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data/files/A000Z/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000Z",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1I5K",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1I5K"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00747",
|
| 31 |
+
"P49054"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EKLTADAELQRLKNERHEEAELERLK",
|
| 38 |
+
"EECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRC",
|
| 39 |
+
"ECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRC"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Plasminogen",
|
| 44 |
+
"Plasmin heavy chain A",
|
| 45 |
+
"Angiostatin",
|
| 46 |
+
"Plasmin heavy chain A, short form",
|
| 47 |
+
"Kringle 2",
|
| 48 |
+
"Plasminogen-binding group A streptococcal M-like protein PAM",
|
| 49 |
+
"Able to bind plasminogen",
|
| 50 |
+
"2 X approximate tandem repeats, type a",
|
| 51 |
+
"Disordered"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
+
"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 3391,
|
| 63 |
+
"SYSTRES": 211,
|
| 64 |
+
"PROTATS": 3391,
|
| 65 |
+
"PROTRES": 211,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "protein-protein interaction C-B",
|
| 80 |
+
"agent_1": "protein C",
|
| 81 |
+
"agent_2": "protein B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
+
"name": "protein-protein interaction C-D",
|
| 88 |
+
"agent_1": "protein C",
|
| 89 |
+
"agent_2": "protein D",
|
| 90 |
+
"selection_1": "chain A",
|
| 91 |
+
"selection_2": "chain C",
|
| 92 |
+
"type": "protein-protein"
|
| 93 |
+
},
|
| 94 |
+
{
|
| 95 |
+
"name": "protein-protein interaction C-A",
|
| 96 |
+
"agent_1": "protein C",
|
| 97 |
+
"agent_2": "protein A",
|
| 98 |
+
"selection_1": "chain A",
|
| 99 |
+
"selection_2": "chain D",
|
| 100 |
+
"type": "protein-protein"
|
| 101 |
+
},
|
| 102 |
+
{
|
| 103 |
+
"name": "protein-protein interaction B-D",
|
| 104 |
+
"agent_1": "protein B",
|
| 105 |
+
"agent_2": "protein D",
|
| 106 |
+
"selection_1": "chain B",
|
| 107 |
+
"selection_2": "chain C",
|
| 108 |
+
"type": "protein-protein"
|
| 109 |
+
},
|
| 110 |
+
{
|
| 111 |
+
"name": "protein-protein interaction B-A",
|
| 112 |
+
"agent_1": "protein B",
|
| 113 |
+
"agent_2": "protein A",
|
| 114 |
+
"selection_1": "chain B",
|
| 115 |
+
"selection_2": "chain D",
|
| 116 |
+
"type": "protein-protein"
|
| 117 |
+
},
|
| 118 |
+
{
|
| 119 |
+
"name": "protein-protein interaction D-A",
|
| 120 |
+
"agent_1": "protein D",
|
| 121 |
+
"agent_2": "protein A",
|
| 122 |
+
"selection_1": "chain C",
|
| 123 |
+
"selection_2": "chain D",
|
| 124 |
+
"type": "protein-protein"
|
| 125 |
+
}
|
| 126 |
+
],
|
| 127 |
+
"PBC_SELECTION": null,
|
| 128 |
+
"CHAINNAMES": null,
|
| 129 |
+
"MEMBRANES": null,
|
| 130 |
+
"CUSTOMS": null,
|
| 131 |
+
"ORIENTATION": null,
|
| 132 |
+
"PTM": [],
|
| 133 |
+
"MULTIMERIC": null,
|
| 134 |
+
"COLLECTIONS": "dynarepo",
|
| 135 |
+
"WARNINGS": [],
|
| 136 |
+
"BOXSIZEX": 9.13395,
|
| 137 |
+
"BOXSIZEY": 9.13395,
|
| 138 |
+
"BOXSIZEZ": 6.42953,
|
| 139 |
+
"mdName": "replica 1",
|
| 140 |
+
"mdAtoms": 3391,
|
| 141 |
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"mdFrames": 5001
|
| 142 |
+
},
|
| 143 |
+
"mds": [
|
| 144 |
+
"replica 1",
|
| 145 |
+
"replica 2",
|
| 146 |
+
"replica 3"
|
| 147 |
+
],
|
| 148 |
+
"mdref": 0,
|
| 149 |
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"files": [
|
| 150 |
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"topology.tpr",
|
| 151 |
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"screenshot.jpg",
|
| 152 |
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"trajectory.bin",
|
| 153 |
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"pca_trajectory_01.bin",
|
| 154 |
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"pca_trajectory_02.bin",
|
| 155 |
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"pca_trajectory_03.bin",
|
| 156 |
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"structure.pdb",
|
| 157 |
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"trajectory.xtc",
|
| 158 |
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"clusters_00_screenshot_00.jpg",
|
| 159 |
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| 160 |
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| 168 |
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| 169 |
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data/files/A000Z/records.jsonl
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| 1 |
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{
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| 2 |
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| 6 |
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| 9 |
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| 10 |
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| 11 |
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"pocket_01.pdb",
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"fluctuation",
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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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data/files/A0010/records.jsonl
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| 1 |
+
{
|
| 2 |
+
"accession": "A0011",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1IB1",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
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| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
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| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
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| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
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| 20 |
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"LICENSE": "Apache License 2.0",
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| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
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| 24 |
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| 25 |
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| 26 |
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"1IB1"
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| 27 |
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],
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| 28 |
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| 29 |
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"REFERENCES": [
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| 30 |
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"P63104",
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| 31 |
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"Q29495"
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| 32 |
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],
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| 33 |
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"INPUT_LIGANDS": null,
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| 34 |
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"LIGANDS": [],
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| 35 |
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| 36 |
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| 37 |
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"SGIPGSPGRQRRHTLPANEFRCLTPEDAAGVFEIEREAFISVSGNCPLNLDEVQHFLTLCPELSLGWFVEGRLVAFIIGSLWDEERLTQESLALHRPRGHSAHLHALAVHRSFRQQGKGSVLLWRYLHHVGAQPAVRRAVLMCEDALVPFYQRFGFHPAGPCAIVVGSLTFTEMHCSLR",
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| 39 |
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],
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| 40 |
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|
| 41 |
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"DOMAINS": [
|
| 42 |
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"14-3-3 protein zeta/delta",
|
| 43 |
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"Interaction with phosphoserine on interacting protein",
|
| 44 |
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"Serotonin N-acetyltransferase",
|
| 45 |
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"N-acetyltransferase",
|
| 46 |
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"Disordered",
|
| 47 |
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"YWHAZ-binding",
|
| 48 |
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"Important for the catalytic mechanism; involved in substrate deprotonation"
|
| 49 |
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],
|
| 50 |
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| 51 |
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|
| 52 |
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| 53 |
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| 54 |
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| 55 |
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"CHARMM36m"
|
| 56 |
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],
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| 57 |
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"WAT": "TIP3P",
|
| 58 |
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"BOXTYPE": "Dodecahedron",
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| 59 |
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|
| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 64 |
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|
| 65 |
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| 66 |
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| 67 |
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| 68 |
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| 69 |
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| 70 |
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| 71 |
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| 72 |
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| 73 |
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| 74 |
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|
| 75 |
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{
|
| 76 |
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"name": "protein-protein interaction D-C",
|
| 77 |
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"agent_1": "protein D",
|
| 78 |
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|
| 79 |
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"selection_1": "chain A",
|
| 80 |
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|
| 81 |
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"type": "protein-protein"
|
| 82 |
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},
|
| 83 |
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{
|
| 84 |
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"name": "protein-protein interaction D-A",
|
| 85 |
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| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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"type": "protein-protein"
|
| 90 |
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},
|
| 91 |
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{
|
| 92 |
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"name": "protein-protein interaction D-B",
|
| 93 |
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| 94 |
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| 95 |
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| 96 |
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|
| 97 |
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"type": "protein-protein"
|
| 98 |
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},
|
| 99 |
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{
|
| 100 |
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"name": "protein-protein interaction C-A",
|
| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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"type": "protein-protein"
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| 106 |
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| 107 |
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{
|
| 108 |
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"name": "protein-protein interaction C-B",
|
| 109 |
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| 110 |
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| 111 |
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| 112 |
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|
| 113 |
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"type": "protein-protein"
|
| 114 |
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},
|
| 115 |
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{
|
| 116 |
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"name": "protein-protein interaction A-B",
|
| 117 |
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|
| 118 |
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|
| 119 |
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|
| 120 |
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|
| 121 |
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"type": "protein-protein"
|
| 122 |
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}
|
| 123 |
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],
|
| 124 |
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|
| 125 |
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|
| 126 |
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| 127 |
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| 128 |
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| 131 |
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| 132 |
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| 139 |
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},
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| 140 |
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| 141 |
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| 142 |
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| 143 |
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| 144 |
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| 146 |
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|
| 282 |
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"clusters_05_screenshot_16.jpg",
|
| 283 |
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"clusters_05_screenshot_17.jpg",
|
| 284 |
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"clusters_05_screenshot_18.jpg",
|
| 285 |
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"clusters_05_screenshot_19.jpg",
|
| 286 |
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"clusters_05_screenshot_20.jpg",
|
| 287 |
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"clusters_06_screenshot_00.jpg",
|
| 288 |
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"clusters_06_screenshot_01.jpg",
|
| 289 |
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"clusters_06_screenshot_02.jpg",
|
| 290 |
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"clusters_06_screenshot_03.jpg",
|
| 291 |
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"clusters_06_screenshot_04.jpg",
|
| 292 |
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"clusters_06_screenshot_05.jpg",
|
| 293 |
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"clusters_06_screenshot_06.jpg",
|
| 294 |
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"clusters_06_screenshot_07.jpg",
|
| 295 |
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"clusters_06_screenshot_08.jpg",
|
| 296 |
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"clusters_06_screenshot_09.jpg",
|
| 297 |
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"clusters_06_screenshot_10.jpg",
|
| 298 |
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"clusters_06_screenshot_11.jpg",
|
| 299 |
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"clusters_06_screenshot_12.jpg",
|
| 300 |
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"clusters_06_screenshot_13.jpg",
|
| 301 |
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"clusters_06_screenshot_14.jpg",
|
| 302 |
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"clusters_06_screenshot_15.jpg",
|
| 303 |
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"clusters_06_screenshot_16.jpg",
|
| 304 |
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"clusters_06_screenshot_17.jpg",
|
| 305 |
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"clusters_06_screenshot_18.jpg",
|
| 306 |
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"clusters_06_screenshot_19.jpg",
|
| 307 |
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"pocket_01.pdb",
|
| 308 |
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"pocket_02.pdb",
|
| 309 |
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"pocket_03.pdb",
|
| 310 |
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"pocket_04.pdb",
|
| 311 |
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"pocket_05.pdb",
|
| 312 |
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"pocket_06.pdb",
|
| 313 |
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"pocket_07.pdb",
|
| 314 |
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"pocket_08.pdb",
|
| 315 |
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"pocket_09.pdb",
|
| 316 |
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"pocket_10.pdb"
