| { | |
| "accession": "A000S", | |
| "published": true, | |
| "metadata": { | |
| "NAME": "Dynarepo 1FLT", | |
| "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": [ | |
| "1FLT" | |
| ], | |
| "FORCED_REFERENCES": null, | |
| "REFERENCES": [ | |
| "P15692", | |
| "P17948" | |
| ], | |
| "INPUT_LIGANDS": null, | |
| "LIGANDS": [], | |
| "LIGANDNAMES": null, | |
| "PROTSEQ": [ | |
| "GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQ", | |
| "EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK", | |
| "GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT", | |
| "HEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD" | |
| ], | |
| "NUCLSEQ": [], | |
| "DOMAINS": [ | |
| "Vascular endothelial growth factor A, long form", | |
| "Disordered", | |
| "Vascular endothelial growth factor receptor 1", | |
| "Ig-like C2-type 2" | |
| ], | |
| "FRAMESTEP": 0.1, | |
| "TIMESTEP": 2, | |
| "TEMP": 310, | |
| "ENSEMBLE": "NPT", | |
| "FF": [ | |
| "CHARMM36m" | |
| ], | |
| "WAT": "TIP3P", | |
| "BOXTYPE": "Dodecahedron", | |
| "SYSTATS": 6155, | |
| "SYSTRES": 382, | |
| "PROTATS": 6155, | |
| "PROTRES": 382, | |
| "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-D", | |
| "agent_1": "protein A", | |
| "agent_2": "protein D", | |
| "selection_1": "chain A", | |
| "selection_2": "chain B", | |
| "type": "protein-protein" | |
| }, | |
| { | |
| "name": "protein-protein interaction A-B", | |
| "agent_1": "protein A", | |
| "agent_2": "protein B", | |
| "selection_1": "chain A", | |
| "selection_2": "chain C", | |
| "type": "protein-protein" | |
| }, | |
| { | |
| "name": "protein-protein interaction A-C", | |
| "agent_1": "protein A", | |
| "agent_2": "protein C", | |
| "selection_1": "chain A", | |
| "selection_2": "chain D", | |
| "type": "protein-protein" | |
| }, | |
| { | |
| "name": "protein-protein interaction D-B", | |
| "agent_1": "protein D", | |
| "agent_2": "protein B", | |
| "selection_1": "chain B", | |
| "selection_2": "chain C", | |
| "type": "protein-protein" | |
| }, | |
| { | |
| "name": "protein-protein interaction B-C", | |
| "agent_1": "protein B", | |
| "agent_2": "protein C", | |
| "selection_1": "chain B", | |
| "selection_2": "chain D", | |
| "type": "protein-protein" | |
| } | |
| ], | |
| "PBC_SELECTION": null, | |
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| "CUSTOMS": null, | |
| "ORIENTATION": null, | |
| "PTM": [], | |
| "MULTIMERIC": null, | |
| "COLLECTIONS": "dynarepo", | |
| "WARNINGS": [], | |
| "BOXSIZEX": 12.2762, | |
| "BOXSIZEY": 12.2762, | |
| "BOXSIZEZ": 8.68755, | |
| "mdName": "replica 1", | |
| "mdAtoms": 6155, | |
| "mdFrames": 5001 | |
| }, | |
| "mds": [ | |
| "replica 1", | |
| "replica 2", | |
| "replica 3" | |
| ], | |
| "mdref": 0, | |
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