null, | |
| "CUSTOMS": null, | |
| "ORIENTATION": null, | |
| "PTM": [], | |
| "MULTIMERIC": null, | |
| "COLLECTIONS": "dynarepo", | |
| "WARNINGS": [], | |
| "BOXSIZEX": 12.7499, | |
| "BOXSIZEY": 12.7499, | |
| "BOXSIZEZ": 9.02727, | |
| "mdName": "replica 1", | |
| "mdAtoms": 11179, | |
| "mdFrames": 5001 | |
| }, | |
| "mds": [ | |
| "replica 1", | |
| "replica 2", | |
| "replica 3" | |
| ], | |
| "mdref": 0, | |
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| "analyses": [ | |
| "clusters", | |
| "clusters-00", | |
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| "energies", | |
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| "internalId": "683f431894c5b2a431903d8d", | |
| "creationDate": "2025-06-03T18:46:48.000Z", | |
| "identifier": "A0017" | |
| } |