|
| 317 |
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],
|
| 318 |
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"analyses": [
|
| 319 |
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"clusters",
|
| 320 |
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"clusters-00",
|
| 321 |
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"clusters-01",
|
| 322 |
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"clusters-02",
|
| 323 |
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"clusters-03",
|
| 324 |
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"clusters-04",
|
| 325 |
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"clusters-05",
|
| 326 |
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"clusters-06",
|
| 327 |
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"dist-perres",
|
| 328 |
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"energies",
|
| 329 |
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"fluctuation",
|
| 330 |
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"hbonds",
|
| 331 |
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"interactions",
|
| 332 |
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"pca",
|
| 333 |
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"pockets",
|
| 334 |
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"rgyr",
|
| 335 |
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"rmsd-pairwise",
|
| 336 |
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"rmsd-perres",
|
| 337 |
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"rmsds",
|
| 338 |
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"sasa",
|
| 339 |
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"tmscores"
|
| 340 |
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|
| 341 |
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|
| 342 |
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| 343 |
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| 344 |
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| 345 |
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"creationDate": "2025-06-03T17:51:07.000Z",
|
| 346 |
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"identifier": "A0011"
|
| 347 |
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}
|
data/files/A0011/records.jsonl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
data/files/A0012/project.json
ADDED
|
@@ -0,0 +1,263 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0012",
|
| 3 |
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"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1ICF",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"1ICF"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P07711",
|
| 31 |
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"P04233"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFEST",
|
| 38 |
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|
| 39 |
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|
| 40 |
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],
|
| 41 |
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"NUCLSEQ": [],
|
| 42 |
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"DOMAINS": [
|
| 43 |
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"Cathepsin L",
|
| 44 |
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"Cathepsin L heavy chain",
|
| 45 |
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"Cathepsin L light chain",
|
| 46 |
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"Cleavage; by autolysis",
|
| 47 |
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"HLA class II histocompatibility antigen gamma chain",
|
| 48 |
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"Thyroglobulin type-1",
|
| 49 |
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"Disordered",
|
| 50 |
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"Required for interaction with CTSL"
|
| 51 |
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],
|
| 52 |
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|
| 53 |
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"TIMESTEP": 2,
|
| 54 |
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|
| 55 |
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|
| 56 |
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"FF": [
|
| 57 |
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"CHARMM36m"
|
| 58 |
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],
|
| 59 |
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"WAT": "TIP3P",
|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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| 67 |
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| 68 |
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| 69 |
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|
| 71 |
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| 72 |
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| 73 |
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|
| 75 |
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|
| 76 |
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|
| 77 |
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{
|
| 78 |
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"name": "protein-protein interaction A-B",
|
| 79 |
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|
| 80 |
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|
| 81 |
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"selection_1": "chain A",
|
| 82 |
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"selection_2": "chain B",
|
| 83 |
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"type": "protein-protein"
|
| 84 |
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},
|
| 85 |
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{
|
| 86 |
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"name": "protein-protein interaction A-C",
|
| 87 |
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"agent_1": "protein A",
|
| 88 |
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|
| 89 |
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"selection_1": "chain A",
|
| 90 |
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|
| 91 |
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"type": "protein-protein"
|
| 92 |
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},
|
| 93 |
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{
|
| 94 |
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"name": "protein-protein interaction B-C",
|
| 95 |
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"agent_1": "protein B",
|
| 96 |
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|
| 97 |
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"selection_1": "chain B",
|
| 98 |
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"selection_2": "chain C",
|
| 99 |
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"type": "protein-protein"
|
| 100 |
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}
|
| 101 |
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],
|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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|
| 106 |
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|
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
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|
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},
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|
| 119 |
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|
| 120 |
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|
| 121 |
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|
| 122 |
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],
|
| 123 |
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|
| 124 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 185 |
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.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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| 241 |
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"clusters-02",
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"clusters-03",
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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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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f383a614edc1219cdccf7",
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"creationDate": "2025-06-03T18:00:26.000Z",
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"identifier": "A0012"
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+
}
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data/files/A0012/records.jsonl
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data/files/A0013/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0013",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1J7D",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1J7D"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q15819",
|
| 31 |
+
"P61088"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN",
|
| 38 |
+
"GVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ubiquitin-conjugating enzyme E2 variant 2",
|
| 43 |
+
"UBC core",
|
| 44 |
+
"Ubiquitin-conjugating enzyme E2 N",
|
| 45 |
+
"UBC core"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 4609,
|
| 57 |
+
"SYSTRES": 289,
|
| 58 |
+
"PROTATS": 4609,
|
| 59 |
+
"PROTRES": 289,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
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"CARBATS": 0,
|
| 65 |
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"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "protein-protein interaction B-A",
|
| 74 |
+
"agent_1": "protein B",
|
| 75 |
+
"agent_2": "protein A",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
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}
|
| 80 |
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],
|
| 81 |
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"PBC_SELECTION": null,
|
| 82 |
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|
| 83 |
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|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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"MULTIMERIC": null,
|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
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"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
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],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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| 105 |
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"screenshot.jpg",
|
| 106 |
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"trajectory.bin",
|
| 107 |
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"pca_trajectory_01.bin",
|
| 108 |
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"pca_trajectory_02.bin",
|
| 109 |
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"pca_trajectory_03.bin",
|
| 110 |
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"pca_trajectory_04.bin",
|
| 111 |
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"pca_trajectory_05.bin",
|
| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
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"pca_trajectory_07.bin",
|
| 114 |
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"pca_trajectory_08.bin",
|
| 115 |
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"pca_trajectory_09.bin",
|
| 116 |
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"pca_trajectory_10.bin",
|
| 117 |
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"pca_trajectory_11.bin",
|
| 118 |
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"pca_trajectory_12.bin",
|
| 119 |
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"pca_trajectory_13.bin",
|
| 120 |
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"pca_trajectory_14.bin",
|
| 121 |
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"pca_trajectory_15.bin",
|
| 122 |
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"pca_trajectory_16.bin",
|
| 123 |
+
"pca_trajectory_17.bin",
|
| 124 |
+
"pca_trajectory_18.bin",
|
| 125 |
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"structure.pdb",
|
| 126 |
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"trajectory.xtc",
|
| 127 |
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"clusters_00_screenshot_00.jpg",
|
| 128 |
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"clusters_00_screenshot_01.jpg",
|
| 129 |
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|
| 130 |
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"clusters_00_screenshot_03.jpg",
|
| 131 |
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|
| 132 |
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|
| 133 |
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"clusters_00_screenshot_06.jpg",
|
| 134 |
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"clusters_00_screenshot_07.jpg",
|
| 135 |
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|
| 136 |
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|
| 137 |
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"clusters_00_screenshot_10.jpg",
|
| 138 |
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"clusters_00_screenshot_11.jpg",
|
| 139 |
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"clusters_00_screenshot_12.jpg",
|
| 140 |
+
"clusters_00_screenshot_13.jpg",
|
| 141 |
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"clusters_00_screenshot_14.jpg",
|
| 142 |
+
"clusters_00_screenshot_15.jpg",
|
| 143 |
+
"clusters_00_screenshot_16.jpg",
|
| 144 |
+
"clusters_00_screenshot_17.jpg",
|
| 145 |
+
"clusters_00_screenshot_18.jpg",
|
| 146 |
+
"clusters_01_screenshot_00.jpg",
|
| 147 |
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"clusters_01_screenshot_01.jpg",
|
| 148 |
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"clusters_01_screenshot_02.jpg",
|
| 149 |
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"clusters_01_screenshot_03.jpg",
|
| 150 |
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"clusters_01_screenshot_04.jpg",
|
| 151 |
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"clusters_01_screenshot_05.jpg",
|
| 152 |
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"clusters_01_screenshot_06.jpg",
|
| 153 |
+
"clusters_01_screenshot_07.jpg",
|
| 154 |
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"clusters_01_screenshot_08.jpg",
|
| 155 |
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"clusters_01_screenshot_09.jpg",
|
| 156 |
+
"clusters_01_screenshot_10.jpg",
|
| 157 |
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"clusters_01_screenshot_11.jpg",
|
| 158 |
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"clusters_01_screenshot_12.jpg",
|
| 159 |
+
"clusters_01_screenshot_13.jpg",
|
| 160 |
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"clusters_01_screenshot_14.jpg",
|
| 161 |
+
"clusters_01_screenshot_15.jpg",
|
| 162 |
+
"clusters_01_screenshot_16.jpg",
|
| 163 |
+
"clusters_01_screenshot_17.jpg",
|
| 164 |
+
"clusters_01_screenshot_18.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb"
|
| 171 |
+
],
|
| 172 |
+
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|
| 173 |
+
"clusters",
|
| 174 |
+
"clusters-00",
|
| 175 |
+
"clusters-01",
|
| 176 |
+
"dist-perres",
|
| 177 |
+
"energies",
|
| 178 |
+
"fluctuation",
|
| 179 |
+
"hbonds",
|
| 180 |
+
"interactions",
|
| 181 |
+
"pca",
|
| 182 |
+
"pockets",
|
| 183 |
+
"rgyr",
|
| 184 |
+
"rmsd-pairwise",
|
| 185 |
+
"rmsd-perres",
|
| 186 |
+
"rmsds",
|
| 187 |
+
"sasa",
|
| 188 |
+
"tmscores"
|
| 189 |
+
],
|
| 190 |
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"mdIndex": 0,
|
| 191 |
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"mdNumber": 1,
|
| 192 |
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|
| 193 |
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"internalId": "683f39723fbce78ed0de2e0d",
|
| 194 |
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"creationDate": "2025-06-03T18:05:38.000Z",
|
| 195 |
+
"identifier": "A0013"
|
| 196 |
+
}
|
data/files/A0013/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
{"project_identifier": "A0013", "accession": "A0013", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "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"], 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data/files/A0014/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A0014",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1JIW",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"1JIW"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q03023",
|
| 31 |
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"Q03026"
|
| 32 |
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],
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| 33 |
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|
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| 36 |
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| 37 |
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| 38 |
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| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Serralysin",
|
| 43 |
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"Proteinase inhibitor"
|
| 44 |
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],
|
| 45 |
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"FRAMESTEP": 0.1,
|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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"FF": [
|
| 50 |
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"CHARMM36m"
|
| 51 |
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],
|
| 52 |
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"WAT": "TIP3P",
|
| 53 |
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| 54 |
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| 55 |
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| 56 |
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| 68 |
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|
| 69 |
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|
| 70 |
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{
|
| 71 |
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"name": "protein-protein interaction B-A",
|
| 72 |
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"agent_1": "protein B",
|
| 73 |
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|
| 74 |
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"selection_1": "chain A",
|
| 75 |
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|
| 76 |
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"type": "protein-protein"
|
| 77 |
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}
|
| 78 |
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],
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| 79 |
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| 80 |
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| 81 |
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| 84 |
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| 86 |
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| 87 |
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| 164 |
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|
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|
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|
| 170 |
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|
| 171 |
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|
| 172 |
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|
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|
| 174 |
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],
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"analyses": [
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|
| 189 |
+
"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f3b10632a89b6cbbd235c",
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"creationDate": "2025-06-03T18:12:32.000Z",
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"identifier": "A0014"
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}
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| 1 |
+
{
|
| 2 |
+
"accession": "A0015",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1JTD",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1JTD"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P62593",
|
| 31 |
+
"O87916"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"PETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW",
|
| 38 |
+
"VAATSVVAWGGNNDWGEATVPAEAQSGVDAIAGGYFHGLALKGGKVLGWGANLNGQLTMPAATQSGVDAIAAGNYHSLALKDGEVIAWGGNEDGQTTVPAEARSGVDAIAAGAWASYALKDGKVIAWGDDSDGQTTVPAEAQSGVTALDGGVYTALAVKNGGVIAWGDNYFGQTTVPAEAQSGVDDVAGGIFHSLALKDGKVIAWGDNRYKQTTVPTEALSGVSAIASGEWYSLALKNGKVIAWGSSRTAPSSVQSGVSSIEAGPNAAYALKG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Beta-lactamase TEM",
|
| 43 |
+
""
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
"SYSTATS": 7838,
|
| 55 |
+
"SYSTRES": 535,
|
| 56 |
+
"PROTATS": 7838,
|
| 57 |
+
"PROTRES": 535,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
+
"SOLVRES": 0,
|
| 66 |
+
"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "protein-protein interaction B-A",
|
| 72 |
+
"agent_1": "protein B",
|
| 73 |
+
"agent_2": "protein A",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
+
"MEMBRANES": null,
|
| 82 |
+
"CUSTOMS": null,
|
| 83 |
+
"ORIENTATION": null,
|
| 84 |
+
"PTM": [],
|
| 85 |
+
"MULTIMERIC": null,
|
| 86 |
+
"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
+
"BOXSIZEX": 10.2974,
|
| 89 |
+
"BOXSIZEY": 10.2974,
|
| 90 |
+
"BOXSIZEZ": 7.25218,
|
| 91 |
+
"mdName": "replica 1",
|
| 92 |
+
"mdAtoms": 7838,
|
| 93 |
+
"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
+
"mdref": 0,
|
| 101 |
+
"files": [
|
| 102 |
+
"topology.tpr",
|
| 103 |
+
"screenshot.jpg",
|
| 104 |
+
"trajectory.bin",
|
| 105 |
+
"pca_trajectory_01.bin",
|
| 106 |
+
"pca_trajectory_02.bin",
|
| 107 |
+
"pca_trajectory_03.bin",
|
| 108 |
+
"pca_trajectory_04.bin",
|
| 109 |
+
"pca_trajectory_05.bin",
|
| 110 |
+
"pca_trajectory_06.bin",
|
| 111 |
+
"pca_trajectory_07.bin",
|
| 112 |
+
"structure.pdb",
|
| 113 |
+
"trajectory.xtc",
|
| 114 |
+
"clusters_00_screenshot_00.jpg",
|
| 115 |
+
"clusters_00_screenshot_01.jpg",
|
| 116 |
+
"clusters_00_screenshot_02.jpg",
|
| 117 |
+
"clusters_00_screenshot_03.jpg",
|
| 118 |
+
"clusters_00_screenshot_04.jpg",
|
| 119 |
+
"clusters_00_screenshot_05.jpg",
|
| 120 |
+
"clusters_00_screenshot_06.jpg",
|
| 121 |
+
"clusters_00_screenshot_07.jpg",
|
| 122 |
+
"clusters_00_screenshot_08.jpg",
|
| 123 |
+
"clusters_00_screenshot_09.jpg",
|
| 124 |
+
"clusters_00_screenshot_10.jpg",
|
| 125 |
+
"clusters_00_screenshot_11.jpg",
|
| 126 |
+
"clusters_00_screenshot_12.jpg",
|
| 127 |
+
"clusters_00_screenshot_13.jpg",
|
| 128 |
+
"clusters_00_screenshot_14.jpg",
|
| 129 |
+
"clusters_00_screenshot_15.jpg",
|
| 130 |
+
"clusters_00_screenshot_16.jpg",
|
| 131 |
+
"clusters_00_screenshot_17.jpg",
|
| 132 |
+
"clusters_00_screenshot_18.jpg",
|
| 133 |
+
"clusters_00_screenshot_19.jpg",
|
| 134 |
+
"clusters_00_screenshot_20.jpg",
|
| 135 |
+
"clusters_00_screenshot_21.jpg",
|
| 136 |
+
"clusters_00_screenshot_22.jpg",
|
| 137 |
+
"clusters_01_screenshot_00.jpg",
|
| 138 |
+
"clusters_01_screenshot_01.jpg",
|
| 139 |
+
"clusters_01_screenshot_02.jpg",
|
| 140 |
+
"clusters_01_screenshot_03.jpg",
|
| 141 |
+
"clusters_01_screenshot_04.jpg",
|
| 142 |
+
"clusters_01_screenshot_05.jpg",
|
| 143 |
+
"clusters_01_screenshot_06.jpg",
|
| 144 |
+
"clusters_01_screenshot_07.jpg",
|
| 145 |
+
"clusters_01_screenshot_08.jpg",
|
| 146 |
+
"clusters_01_screenshot_09.jpg",
|
| 147 |
+
"clusters_01_screenshot_10.jpg",
|
| 148 |
+
"clusters_01_screenshot_11.jpg",
|
| 149 |
+
"clusters_01_screenshot_12.jpg",
|
| 150 |
+
"clusters_01_screenshot_13.jpg",
|
| 151 |
+
"clusters_01_screenshot_14.jpg",
|
| 152 |
+
"clusters_01_screenshot_15.jpg",
|
| 153 |
+
"clusters_01_screenshot_16.jpg",
|
| 154 |
+
"clusters_01_screenshot_17.jpg",
|
| 155 |
+
"clusters_01_screenshot_18.jpg",
|
| 156 |
+
"clusters_01_screenshot_19.jpg",
|
| 157 |
+
"pocket_01.pdb",
|
| 158 |
+
"pocket_02.pdb",
|
| 159 |
+
"pocket_03.pdb",
|
| 160 |
+
"pocket_04.pdb",
|
| 161 |
+
"pocket_05.pdb",
|
| 162 |
+
"pocket_06.pdb",
|
| 163 |
+
"pocket_07.pdb",
|
| 164 |
+
"pocket_08.pdb"
|
| 165 |
+
],
|
| 166 |
+
"analyses": [
|
| 167 |
+
"clusters",
|
| 168 |
+
"clusters-00",
|
| 169 |
+
"clusters-01",
|
| 170 |
+
"dist-perres",
|
| 171 |
+
"energies",
|
| 172 |
+
"fluctuation",
|
| 173 |
+
"hbonds",
|
| 174 |
+
"interactions",
|
| 175 |
+
"pca",
|
| 176 |
+
"pockets",
|
| 177 |
+
"rgyr",
|
| 178 |
+
"rmsd-pairwise",
|
| 179 |
+
"rmsd-perres",
|
| 180 |
+
"rmsds",
|
| 181 |
+
"sasa",
|
| 182 |
+
"tmscores"
|
| 183 |
+
],
|
| 184 |
+
"mdIndex": 0,
|
| 185 |
+
"mdNumber": 1,
|
| 186 |
+
"refframe": 0,
|
| 187 |
+
"internalId": "683f3d0c6d9444d2dc316110",
|
| 188 |
+
"creationDate": "2025-06-03T18:21:00.000Z",
|
| 189 |
+
"identifier": "A0015"
|
| 190 |
+
}
|
data/files/A0015/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0015", "accession": "A0015", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1JTD", "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": ["1JTD"], "FORCED_REFERENCES": null, "REFERENCES": ["P62593", "O87916"], 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data/files/A0016/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0016",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1JWH",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1JWH"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P68400",
|
| 31 |
+
"P67870"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS",
|
| 38 |
+
"EVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYXPRVYXENQPMLPIGLSDIPGEAMVKLYXPKXMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHPMAYQLQLQAAS",
|
| 39 |
+
"SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS",
|
| 40 |
+
"SSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYXPRVYXENQPMLPIGLSDIPGEAMVKLYXPKXMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHPMAYQLQLQAAS"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Casein kinase II subunit alpha",
|
| 45 |
+
"Protein kinase",
|
| 46 |
+
"Interaction with beta subunit",
|
| 47 |
+
"Casein kinase II subunit beta",
|
| 48 |
+
"Interaction with alpha subunit",
|
| 49 |
+
"KSSR motif"
|
| 50 |
+
],
|
| 51 |
+
"FRAMESTEP": 0.1,
|
| 52 |
+
"TIMESTEP": 2,
|
| 53 |
+
"TEMP": 310,
|
| 54 |
+
"ENSEMBLE": "NPT",
|
| 55 |
+
"FF": [
|
| 56 |
+
"CHARMM36m"
|
| 57 |
+
],
|
| 58 |
+
"WAT": "TIP3P",
|
| 59 |
+
"BOXTYPE": "Dodecahedron",
|
| 60 |
+
"SYSTATS": 17609,
|
| 61 |
+
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|
| 76 |
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{
|
| 77 |
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|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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|
| 82 |
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|
| 83 |
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|
| 84 |
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{
|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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{
|
| 93 |
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"name": "protein-protein interaction B-D",
|
| 94 |
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|
| 95 |
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|
| 96 |
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"selection_1": "chain A",
|
| 97 |
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|
| 98 |
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"type": "protein-protein"
|
| 99 |
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},
|
| 100 |
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{
|
| 101 |
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"name": "protein-protein interaction B-C",
|
| 102 |
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"agent_1": "protein B",
|
| 103 |
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|
| 104 |
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"selection_1": "chain B",
|
| 105 |
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|
| 106 |
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"type": "protein-protein"
|
| 107 |
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},
|
| 108 |
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{
|
| 109 |
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"name": "protein-protein interaction D-C",
|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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|
| 114 |
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"type": "protein-protein"
|
| 115 |
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}
|
| 116 |
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],
|
| 117 |
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|
| 118 |
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|
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|
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|
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|
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|
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|
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|
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|
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},
|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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],
|
| 138 |
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"mdref": 0,
|
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|
| 140 |
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|
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|
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| 146 |
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| 147 |
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| 150 |
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|
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|
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| 232 |
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| 234 |
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| 235 |
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| 236 |
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| 237 |
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|
| 239 |
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|
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|
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|
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|
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|
| 259 |
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|
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|
| 263 |
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|
| 264 |
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|
| 265 |
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|
| 266 |
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|
| 267 |
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|
| 268 |
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|
| 269 |
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|
| 270 |
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|
| 271 |
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|
| 272 |
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|
| 273 |
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|
| 274 |
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|
| 275 |
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|
| 276 |
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|
| 277 |
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|
| 278 |
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"clusters_05_screenshot_19.jpg",
|
| 279 |
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"pocket_01.pdb",
|
| 280 |
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|
| 281 |
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"pocket_03.pdb",
|
| 282 |
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"pocket_04.pdb",
|
| 283 |
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"pocket_05.pdb",
|
| 284 |
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"pocket_06.pdb",
|
| 285 |
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"pocket_07.pdb",
|
| 286 |
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"pocket_08.pdb",
|
| 287 |
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"pocket_09.pdb",
|
| 288 |
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"pocket_10.pdb"
|
| 289 |
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],
|
| 290 |
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"analyses": [
|
| 291 |
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"clusters",
|
| 292 |
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"clusters-00",
|
| 293 |
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"clusters-01",
|
| 294 |
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"clusters-02",
|
| 295 |
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"clusters-03",
|
| 296 |
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"clusters-04",
|
| 297 |
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"clusters-05",
|
| 298 |
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"dist-perres",
|
| 299 |
+
"energies",
|
| 300 |
+
"fluctuation",
|
| 301 |
+
"hbonds",
|
| 302 |
+
"interactions",
|
| 303 |
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"pca",
|
| 304 |
+
"pockets",
|
| 305 |
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"rgyr",
|
| 306 |
+
"rmsd-pairwise",
|
| 307 |
+
"rmsd-perres",
|
| 308 |
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"rmsds",
|
| 309 |
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"sasa",
|
| 310 |
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"tmscores"
|
| 311 |
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],
|
| 312 |
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|
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|
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|
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"internalId": "683f3fd4e82f4ec7d5ececad",
|
| 316 |
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"creationDate": "2025-06-03T18:32:52.000Z",
|
| 317 |
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"identifier": "A0016"
|
| 318 |
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}
|
data/files/A0016/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
data/files/A0017/project.json
ADDED
|
@@ -0,0 +1,263 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0017",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1K5D",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1K5D"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P62826",
|
| 31 |
+
"P43487",
|
| 32 |
+
"P41391"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"NHDPQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDLPEWKERGTGDVKLLKHKEKGAIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADECPKPELLAIRFLNAENAQKFKTKFEECRKEIEEREK",
|
| 39 |
+
"QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDED",
|
| 40 |
+
"ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEE"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"GTP-binding nuclear protein Ran",
|
| 45 |
+
"Interaction with RANBP1",
|
| 46 |
+
"Essential for GTP hydrolysis",
|
| 47 |
+
"Ran-specific GTPase-activating protein",
|
| 48 |
+
"RanBD1",
|
| 49 |
+
"Disordered",
|
| 50 |
+
"Ran GTPase-activating protein 1",
|
| 51 |
+
"Disordered",
|
| 52 |
+
"Critical residue for GTP hydrolysis"
|
| 53 |
+
],
|
| 54 |
+
"FRAMESTEP": 0.1,
|
| 55 |
+
"TIMESTEP": 2,
|
| 56 |
+
"TEMP": 310,
|
| 57 |
+
"ENSEMBLE": "NPT",
|
| 58 |
+
"FF": [
|
| 59 |
+
"CHARMM36m"
|
| 60 |
+
],
|
| 61 |
+
"WAT": "TIP3P",
|
| 62 |
+
"BOXTYPE": "Dodecahedron",
|
| 63 |
+
"SYSTATS": 11179,
|
| 64 |
+
"SYSTRES": 696,
|
| 65 |
+
"PROTATS": 11179,
|
| 66 |
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"PROTRES": 696,
|
| 67 |
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"NUCLATS": 0,
|
| 68 |
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"NUCLRES": 0,
|
| 69 |
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"LIPIATS": 0,
|
| 70 |
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"LIPIRES": 0,
|
| 71 |
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"CARBATS": 0,
|
| 72 |
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"CARBRES": 0,
|
| 73 |
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"SOLVATS": 0,
|
| 74 |
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"SOLVRES": 0,
|
| 75 |
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"COUNCAT": 0,
|
| 76 |
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"COUNANI": 0,
|
| 77 |
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"COUNION": 0,
|
| 78 |
+
"INTERACTIONS": [
|
| 79 |
+
{
|
| 80 |
+
"name": "chain A-chain B interaction",
|
| 81 |
+
"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain B",
|
| 83 |
+
"selection_1": "chain A",
|
| 84 |
+
"selection_2": "chain B",
|
| 85 |
+
"type": "protein-protein"
|
| 86 |
+
},
|
| 87 |
+
{
|
| 88 |
+
"name": "chain A-chain C interaction",
|
| 89 |
+
"agent_1": "chain A",
|
| 90 |
+
"agent_2": "chain C",
|
| 91 |
+
"selection_1": "chain A",
|
| 92 |
+
"selection_2": "chain C",
|
| 93 |
+
"type": "protein-protein"
|
| 94 |
+
},
|
| 95 |
+
{
|
| 96 |
+
"name": "chain B-chain C interaction",
|
| 97 |
+
"agent_1": "chain B",
|
| 98 |
+
"agent_2": "chain C",
|
| 99 |
+
"selection_1": "chain B",
|
| 100 |
+
"selection_2": "chain C",
|
| 101 |
+
"type": "protein-protein"
|
| 102 |
+
}
|
| 103 |
+
],
|
| 104 |
+
"PBC_SELECTION": null,
|
| 105 |
+
"CHAINNAMES": null,
|
| 106 |
+
"MEMBRANES": null,
|
| 107 |
+
"CUSTOMS": null,
|
| 108 |
+
"ORIENTATION": null,
|
| 109 |
+
"PTM": [],
|
| 110 |
+
"MULTIMERIC": null,
|
| 111 |
+
"COLLECTIONS": "dynarepo",
|
| 112 |
+
"WARNINGS": [],
|
| 113 |
+
"BOXSIZEX": 12.7499,
|
| 114 |
+
"BOXSIZEY": 12.7499,
|
| 115 |
+
"BOXSIZEZ": 9.02727,
|
| 116 |
+
"mdName": "replica 1",
|
| 117 |
+
"mdAtoms": 11179,
|
| 118 |
+
"mdFrames": 5001
|
| 119 |
+
},
|
| 120 |
+
"mds": [
|
| 121 |
+
"replica 1",
|
| 122 |
+
"replica 2",
|
| 123 |
+
"replica 3"
|
| 124 |
+
],
|
| 125 |
+
"mdref": 0,
|
| 126 |
+
"files": [
|
| 127 |
+
"topology.tpr",
|
| 128 |
+
"screenshot.jpg",
|
| 129 |
+
"trajectory.bin",
|
| 130 |
+
"pca_trajectory_01.bin",
|
| 131 |
+
"pca_trajectory_02.bin",
|
| 132 |
+
"pca_trajectory_03.bin",
|
| 133 |
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"pca_trajectory_04.bin",
|
| 134 |
+
"pca_trajectory_05.bin",
|
| 135 |
+
"pca_trajectory_06.bin",
|
| 136 |
+
"pca_trajectory_07.bin",
|
| 137 |
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"pca_trajectory_08.bin",
|
| 138 |
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"pca_trajectory_09.bin",
|
| 139 |
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"pca_trajectory_10.bin",
|
| 140 |
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"pca_trajectory_11.bin",
|
| 141 |
+
"pca_trajectory_12.bin",
|
| 142 |
+
"pca_trajectory_13.bin",
|
| 143 |
+
"structure.pdb",
|
| 144 |
+
"trajectory.xtc",
|
| 145 |
+
"clusters_00_screenshot_00.jpg",
|
| 146 |
+
"clusters_00_screenshot_01.jpg",
|
| 147 |
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"clusters_00_screenshot_02.jpg",
|
| 148 |
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"clusters_00_screenshot_03.jpg",
|
| 149 |
+
"clusters_00_screenshot_04.jpg",
|
| 150 |
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"clusters_00_screenshot_05.jpg",
|
| 151 |
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"clusters_00_screenshot_06.jpg",
|
| 152 |
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"clusters_00_screenshot_07.jpg",
|
| 153 |
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"clusters_00_screenshot_08.jpg",
|
| 154 |
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"clusters_00_screenshot_09.jpg",
|
| 155 |
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"clusters_00_screenshot_10.jpg",
|
| 156 |
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"clusters_00_screenshot_11.jpg",
|
| 157 |
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"clusters_00_screenshot_12.jpg",
|
| 158 |
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"clusters_00_screenshot_13.jpg",
|
| 159 |
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"clusters_00_screenshot_14.jpg",
|
| 160 |
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"clusters_00_screenshot_15.jpg",
|
| 161 |
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"clusters_00_screenshot_16.jpg",
|
| 162 |
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"clusters_00_screenshot_17.jpg",
|
| 163 |
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"clusters_00_screenshot_18.jpg",
|
| 164 |
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"clusters_00_screenshot_19.jpg",
|
| 165 |
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"clusters_01_screenshot_00.jpg",
|
| 166 |
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"clusters_01_screenshot_01.jpg",
|
| 167 |
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"clusters_01_screenshot_02.jpg",
|
| 168 |
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"clusters_01_screenshot_03.jpg",
|
| 169 |
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"clusters_01_screenshot_04.jpg",
|
| 170 |
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"clusters_01_screenshot_05.jpg",
|
| 171 |
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"clusters_01_screenshot_06.jpg",
|
| 172 |
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"clusters_01_screenshot_07.jpg",
|
| 173 |
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"clusters_01_screenshot_08.jpg",
|
| 174 |
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"clusters_01_screenshot_09.jpg",
|
| 175 |
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"clusters_01_screenshot_10.jpg",
|
| 176 |
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"clusters_01_screenshot_11.jpg",
|
| 177 |
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"clusters_01_screenshot_12.jpg",
|
| 178 |
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"clusters_01_screenshot_13.jpg",
|
| 179 |
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"clusters_01_screenshot_14.jpg",
|
| 180 |
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"clusters_01_screenshot_15.jpg",
|
| 181 |
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"clusters_01_screenshot_16.jpg",
|
| 182 |
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"clusters_01_screenshot_17.jpg",
|
| 183 |
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"clusters_01_screenshot_18.jpg",
|
| 184 |
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"clusters_01_screenshot_19.jpg",
|
| 185 |
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"clusters_01_screenshot_20.jpg",
|
| 186 |
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"clusters_02_screenshot_00.jpg",
|
| 187 |
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"clusters_02_screenshot_01.jpg",
|
| 188 |
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"clusters_02_screenshot_02.jpg",
|
| 189 |
+
"clusters_02_screenshot_03.jpg",
|
| 190 |
+
"clusters_02_screenshot_04.jpg",
|
| 191 |
+
"clusters_02_screenshot_05.jpg",
|
| 192 |
+
"clusters_02_screenshot_06.jpg",
|
| 193 |
+
"clusters_02_screenshot_07.jpg",
|
| 194 |
+
"clusters_02_screenshot_08.jpg",
|
| 195 |
+
"clusters_02_screenshot_09.jpg",
|
| 196 |
+
"clusters_02_screenshot_10.jpg",
|
| 197 |
+
"clusters_02_screenshot_11.jpg",
|
| 198 |
+
"clusters_02_screenshot_12.jpg",
|
| 199 |
+
"clusters_02_screenshot_13.jpg",
|
| 200 |
+
"clusters_02_screenshot_14.jpg",
|
| 201 |
+
"clusters_02_screenshot_15.jpg",
|
| 202 |
+
"clusters_02_screenshot_16.jpg",
|
| 203 |
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"clusters_02_screenshot_17.jpg",
|
| 204 |
+
"clusters_02_screenshot_18.jpg",
|
| 205 |
+
"clusters_02_screenshot_19.jpg",
|
| 206 |
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"clusters_03_screenshot_00.jpg",
|
| 207 |
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"clusters_03_screenshot_01.jpg",
|
| 208 |
+
"clusters_03_screenshot_02.jpg",
|
| 209 |
+
"clusters_03_screenshot_03.jpg",
|
| 210 |
+
"clusters_03_screenshot_04.jpg",
|
| 211 |
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"clusters_03_screenshot_05.jpg",
|
| 212 |
+
"clusters_03_screenshot_06.jpg",
|
| 213 |
+
"clusters_03_screenshot_07.jpg",
|
| 214 |
+
"clusters_03_screenshot_08.jpg",
|
| 215 |
+
"clusters_03_screenshot_09.jpg",
|
| 216 |
+
"clusters_03_screenshot_10.jpg",
|
| 217 |
+
"clusters_03_screenshot_11.jpg",
|
| 218 |
+
"clusters_03_screenshot_12.jpg",
|
| 219 |
+
"clusters_03_screenshot_13.jpg",
|
| 220 |
+
"clusters_03_screenshot_14.jpg",
|
| 221 |
+
"clusters_03_screenshot_15.jpg",
|
| 222 |
+
"clusters_03_screenshot_16.jpg",
|
| 223 |
+
"clusters_03_screenshot_17.jpg",
|
| 224 |
+
"clusters_03_screenshot_18.jpg",
|
| 225 |
+
"clusters_03_screenshot_19.jpg",
|
| 226 |
+
"pocket_01.pdb",
|
| 227 |
+
"pocket_02.pdb",
|
| 228 |
+
"pocket_03.pdb",
|
| 229 |
+
"pocket_04.pdb",
|
| 230 |
+
"pocket_05.pdb",
|
| 231 |
+
"pocket_06.pdb",
|
| 232 |
+
"pocket_07.pdb",
|
| 233 |
+
"pocket_08.pdb",
|
| 234 |
+
"pocket_09.pdb",
|
| 235 |
+
"pocket_10.pdb"
|
| 236 |
+
],
|
| 237 |
+
"analyses": [
|
| 238 |
+
"clusters",
|
| 239 |
+
"clusters-00",
|
| 240 |
+
"clusters-01",
|
| 241 |
+
"clusters-02",
|
| 242 |
+
"clusters-03",
|
| 243 |
+
"dist-perres",
|
| 244 |
+
"energies",
|
| 245 |
+
"fluctuation",
|
| 246 |
+
"hbonds",
|
| 247 |
+
"interactions",
|
| 248 |
+
"pca",
|
| 249 |
+
"pockets",
|
| 250 |
+
"rgyr",
|
| 251 |
+
"rmsd-pairwise",
|
| 252 |
+
"rmsd-perres",
|
| 253 |
+
"rmsds",
|
| 254 |
+
"sasa",
|
| 255 |
+
"tmscores"
|
| 256 |
+
],
|
| 257 |
+
"mdIndex": 0,
|
| 258 |
+
"mdNumber": 1,
|
| 259 |
+
"refframe": 0,
|
| 260 |
+
"internalId": "683f431894c5b2a431903d8d",
|
| 261 |
+
"creationDate": "2025-06-03T18:46:48.000Z",
|
| 262 |
+
"identifier": "A0017"
|
| 263 |
+
}
|
data/files/A0017/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0017", "accession": "A0017", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "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": 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data/files/A0018/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0018",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1KAC",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1KAC"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P36711",
|
| 31 |
+
"P78310"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"GITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQVIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVKPSGA",
|
| 38 |
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"TPYDPLTLWTTPDPPPNCSLIQELDAKLTLCLTKNGSIVNGIVSLVGVKGNLLNIQSTTTTVGVHLVFDEQGRLITSTPTALVPQASWGYRQGQSVSTNTVTNGLGFMPNVSAYPRPNASEAKSQMVSLTYLQGDTSKPITMKVAFNGITSLNGYSLTFMWSGLSNYINQPFSTPSCSFSYITQE"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Fiber protein",
|
| 43 |
+
"Coxsackievirus and adenovirus receptor",
|
| 44 |
+
"Ig-like C2-type 1",
|
| 45 |
+
"Ig-like C2-type 2"
|
| 46 |
+
],
|
| 47 |
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"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
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"TEMP": 310,
|
| 50 |
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"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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"WAT": "TIP3P",
|
| 55 |
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"BOXTYPE": "Dodecahedron",
|
| 56 |
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"SYSTATS": 4718,
|
| 57 |
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"SYSTRES": 309,
|
| 58 |
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"PROTATS": 4718,
|
| 59 |
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"PROTRES": 309,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
|
| 63 |
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"LIPIRES": 0,
|
| 64 |
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"CARBATS": 0,
|
| 65 |
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"CARBRES": 0,
|
| 66 |
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"SOLVATS": 0,
|
| 67 |
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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
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"COUNANI": 0,
|
| 70 |
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"COUNION": 0,
|
| 71 |
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"INTERACTIONS": [
|
| 72 |
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{
|
| 73 |
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"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
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],
|
| 81 |
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"PBC_SELECTION": null,
|
| 82 |
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"CHAINNAMES": null,
|
| 83 |
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"MEMBRANES": null,
|
| 84 |
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"CUSTOMS": null,
|
| 85 |
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"ORIENTATION": null,
|
| 86 |
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"PTM": [],
|
| 87 |
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"MULTIMERIC": null,
|
| 88 |
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"COLLECTIONS": "dynarepo",
|
| 89 |
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"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 9.93136,
|
| 91 |
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"BOXSIZEY": 9.93136,
|
| 92 |
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"BOXSIZEZ": 7.03317,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 4718,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
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"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
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],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
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| 104 |
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|
| 105 |
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"screenshot.jpg",
|
| 106 |
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"trajectory.bin",
|
| 107 |
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"pca_trajectory_01.bin",
|
| 108 |
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"pca_trajectory_02.bin",
|
| 109 |
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"pca_trajectory_03.bin",
|
| 110 |
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"pca_trajectory_04.bin",
|
| 111 |
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"pca_trajectory_05.bin",
|
| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
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"pca_trajectory_07.bin",
|
| 114 |
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| 115 |
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| 116 |
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| 117 |
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| 118 |
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"pca_trajectory_12.bin",
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"clusters_01_screenshot_18.jpg",
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"clusters_01_screenshot_19.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.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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| 178 |
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"clusters-00",
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"clusters-01",
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| 180 |
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"dist-perres",
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| 181 |
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"energies",
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"fluctuation",
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| 183 |
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"hbonds",
|
| 184 |
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"interactions",
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"pca",
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| 186 |
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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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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f4524731f82fa10c92d5a",
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"creationDate": "2025-06-03T18:55:32.000Z",
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"identifier": "A0018"
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}
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data/files/A0018/records.jsonl
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| 3 |
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data/files/A0019/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0019",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1KGY",
|
| 6 |
+
"DESCRIPTION": "Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Author Omid Mokhtari",
|
| 9 |
+
"Author Hamed Khakzad",
|
| 10 |
+
"Author Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": [
|
| 25 |
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{
|
| 26 |
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"name": "Link_name",
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| 27 |
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"url": "www.link-name.org"
|
| 28 |
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}
|
| 29 |
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],
|
| 30 |
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"PDBIDS": [
|
| 31 |
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"1KGY"
|
| 32 |
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],
|
| 33 |
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"FORCED_REFERENCES": null,
|
| 34 |
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"REFERENCES": [
|
| 35 |
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"P54763",
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| 36 |
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"P52800"
|
| 37 |
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],
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| 38 |
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"INPUT_LIGANDS": null,
|
| 39 |
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"LIGANDS": [],
|
| 40 |
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"LIGANDNAMES": null,
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| 41 |
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"PROTSEQ": [
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| 42 |
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"IVLEPIYWNSSNSKFLPGGGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQADRCTIKKENTPLLNCARPDQDVKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLDNQEGGVCQTRAMKILMKVG",
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| 43 |
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| 44 |
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],
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| 45 |
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"NUCLSEQ": [],
|
| 46 |
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"DOMAINS": [
|
| 47 |
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"Ephrin type-B receptor 2",
|
| 48 |
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"Eph LBD",
|
| 49 |
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"Ephrin-B2",
|
| 50 |
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"Ephrin RBD"
|
| 51 |
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],
|
| 52 |
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"FRAMESTEP": 0.02,
|
| 53 |
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"TIMESTEP": 5000,
|
| 54 |
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"TEMP": 310,
|
| 55 |
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"ENSEMBLE": "NPT",
|
| 56 |
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"FF": [
|
| 57 |
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"CHARMM36m"
|
| 58 |
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],
|
| 59 |
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"WAT": "TIP3P",
|
| 60 |
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"BOXTYPE": "Dodecahedron",
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| 61 |
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"SYSTATS": 10116,
|
| 62 |
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"SYSTRES": 638,
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| 63 |
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"PROTATS": 10116,
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| 64 |
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"PROTRES": 638,
|
| 65 |
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"NUCLATS": 0,
|
| 66 |
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"NUCLRES": 0,
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| 67 |
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"LIPIATS": 0,
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| 68 |
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| 69 |
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"CARBATS": 0,
|
| 70 |
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"CARBRES": 0,
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| 71 |
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"SOLVATS": 0,
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| 72 |
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"SOLVRES": 0,
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| 73 |
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"COUNCAT": 0,
|
| 74 |
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"COUNANI": 0,
|
| 75 |
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"COUNION": 0,
|
| 76 |
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"INTERACTIONS": [
|
| 77 |
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{
|
| 78 |
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"name": "chain A-chain B interaction",
|
| 79 |
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"agent_1": "chain A",
|
| 80 |
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"agent_2": "chain B",
|
| 81 |
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"selection_1": "chain A",
|
| 82 |
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"selection_2": "chain B",
|
| 83 |
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"type": "protein-protein"
|
| 84 |
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},
|
| 85 |
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{
|
| 86 |
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"name": "chain A-chain C interaction",
|
| 87 |
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"agent_1": "chain A",
|
| 88 |
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"agent_2": "chain C",
|
| 89 |
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"selection_1": "chain A",
|
| 90 |
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"selection_2": "chain C",
|
| 91 |
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"type": "protein-protein"
|
| 92 |
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},
|
| 93 |
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{
|
| 94 |
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"name": "chain A-chain D interaction",
|
| 95 |
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"agent_1": "chain A",
|
| 96 |
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"agent_2": "chain D",
|
| 97 |
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"selection_1": "chain A",
|
| 98 |
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"selection_2": "chain D",
|
| 99 |
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"type": "protein-protein"
|
| 100 |
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},
|
| 101 |
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{
|
| 102 |
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"name": "chain B-chain C interaction",
|
| 103 |
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"agent_1": "chain B",
|
| 104 |
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"agent_2": "chain C",
|
| 105 |
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"selection_1": "chain B",
|
| 106 |
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"selection_2": "chain C",
|
| 107 |
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"type": "protein-protein"
|
| 108 |
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},
|
| 109 |
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{
|
| 110 |
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"name": "chain B-chain D interaction",
|
| 111 |
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"agent_1": "chain B",
|
| 112 |
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"agent_2": "chain D",
|
| 113 |
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"selection_1": "chain B",
|
| 114 |
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"selection_2": "chain D",
|
| 115 |
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"type": "protein-protein"
|
| 116 |
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}
|
| 117 |
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],
|
| 118 |
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"PBC_SELECTION": null,
|
| 119 |
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"CHAINNAMES": null,
|
| 120 |
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"MEMBRANES": null,
|
| 121 |
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"CUSTOMS": null,
|
| 122 |
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"ORIENTATION": null,
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| 123 |
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"PTM": [],
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| 124 |
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"MULTIMERIC": null,
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| 125 |
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"COLLECTIONS": "dynarepo",
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| 126 |
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"WARNINGS": [],
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| 127 |
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"BOXSIZEX": 11.6619,
|
| 128 |
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"BOXSIZEY": 11.6619,
|
| 129 |
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"BOXSIZEZ": 8.28273,
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| 130 |
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"mdName": "replica 1",
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| 131 |
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"mdAtoms": 10116,
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| 132 |
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"mdFrames": 5001
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| 133 |
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},
|
| 134 |
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"mds": [
|
| 135 |
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"replica 1",
|
| 136 |
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"replica 2",
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| 137 |
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"replica 3"
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| 138 |
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],
|
| 139 |
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"mdref": 0,
|
| 140 |
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"files": [
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| 141 |
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| 142 |
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| 272 |
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| 273 |
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| 274 |
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"pocket_01.pdb",
|
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|
| 276 |
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"pocket_03.pdb",
|
| 277 |
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|
| 278 |
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"pocket_05.pdb",
|
| 279 |
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"pocket_06.pdb",
|
| 280 |
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"pocket_07.pdb"
|
| 281 |
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|
| 282 |
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|
| 283 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 294 |
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|
| 295 |
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|
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|
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|
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|
| 299 |
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|
| 300 |
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|
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|
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|
| 310 |
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}
|
data/files/A0019/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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|
data/files/A001A/project.json
ADDED
|
@@ -0,0 +1,203 @@
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|
| 1 |
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{
|
| 2 |
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"accession": "A001A",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1KXT",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
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| 15 |
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|
| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 24 |
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| 109 |
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|
| 114 |
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|
| 115 |
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|
| 116 |
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"pca_trajectory_08.bin",
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|
| 125 |
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| 126 |
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| 127 |
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|
| 128 |
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|
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|
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"clusters_01_screenshot_01.jpg",
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"clusters_01_screenshot_02.jpg",
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|
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|
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|
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| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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|
| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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"clusters_01_screenshot_18.jpg",
|
| 167 |
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"clusters_01_screenshot_19.jpg",
|
| 168 |
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"pocket_01.pdb",
|
| 169 |
+
"pocket_02.pdb",
|
| 170 |
+
"pocket_03.pdb",
|
| 171 |
+
"pocket_04.pdb",
|
| 172 |
+
"pocket_05.pdb",
|
| 173 |
+
"pocket_06.pdb",
|
| 174 |
+
"pocket_07.pdb",
|
| 175 |
+
"pocket_08.pdb",
|
| 176 |
+
"pocket_09.pdb",
|
| 177 |
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"pocket_10.pdb"
|
| 178 |
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],
|
| 179 |
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|
| 180 |
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"clusters",
|
| 181 |
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"clusters-00",
|
| 182 |
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"clusters-01",
|
| 183 |
+
"dist-perres",
|
| 184 |
+
"energies",
|
| 185 |
+
"fluctuation",
|
| 186 |
+
"hbonds",
|
| 187 |
+
"interactions",
|
| 188 |
+
"pca",
|
| 189 |
+
"pockets",
|
| 190 |
+
"rgyr",
|
| 191 |
+
"rmsd-pairwise",
|
| 192 |
+
"rmsd-perres",
|
| 193 |
+
"rmsds",
|
| 194 |
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"sasa",
|
| 195 |
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"tmscores"
|
| 196 |
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|
| 197 |
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|
| 202 |
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"identifier": "A001A"
|
| 203 |
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}
|
data/files/A001A/records.jsonl
ADDED
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data/files/A001B/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001B",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1L2W",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1L2W"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"A0A0N9NJF3",
|
| 31 |
+
"P08008"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"MGYSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQTSS",
|
| 38 |
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"YSFEQAITQLFQQLSLSIPDTIEPVIGVKVGEFACHITEHPVGQILMFTLPSLDNNDEKETLLSHNIFSQDILKPILSWDEVGGHPVLWNRQPLNSLDNNSLYTQLEMLVQGAERLQ",
|
| 39 |
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"SVGEMSGRSVSQQTSDQYANNLAGRTESPQGSSLASRIIERLSSVAHSVIGFIQRMF"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Outer membrane virulence protein YopE",
|
| 44 |
+
"Disordered"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 4619,
|
| 56 |
+
"SYSTRES": 296,
|
| 57 |
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"PROTATS": 4619,
|
| 58 |
+
"PROTRES": 296,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
},
|
| 79 |
+
{
|
| 80 |
+
"name": "chain A-chain C interaction",
|
| 81 |
+
"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain C",
|
| 83 |
+
"selection_1": "chain A",
|
| 84 |
+
"selection_2": "chain C",
|
| 85 |
+
"type": "protein-protein"
|
| 86 |
+
},
|
| 87 |
+
{
|
| 88 |
+
"name": "chain B-chain C interaction",
|
| 89 |
+
"agent_1": "chain B",
|
| 90 |
+
"agent_2": "chain C",
|
| 91 |
+
"selection_1": "chain B",
|
| 92 |
+
"selection_2": "chain C",
|
| 93 |
+
"type": "protein-protein"
|
| 94 |
+
}
|
| 95 |
+
],
|
| 96 |
+
"PBC_SELECTION": null,
|
| 97 |
+
"CHAINNAMES": null,
|
| 98 |
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"MEMBRANES": null,
|
| 99 |
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"CUSTOMS": null,
|
| 100 |
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"ORIENTATION": null,
|
| 101 |
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"PTM": [],
|
| 102 |
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"MULTIMERIC": null,
|
| 103 |
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"COLLECTIONS": "dynarepo",
|
| 104 |
+
"WARNINGS": [],
|
| 105 |
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"BOXSIZEX": 8.87367,
|
| 106 |
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"BOXSIZEY": 8.87367,
|
| 107 |
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"BOXSIZEZ": 6.31214,
|
| 108 |
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"mdName": "replica 1",
|
| 109 |
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"mdAtoms": 4619,
|
| 110 |
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"mdFrames": 5001
|
| 111 |
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},
|
| 112 |
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"mds": [
|
| 113 |
+
"replica 1",
|
| 114 |
+
"replica 2",
|
| 115 |
+
"replica 3"
|
| 116 |
+
],
|
| 117 |
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"mdref": 0,
|
| 118 |
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"files": [
|
| 119 |
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"topology.tpr",
|
| 120 |
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"screenshot.jpg",
|
| 121 |
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"trajectory.bin",
|
| 122 |
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"pca_trajectory_01.bin",
|
| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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"pca_trajectory_16.bin",
|
| 138 |
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"structure.pdb",
|
| 139 |
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|
| 140 |
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|
| 141 |
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| 142 |
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| 143 |
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| 144 |
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| 153 |
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| 154 |
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| 157 |
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| 166 |
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"clusters_03_screenshot_18.jpg",
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"clusters_03_screenshot_19.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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+
"pocket_03.pdb",
|
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb",
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"pocket_08.pdb",
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"pocket_09.pdb",
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"pocket_10.pdb"
|
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+
],
|
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+
"analyses": [
|
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+
"clusters",
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+
"clusters-00",
|
| 231 |
+
"clusters-01",
|
| 232 |
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"clusters-02",
|
| 233 |
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"clusters-03",
|
| 234 |
+
"dist-perres",
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"energies",
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| 236 |
+
"fluctuation",
|
| 237 |
+
"hbonds",
|
| 238 |
+
"interactions",
|
| 239 |
+
"pca",
|
| 240 |
+
"pockets",
|
| 241 |
+
"rgyr",
|
| 242 |
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"rmsd-pairwise",
|
| 243 |
+
"rmsd-perres",
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"rmsds",
|
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+
"sasa",
|
| 246 |
+
"tmscores"
|
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+
],
|
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+
"mdIndex": 0,
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+
"mdNumber": 1,
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+
"refframe": 0,
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+
"internalId": "683f4b4fdd9423956f1914ee",
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+
"creationDate": "2025-06-03T19:21:51.000Z",
|
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+
"identifier": "A001B"
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+
}
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data/files/A001B/records.jsonl
ADDED
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data/files/A001C/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001C",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1LFD",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1LFD"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q03386",
|
| 31 |
+
"P01112"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"GDCCIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELLQIISEDHKLKIPENANVFYAMNSAANYDFILKKR",
|
| 38 |
+
"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDKYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ral guanine nucleotide dissociation stimulator",
|
| 43 |
+
"Ras-associating",
|
| 44 |
+
"GTPase HRas",
|
| 45 |
+
"GTPase HRas, N-terminally processed",
|
| 46 |
+
"Hypervariable region",
|
| 47 |
+
"Effector region"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 4036,
|
| 59 |
+
"SYSTRES": 254,
|
| 60 |
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"PROTATS": 4036,
|
| 61 |
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"PROTRES": 254,
|
| 62 |
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"NUCLATS": 0,
|
| 63 |
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"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
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| 65 |
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"LIPIRES": 0,
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| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
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"SOLVRES": 0,
|
| 70 |
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|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
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}
|
| 82 |
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],
|
| 83 |
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|
| 84 |
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"CHAINNAMES": null,
|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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|
| 97 |
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|
| 98 |
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},
|
| 99 |
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"mds": [
|
| 100 |
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"replica 1",
|
| 101 |
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"replica 2",
|
| 102 |
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"replica 3"
|
| 103 |
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|
| 104 |
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"mdref": 0,
|
| 105 |
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"files": [
|
| 106 |
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|
| 109 |
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"pca_trajectory_01.bin",
|
| 110 |
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"pca_trajectory_02.bin",
|
| 111 |
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"pca_trajectory_03.bin",
|
| 112 |
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"pca_trajectory_04.bin",
|
| 113 |
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"pca_trajectory_05.bin",
|
| 114 |
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"pca_trajectory_06.bin",
|
| 115 |
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"pca_trajectory_07.bin",
|
| 116 |
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"pca_trajectory_08.bin",
|
| 117 |
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"pca_trajectory_09.bin",
|
| 118 |
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"pca_trajectory_10.bin",
|
| 119 |
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"pca_trajectory_11.bin",
|
| 120 |
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"pca_trajectory_12.bin",
|
| 121 |
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"pca_trajectory_13.bin",
|
| 122 |
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"pca_trajectory_14.bin",
|
| 123 |
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"structure.pdb",
|
| 124 |
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"trajectory.xtc",
|
| 125 |
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"clusters_00_screenshot_00.jpg",
|
| 126 |
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"clusters_00_screenshot_01.jpg",
|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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|
| 134 |
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|
| 135 |
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| 136 |
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|
| 137 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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"clusters_00_screenshot_17.jpg",
|
| 143 |
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"clusters_00_screenshot_18.jpg",
|
| 144 |
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"clusters_00_screenshot_19.jpg",
|
| 145 |
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"clusters_01_screenshot_00.jpg",
|
| 146 |
+
"clusters_01_screenshot_01.jpg",
|
| 147 |
+
"clusters_01_screenshot_02.jpg",
|
| 148 |
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"clusters_01_screenshot_03.jpg",
|
| 149 |
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"clusters_01_screenshot_04.jpg",
|
| 150 |
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"clusters_01_screenshot_05.jpg",
|
| 151 |
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"clusters_01_screenshot_06.jpg",
|
| 152 |
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"clusters_01_screenshot_07.jpg",
|
| 153 |
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"clusters_01_screenshot_08.jpg",
|
| 154 |
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"clusters_01_screenshot_09.jpg",
|
| 155 |
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"clusters_01_screenshot_10.jpg",
|
| 156 |
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"clusters_01_screenshot_11.jpg",
|
| 157 |
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"clusters_01_screenshot_12.jpg",
|
| 158 |
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"clusters_01_screenshot_13.jpg",
|
| 159 |
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"clusters_01_screenshot_14.jpg",
|
| 160 |
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"clusters_01_screenshot_15.jpg",
|
| 161 |
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"clusters_01_screenshot_16.jpg",
|
| 162 |
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"clusters_01_screenshot_17.jpg",
|
| 163 |
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"clusters_01_screenshot_18.jpg",
|
| 164 |
+
"clusters_01_screenshot_19.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb"
|
| 173 |
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],
|
| 174 |
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"analyses": [
|
| 175 |
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"clusters",
|
| 176 |
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"clusters-00",
|
| 177 |
+
"clusters-01",
|
| 178 |
+
"dist-perres",
|
| 179 |
+
"energies",
|
| 180 |
+
"fluctuation",
|
| 181 |
+
"hbonds",
|
| 182 |
+
"interactions",
|
| 183 |
+
"pca",
|
| 184 |
+
"pockets",
|
| 185 |
+
"rgyr",
|
| 186 |
+
"rmsd-pairwise",
|
| 187 |
+
"rmsd-perres",
|
| 188 |
+
"rmsds",
|
| 189 |
+
"sasa",
|
| 190 |
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"tmscores"
|
| 191 |
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],
|
| 192 |
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"mdIndex": 0,
|
| 193 |
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"mdNumber": 1,
|
| 194 |
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|
| 195 |
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|
| 196 |
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"creationDate": "2025-06-03T19:27:03.000Z",
|
| 197 |
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"identifier": "A001C"
|
| 198 |
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}
|
data/files/A001C/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
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data/files/A001D/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001D",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1LJ2",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1LJ2"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P03536",
|
| 31 |
+
"Q04637"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"KTIRIRDPNQGGKDITEEIMSG",
|
| 38 |
+
"PKRERKTIRIRDPNQGGKDITEEIMSG",
|
| 39 |
+
"HSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSF",
|
| 40 |
+
"MHSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSFGSE"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Non-structural protein 3",
|
| 45 |
+
"Dimerization",
|
| 46 |
+
"Interaction with host ZC3H7B",
|
| 47 |
+
"Interaction with host EIF4G1",
|
| 48 |
+
"Eukaryotic translation initiation factor 4 gamma 1",
|
| 49 |
+
"Disordered",
|
| 50 |
+
"PABPC1-binding"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 4321,
|
| 62 |
+
"SYSTRES": 265,
|
| 63 |
+
"PROTATS": 4321,
|
| 64 |
+
"PROTRES": 265,
|
| 65 |
+
"NUCLATS": 0,
|
| 66 |
+
"NUCLRES": 0,
|
| 67 |
+
"LIPIATS": 0,
|
| 68 |
+
"LIPIRES": 0,
|
| 69 |
+
"CARBATS": 0,
|
| 70 |
+
"CARBRES": 0,
|
| 71 |
+
"SOLVATS": 0,
|
| 72 |
+
"SOLVRES": 0,
|
| 73 |
+
"COUNCAT": 0,
|
| 74 |
+
"COUNANI": 0,
|
| 75 |
+
"COUNION": 0,
|
| 76 |
+
"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
},
|
| 85 |
+
{
|
| 86 |
+
"name": "chain A-chain C interaction",
|
| 87 |
+
"agent_1": "chain A",
|
| 88 |
+
"agent_2": "chain C",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain C",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "chain A-chain D interaction",
|
| 95 |
+
"agent_1": "chain A",
|
| 96 |
+
"agent_2": "chain D",
|
| 97 |
+
"selection_1": "chain A",
|
| 98 |
+
"selection_2": "chain D",
|
| 99 |
+
"type": "protein-protein"
|
| 100 |
+
},
|
| 101 |
+
{
|
| 102 |
+
"name": "chain B-chain C interaction",
|
| 103 |
+
"agent_1": "chain B",
|
| 104 |
+
"agent_2": "chain C",
|
| 105 |
+
"selection_1": "chain B",
|
| 106 |
+
"selection_2": "chain C",
|
| 107 |
+
"type": "protein-protein"
|
| 108 |
+
},
|
| 109 |
+
{
|
| 110 |
+
"name": "chain B-chain D interaction",
|
| 111 |
+
"agent_1": "chain B",
|
| 112 |
+
"agent_2": "chain D",
|
| 113 |
+
"selection_1": "chain B",
|
| 114 |
+
"selection_2": "chain D",
|
| 115 |
+
"type": "protein-protein"
|
| 116 |
+
}
|
| 117 |
+
],
|
| 118 |
+
"PBC_SELECTION": null,
|
| 119 |
+
"CHAINNAMES": null,
|
| 120 |
+
"MEMBRANES": null,
|
| 121 |
+
"CUSTOMS": null,
|
| 122 |
+
"ORIENTATION": null,
|
| 123 |
+
"PTM": [],
|
| 124 |
+
"MULTIMERIC": null,
|
| 125 |
+
"COLLECTIONS": "dynarepo",
|
| 126 |
+
"WARNINGS": [],
|
| 127 |
+
"BOXSIZEX": 12.1659,
|
| 128 |
+
"BOXSIZEY": 12.1659,
|
| 129 |
+
"BOXSIZEZ": 8.6127,
|
| 130 |
+
"mdName": "replica 1",
|
| 131 |
+
"mdAtoms": 4321,
|
| 132 |
+
"mdFrames": 5001
|
| 133 |
+
},
|
| 134 |
+
"mds": [
|
| 135 |
+
"replica 1",
|
| 136 |
+
"replica 2",
|
| 137 |
+
"replica 3"
|
| 138 |
+
],
|
| 139 |
+
"mdref": 0,
|
| 140 |
+
"files": [
|
| 141 |
+
"topology.tpr",
|
| 142 |
+
"screenshot.jpg",
|
| 143 |
+
"trajectory.bin",
|
| 144 |
+
"pca_trajectory_01.bin",
|
| 145 |
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"pca_trajectory_02.bin",
|
| 146 |
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"pca_trajectory_03.bin",
|
| 147 |
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"pca_trajectory_04.bin",
|
| 148 |
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"pca_trajectory_05.bin",
|
| 149 |
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"pca_trajectory_06.bin",
|
| 150 |
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"pca_trajectory_07.bin",
|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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"pca_trajectory_12.bin",
|
| 156 |
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"pca_trajectory_13.bin",
|
| 157 |
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"structure.pdb",
|
| 158 |
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"trajectory.xtc",
|
| 159 |
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"clusters_00_screenshot_00.jpg",
|
| 160 |
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"clusters_00_screenshot_01.jpg",
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|
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|
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|
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data/files/A001D/records.jsonl
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data/files/A001E/project.json
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| 1 |
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{
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| 2 |
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| 3 |
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| 7 |
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| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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|
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| 14 |
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| 15 |
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|
| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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"pocket_01.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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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f4eb455e8add357cf5be0",
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"creationDate": "2025-06-03T19:36:20.000Z",
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"identifier": "A001E"
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}
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data/files/A001F/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A001F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1LX5",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"1LX5"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P18075",
|
| 31 |
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"P27038"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"ETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPE",
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| 38 |
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"QACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH"
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| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Bone morphogenetic protein 7",
|
| 43 |
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"Activin receptor type-2A"
|
| 44 |
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],
|
| 45 |
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"FRAMESTEP": 0.1,
|
| 46 |
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"TIMESTEP": 2,
|
| 47 |
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"TEMP": 310,
|
| 48 |
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"ENSEMBLE": "NPT",
|
| 49 |
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"FF": [
|
| 50 |
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"CHARMM36m"
|
| 51 |
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],
|
| 52 |
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"WAT": "TIP3P",
|
| 53 |
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"BOXTYPE": "Dodecahedron",
|
| 54 |
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"SYSTATS": 3094,
|
| 55 |
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"SYSTRES": 198,
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| 56 |
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"PROTATS": 3094,
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| 57 |
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"PROTRES": 198,
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| 58 |
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"NUCLATS": 0,
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| 59 |
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"NUCLRES": 0,
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| 60 |
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"LIPIATS": 0,
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| 61 |
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| 62 |
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"CARBATS": 0,
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| 63 |
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"CARBRES": 0,
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| 64 |
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| 65 |
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"SOLVRES": 0,
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| 66 |
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"COUNCAT": 0,
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| 67 |
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"COUNANI": 0,
|
| 68 |
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"COUNION": 0,
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| 69 |
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"INTERACTIONS": [
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| 70 |
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{
|
| 71 |
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"name": "chain A-chain B interaction",
|
| 72 |
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"agent_1": "chain A",
|
| 73 |
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|
| 74 |
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"selection_1": "chain A",
|
| 75 |
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"selection_2": "chain B",
|
| 76 |
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"type": "protein-protein"
|
| 77 |
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|
| 78 |
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],
|
| 79 |
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|
| 80 |
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|
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|
| 82 |
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|
| 83 |
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|
| 84 |
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|
| 85 |
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|
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| 105 |
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| 106 |
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| 107 |
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| 108 |
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|
| 109 |
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|
| 110 |
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| 112 |
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|
| 113 |
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|
| 114 |
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|
| 115 |
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| 117 |
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| 130 |
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| 132 |
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| 134 |
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| 135 |
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| 137 |
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|
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|
| 139 |
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| 140 |
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| 143 |
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| 145 |
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| 146 |
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| 147 |
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|
| 148 |
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| 149 |
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| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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"clusters_01_screenshot_18.jpg",
|
| 157 |
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"clusters_01_screenshot_19.jpg",
|
| 158 |
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"pocket_01.pdb",
|
| 159 |
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"pocket_02.pdb",
|
| 160 |
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"pocket_03.pdb",
|
| 161 |
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"pocket_04.pdb",
|
| 162 |
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"pocket_05.pdb",
|
| 163 |
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"pocket_06.pdb"
|
| 164 |
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|
| 165 |
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|
| 166 |
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|
| 167 |
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|
| 168 |
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|
| 169 |
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"dist-perres",
|
| 170 |
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"energies",
|
| 171 |
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"fluctuation",
|
| 172 |
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"hbonds",
|
| 173 |
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"interactions",
|
| 174 |
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"pca",
|
| 175 |
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"pockets",
|
| 176 |
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"rgyr",
|
| 177 |
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"rmsd-pairwise",
|
| 178 |
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"rmsd-perres",
|
| 179 |
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"rmsds",
|
| 180 |
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"sasa",
|
| 181 |
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"tmscores"
|
| 182 |
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| 183 |
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|
| 188 |
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|
| 189 |
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|
data/files/A001F/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001G",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1LZW",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1LZW"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0A8Q6",
|
| 31 |
+
"P0ABH9"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVAYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA",
|
| 38 |
+
"MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDE"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"ATP-dependent Clp protease adapter protein ClpS",
|
| 43 |
+
"ATP-dependent Clp protease ATP-binding subunit ClpA",
|
| 44 |
+
"Clp R",
|
| 45 |
+
"Repeat 1",
|
| 46 |
+
"Repeat 2",
|
| 47 |
+
"Disordered"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 3780,
|
| 59 |
+
"SYSTRES": 237,
|
| 60 |
+
"PROTATS": 3780,
|
| 61 |
+
"PROTRES": 237,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
}
|
| 82 |
+
],
|
| 83 |
+
"PBC_SELECTION": null,
|
| 84 |
+
"CHAINNAMES": null,
|
| 85 |
+
"MEMBRANES": null,
|
| 86 |
+
"CUSTOMS": null,
|
| 87 |
+
"ORIENTATION": null,
|
| 88 |
+
"PTM": [],
|
| 89 |
+
"MULTIMERIC": null,
|
| 90 |
+
"COLLECTIONS": "dynarepo",
|
| 91 |
+
"WARNINGS": [],
|
| 92 |
+
"BOXSIZEX": 9.12617,
|
| 93 |
+
"BOXSIZEY": 9.12617,
|
| 94 |
+
"BOXSIZEZ": 6.40912,
|
| 95 |
+
"mdName": "replica 1",
|
| 96 |
+
"mdAtoms": 3780,
|
| 97 |
+
"mdFrames": 5001
|
| 98 |
+
},
|
| 99 |
+
"mds": [
|
| 100 |
+
"replica 1",
|
| 101 |
+
"replica 2",
|
| 102 |
+
"replica 3"
|
| 103 |
+
],
|
| 104 |
+
"mdref": 0,
|
| 105 |
+
"files": [
|
| 106 |
+
"topology.tpr",
|
| 107 |
+
"screenshot.jpg",
|
| 108 |
+
"trajectory.bin",
|
| 109 |
+
"pca_trajectory_01.bin",
|
| 110 |
+
"pca_trajectory_02.bin",
|
| 111 |
+
"pca_trajectory_03.bin",
|
| 112 |
+
"pca_trajectory_04.bin",
|
| 113 |
+
"pca_trajectory_05.bin",
|
| 114 |
+
"pca_trajectory_06.bin",
|
| 115 |
+
"pca_trajectory_07.bin",
|
| 116 |
+
"pca_trajectory_08.bin",
|
| 117 |
+
"pca_trajectory_09.bin",
|
| 118 |
+
"pca_trajectory_10.bin",
|
| 119 |
+
"pca_trajectory_11.bin",
|
| 120 |
+
"pca_trajectory_12.bin",
|
| 121 |
+
"structure.pdb",
|
| 122 |
+
"trajectory.xtc",
|
| 123 |
+
"clusters_00_screenshot_00.jpg",
|
| 124 |
+
"clusters_00_screenshot_01.jpg",
|
| 125 |
+
"clusters_00_screenshot_02.jpg",
|
| 126 |
+
"clusters_00_screenshot_03.jpg",
|
| 127 |
+
"clusters_00_screenshot_04.jpg",
|
| 128 |
+
"clusters_00_screenshot_05.jpg",
|
| 129 |
+
"clusters_00_screenshot_06.jpg",
|
| 130 |
+
"clusters_00_screenshot_07.jpg",
|
| 131 |
+
"clusters_00_screenshot_08.jpg",
|
| 132 |
+
"clusters_00_screenshot_09.jpg",
|
| 133 |
+
"clusters_00_screenshot_10.jpg",
|
| 134 |
+
"clusters_00_screenshot_11.jpg",
|
| 135 |
+
"clusters_00_screenshot_12.jpg",
|
| 136 |
+
"clusters_00_screenshot_13.jpg",
|
| 137 |
+
"clusters_00_screenshot_14.jpg",
|
| 138 |
+
"clusters_00_screenshot_15.jpg",
|
| 139 |
+
"clusters_00_screenshot_16.jpg",
|
| 140 |
+
"clusters_00_screenshot_17.jpg",
|
| 141 |
+
"clusters_00_screenshot_18.jpg",
|
| 142 |
+
"clusters_00_screenshot_19.jpg",
|
| 143 |
+
"clusters_01_screenshot_00.jpg",
|
| 144 |
+
"clusters_01_screenshot_01.jpg",
|
| 145 |
+
"clusters_01_screenshot_02.jpg",
|
| 146 |
+
"clusters_01_screenshot_03.jpg",
|
| 147 |
+
"clusters_01_screenshot_04.jpg",
|
| 148 |
+
"clusters_01_screenshot_05.jpg",
|
| 149 |
+
"clusters_01_screenshot_06.jpg",
|
| 150 |
+
"clusters_01_screenshot_07.jpg",
|
| 151 |
+
"clusters_01_screenshot_08.jpg",
|
| 152 |
+
"clusters_01_screenshot_09.jpg",
|
| 153 |
+
"clusters_01_screenshot_10.jpg",
|
| 154 |
+
"clusters_01_screenshot_11.jpg",
|
| 155 |
+
"clusters_01_screenshot_12.jpg",
|
| 156 |
+
"clusters_01_screenshot_13.jpg",
|
| 157 |
+
"clusters_01_screenshot_14.jpg",
|
| 158 |
+
"clusters_01_screenshot_15.jpg",
|
| 159 |
+
"clusters_01_screenshot_16.jpg",
|
| 160 |
+
"clusters_01_screenshot_17.jpg",
|
| 161 |
+
"clusters_01_screenshot_18.jpg",
|
| 162 |
+
"clusters_01_screenshot_19.jpg",
|
| 163 |
+
"pocket_01.pdb",
|
| 164 |
+
"pocket_02.pdb",
|
| 165 |
+
"pocket_03.pdb",
|
| 166 |
+
"pocket_04.pdb",
|
| 167 |
+
"pocket_05.pdb",
|
| 168 |
+
"pocket_06.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
+
"clusters",
|
| 172 |
+
"clusters-00",
|
| 173 |
+
"clusters-01",
|
| 174 |
+
"dist-perres",
|
| 175 |
+
"energies",
|
| 176 |
+
"fluctuation",
|
| 177 |
+
"hbonds",
|
| 178 |
+
"interactions",
|
| 179 |
+
"pca",
|
| 180 |
+
"pockets",
|
| 181 |
+
"rgyr",
|
| 182 |
+
"rmsd-pairwise",
|
| 183 |
+
"rmsd-perres",
|
| 184 |
+
"rmsds",
|
| 185 |
+
"sasa",
|
| 186 |
+
"tmscores"
|
| 187 |
+
],
|
| 188 |
+
"mdIndex": 0,
|
| 189 |
+
"mdNumber": 1,
|
| 190 |
+
"refframe": 0,
|
| 191 |
+
"internalId": "683f508fe8722aa078718381",
|
| 192 |
+
"creationDate": "2025-06-03T19:44:15.000Z",
|
| 193 |
+
"identifier": "A001G"
|
| 194 |
+
}
|
data/files/A001G/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A001G", "accession": "A001G", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1LZW", "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": ["1LZW"], "FORCED_REFERENCES": null, "REFERENCES": ["P0A8Q6", "P0ABH9"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVAYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA", "MLNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDE"], "NUCLSEQ": [], "DOMAINS": ["ATP-dependent Clp protease adapter protein ClpS", "ATP-dependent Clp protease ATP-binding subunit ClpA", "Clp R", "Repeat 1", "Repeat 2", "Disordered"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3780, "SYSTRES": 237, "PROTATS": 3780, "PROTRES": 237, "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"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.12617, "BOXSIZEY": 9.12617, "BOXSIZEZ": 6.40912, "mdName": "replica 1", "mdAtoms": 3780, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001G/files/topology.tpr", "length": 1323080, "contentType": "application/octet-stream", "metadata": {"project": "683f508fe8722aa078718381", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001G/files/screenshot.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f508fe8722aa078718381", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001G/files/trajectory.bin", "length": 226845360, "contentType": "application/octet-stream", "metadata": {"project": "683f508fe8722aa078718381", "md": 0, "frames": 5001, "atoms": 3780}}, {"name": 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data/files/A001H/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001H",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1M10",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"1M10"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P04275",
|
| 31 |
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"P07359"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"HDFYCSRLLDLVFLLDGSSRLSEAEFEVLKAFVVDMMEQLRISQKWVRVAVVEYHDGSHAYIGLKDRKRPSELRRIASQVKYAGSQVASTSEVLKYTLFQIFSKIDRPEASRIALLLMASQEPQRMSRNFVRYVQGLKKKKVIVIPVGIGPHANLKQIRLIEKQAPENKAFVLSSVDELEQQRDEIVSYLCDLAPEAPP",
|
| 38 |
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"HPICEVSKVASHLEVNCDKRQLTALPPDLPKDTTILHLSENLLYTFSLATLMPYTRLTQLNLDRCELTKLQVDGTLPVLGTLDLSHNQLQSLPLLGQTLPALTVLDVSFNRLTSLPLGALRGLGELQELYLKGNELKTLPPGLLTPTPKLEKLSLANNQLTELPAGLLNGLENLDTLLLQENSLYTIPKGFFGSHLLPFAFLHGNPWLCNCEILYFRRWLQDNAENVYVWKQGVDVKAVTSNVASVQCDNSDKFPVYKYPGKGCPTL"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
+
"von Willebrand factor",
|
| 43 |
+
"VWFA 1; binding site for platelet glycoprotein Ib",
|
| 44 |
+
"Platelet glycoprotein Ib alpha chain",
|
| 45 |
+
"Glycocalicin",
|
| 46 |
+
"LRRNT",
|
| 47 |
+
"LRRCT"
|
| 48 |
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],
|
| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
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"TIMESTEP": 2,
|
| 51 |
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"TEMP": 310,
|
| 52 |
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"ENSEMBLE": "NPT",
|
| 53 |
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"FF": [
|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
|
| 58 |
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"SYSTATS": 7468,
|
| 59 |
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"SYSTRES": 466,
|
| 60 |
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"PROTATS": 7468,
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| 61 |
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"PROTRES": 466,
|
| 62 |
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"NUCLATS": 0,
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| 63 |
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"NUCLRES": 0,
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| 64 |
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| 65 |
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"LIPIRES": 0,
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| 66 |
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"CARBATS": 0,
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| 67 |
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"CARBRES": 0,
|
| 68 |
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| 69 |
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"SOLVRES": 0,
|
| 70 |
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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
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"name": "chain A-chain B interaction",
|
| 76 |
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"agent_1": "chain A",
|
| 77 |
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"agent_2": "chain B",
|
| 78 |
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"selection_1": "chain A",
|
| 79 |
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"selection_2": "chain B",
|
| 80 |
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"type": "protein-protein"
|
| 81 |
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}
|
| 82 |
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],
|
| 83 |
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"PBC_SELECTION": null,
|
| 84 |
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|
| 85 |
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"MEMBRANES": null,
|
| 86 |
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"CUSTOMS": null,
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| 87 |
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| 88 |
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"PTM": [],
|
| 89 |
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"MULTIMERIC": null,
|
| 90 |
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"COLLECTIONS": "dynarepo",
|
| 91 |
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"WARNINGS": [],
|
| 92 |
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"BOXSIZEX": 10.1917,
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| 93 |
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"BOXSIZEY": 10.1917,
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| 94 |
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"BOXSIZEZ": 7.20074,
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| 95 |
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"mdName": "replica 1",
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| 96 |
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| 97 |
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| 98 |
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},
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| 99 |
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"mds": [
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| 100 |
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| 101 |
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| 102 |
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| 103 |
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],
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| 104 |
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|
| 105 |
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"files": [
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| 106 |
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|
| 107 |
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| 108 |
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| 109 |
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| 110 |
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|
| 124 |
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| 125 |
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| 160 |
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"clusters_01_screenshot_16.jpg",
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| 161 |
+
"clusters_01_screenshot_17.jpg",
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| 162 |
+
"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"clusters_01_screenshot_19.jpg",
|
| 164 |
+
"pocket_01.pdb",
|
| 165 |
+
"pocket_02.pdb",
|
| 166 |
+
"pocket_03.pdb",
|
| 167 |
+
"pocket_04.pdb",
|
| 168 |
+
"pocket_05.pdb",
|
| 169 |
+
"pocket_06.pdb",
|
| 170 |
+
"pocket_07.pdb",
|
| 171 |
+
"pocket_08.pdb",
|
| 172 |
+
"pocket_09.pdb",
|
| 173 |
+
"pocket_10.pdb"
|
| 174 |
+
],
|
| 175 |
+
"analyses": [
|
| 176 |
+
"clusters",
|
| 177 |
+
"clusters-00",
|
| 178 |
+
"clusters-01",
|
| 179 |
+
"dist-perres",
|
| 180 |
+
"energies",
|
| 181 |
+
"fluctuation",
|
| 182 |
+
"hbonds",
|
| 183 |
+
"interactions",
|
| 184 |
+
"pca",
|
| 185 |
+
"pockets",
|
| 186 |
+
"rgyr",
|
| 187 |
+
"rmsd-pairwise",
|
| 188 |
+
"rmsd-perres",
|
| 189 |
+
"rmsds",
|
| 190 |
+
"sasa",
|
| 191 |
+
"tmscores"
|
| 192 |
+
],
|
| 193 |
+
"mdIndex": 0,
|
| 194 |
+
"mdNumber": 1,
|
| 195 |
+
"refframe": 0,
|
| 196 |
+
"internalId": "683f51f01c69c04265d3bb2f",
|
| 197 |
+
"creationDate": "2025-06-03T19:50:08.000Z",
|
| 198 |
+
"identifier": "A001H"
|
| 199 |
+
}
|
data/files/A001H/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
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| 1 |
+
{
|
| 2 |
+
"accession": "A001I",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1MQ8",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1MQ8"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P05362",
|
| 31 |
+
"P20701"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"VDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI",
|
| 38 |
+
"QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQT"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Intercellular adhesion molecule 1",
|
| 43 |
+
"Ig-like C2-type 1",
|
| 44 |
+
"Ig-like C2-type 2",
|
| 45 |
+
"Cell attachment site; atypical",
|
| 46 |
+
"Integrin alpha-L",
|
| 47 |
+
"VWFA"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 5705,
|
| 59 |
+
"SYSTRES": 361,
|
| 60 |
+
"PROTATS": 5705,
|
| 61 |
+
"PROTRES": 361,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
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"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
}
|
| 82 |
+
],
|
| 83 |
+
"PBC_SELECTION": null,
|
| 84 |
+
"CHAINNAMES": null,
|
| 85 |
+
"MEMBRANES": null,
|
| 86 |
+
"CUSTOMS": null,
|
| 87 |
+
"ORIENTATION": null,
|
| 88 |
+
"PTM": [],
|
| 89 |
+
"MULTIMERIC": null,
|
| 90 |
+
"COLLECTIONS": "dynarepo",
|
| 91 |
+
"WARNINGS": [],
|
| 92 |
+
"BOXSIZEX": 11.9032,
|
| 93 |
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"BOXSIZEY": 11.9032,
|
| 94 |
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"BOXSIZEZ": 8.40875,
|
| 95 |
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"mdName": "replica 1",
|
| 96 |
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"mdAtoms": 5705,
|
| 97 |
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"mdFrames": 5001
|
| 98 |
+
},
|
| 99 |
+
"mds": [
|
| 100 |
+
"replica 1",
|
| 101 |
+
"replica 2",
|
| 102 |
+
"replica 3"
|
| 103 |
+
],
|
| 104 |
+
"mdref": 0,
|
| 105 |
+
"files": [
|
| 106 |
+
"topology.tpr",
|
| 107 |
+
"screenshot.jpg",
|
| 108 |
+
"trajectory.bin",
|
| 109 |
+
"pca_trajectory_01.bin",
|
| 110 |
+
"pca_trajectory_02.bin",
|
| 111 |
+
"pca_trajectory_03.bin",
|
| 112 |
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"pca_trajectory_04.bin",
|
| 113 |
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"pca_trajectory_05.bin",
|
| 114 |
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"pca_trajectory_06.bin",
|
| 115 |
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"pca_trajectory_07.bin",
|
| 116 |
+
"pca_trajectory_08.bin",
|
| 117 |
+
"structure.pdb",
|
| 118 |
+
"trajectory.xtc",
|
| 119 |
+
"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
+
"clusters_00_screenshot_02.jpg",
|
| 122 |
+
"clusters_00_screenshot_03.jpg",
|
| 123 |
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"clusters_00_screenshot_04.jpg",
|
| 124 |
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"clusters_00_screenshot_05.jpg",
|
| 125 |
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"clusters_00_screenshot_06.jpg",
|
| 126 |
+
"clusters_00_screenshot_07.jpg",
|
| 127 |
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"clusters_00_screenshot_08.jpg",
|
| 128 |
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"clusters_00_screenshot_09.jpg",
|
| 129 |
+
"clusters_00_screenshot_10.jpg",
|
| 130 |
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"clusters_00_screenshot_11.jpg",
|
| 131 |
+
"clusters_00_screenshot_12.jpg",
|
| 132 |
+
"clusters_00_screenshot_13.jpg",
|
| 133 |
+
"clusters_00_screenshot_14.jpg",
|
| 134 |
+
"clusters_00_screenshot_15.jpg",
|
| 135 |
+
"clusters_00_screenshot_16.jpg",
|
| 136 |
+
"clusters_00_screenshot_17.jpg",
|
| 137 |
+
"clusters_00_screenshot_18.jpg",
|
| 138 |
+
"clusters_00_screenshot_19.jpg",
|
| 139 |
+
"clusters_00_screenshot_20.jpg",
|
| 140 |
+
"clusters_00_screenshot_21.jpg",
|
| 141 |
+
"clusters_01_screenshot_00.jpg",
|
| 142 |
+
"clusters_01_screenshot_01.jpg",
|
| 143 |
+
"clusters_01_screenshot_02.jpg",
|
| 144 |
+
"clusters_01_screenshot_03.jpg",
|
| 145 |
+
"clusters_01_screenshot_04.jpg",
|
| 146 |
+
"clusters_01_screenshot_05.jpg",
|
| 147 |
+
"clusters_01_screenshot_06.jpg",
|
| 148 |
+
"clusters_01_screenshot_07.jpg",
|
| 149 |
+
"clusters_01_screenshot_08.jpg",
|
| 150 |
+
"clusters_01_screenshot_09.jpg",
|
| 151 |
+
"clusters_01_screenshot_10.jpg",
|
| 152 |
+
"clusters_01_screenshot_11.jpg",
|
| 153 |
+
"clusters_01_screenshot_12.jpg",
|
| 154 |
+
"clusters_01_screenshot_13.jpg",
|
| 155 |
+
"clusters_01_screenshot_14.jpg",
|
| 156 |
+
"clusters_01_screenshot_15.jpg",
|
| 157 |
+
"clusters_01_screenshot_16.jpg",
|
| 158 |
+
"clusters_01_screenshot_17.jpg",
|
| 159 |
+
"clusters_01_screenshot_18.jpg",
|
| 160 |
+
"clusters_01_screenshot_19.jpg",
|
| 161 |
+
"clusters_01_screenshot_20.jpg",
|
| 162 |
+
"pocket_01.pdb",
|
| 163 |
+
"pocket_02.pdb"
|
| 164 |
+
],
|
| 165 |
+
"analyses": [
|
| 166 |
+
"clusters",
|
| 167 |
+
"clusters-00",
|
| 168 |
+
"clusters-01",
|
| 169 |
+
"dist-perres",
|
| 170 |
+
"energies",
|
| 171 |
+
"fluctuation",
|
| 172 |
+
"hbonds",
|
| 173 |
+
"interactions",
|
| 174 |
+
"pca",
|
| 175 |
+
"pockets",
|
| 176 |
+
"rgyr",
|
| 177 |
+
"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
+
"rmsds",
|
| 180 |
+
"sasa",
|
| 181 |
+
"tmscores"
|
| 182 |
+
],
|
| 183 |
+
"mdIndex": 0,
|
| 184 |
+
"mdNumber": 1,
|
| 185 |
+
"refframe": 0,
|
| 186 |
+
"internalId": "683f53a1b9e3119e941968bb",
|
| 187 |
+
"creationDate": "2025-06-03T19:57:21.000Z",
|
| 188 |
+
"identifier": "A001I"
|
| 189 |
+
}
|
data/files/A001I/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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| 1 |
+
{"project_identifier": "A001I", "accession": "A001I", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1MQ8", "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": ["1MQ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P05362", "P20701"], 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data/files/A001J/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001J",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1MTN",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1MTN"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00766",
|
| 31 |
+
"P00974"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"CGVPAIQPVLS",
|
| 38 |
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"ANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDSGGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN",
|
| 39 |
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"IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGSSSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTTCVTTGWGLTRY",
|
| 40 |
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"RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Chymotrypsin A chain A",
|
| 45 |
+
"Chymotrypsin A chain B",
|
| 46 |
+
"Chymotrypsin A chain C",
|
| 47 |
+
"Peptidase S1",
|
| 48 |
+
"Pancreatic trypsin inhibitor",
|
| 49 |
+
"BPTI/Kunitz inhibitor",
|
| 50 |
+
"Reactive bond for trypsin"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 4389,
|
| 62 |
+
"SYSTRES": 297,
|
| 63 |
+
"PROTATS": 4389,
|
| 64 |
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"PROTRES": 297,
|
| 65 |
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"NUCLATS": 0,
|
| 66 |
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"NUCLRES": 0,
|
| 67 |
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"LIPIATS": 0,
|
| 68 |
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"LIPIRES": 0,
|
| 69 |
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"CARBATS": 0,
|
| 70 |
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"CARBRES": 0,
|
| 71 |
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"SOLVATS": 0,
|
| 72 |
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"SOLVRES": 0,
|
| 73 |
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"COUNCAT": 0,
|
| 74 |
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"COUNANI": 0,
|
| 75 |
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"COUNION": 0,
|
| 76 |
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"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
},
|
| 85 |
+
{
|
| 86 |
+
"name": "chain A-chain C interaction",
|
| 87 |
+
"agent_1": "chain A",
|
| 88 |
+
"agent_2": "chain C",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain C",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "chain B-chain C interaction",
|
| 95 |
+
"agent_1": "chain B",
|
| 96 |
+
"agent_2": "chain C",
|
| 97 |
+
"selection_1": "chain A",
|
| 98 |
+
"selection_2": "chain D",
|
| 99 |
+
"type": "protein-protein"
|
| 100 |
+
},
|
| 101 |
+
{
|
| 102 |
+
"name": "chain B-chain D interaction",
|
| 103 |
+
"agent_1": "chain B",
|
| 104 |
+
"agent_2": "chain D",
|
| 105 |
+
"selection_1": "chain B",
|
| 106 |
+
"selection_2": "chain C",
|
| 107 |
+
"type": "protein-protein"
|
| 108 |
+
},
|
| 109 |
+
{
|
| 110 |
+
"name": "chain C-chain D interaction",
|
| 111 |
+
"agent_1": "chain C",
|
| 112 |
+
"agent_2": "chain D",
|
| 113 |
+
"selection_1": "chain B",
|
| 114 |
+
"selection_2": "chain D",
|
| 115 |
+
"type": "protein-protein"
|
| 116 |
+
}
|
| 117 |
+
],
|
| 118 |
+
"PBC_SELECTION": null,
|
| 119 |
+
"CHAINNAMES": null,
|
| 120 |
+
"MEMBRANES": null,
|
| 121 |
+
"CUSTOMS": null,
|
| 122 |
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"ORIENTATION": null,
|
| 123 |
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"PTM": [],
|
| 124 |
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"MULTIMERIC": null,
|
| 125 |
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"COLLECTIONS": "dynarepo",
|
| 126 |
+
"WARNINGS": [],
|
| 127 |
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"BOXSIZEX": 9.09646,
|
| 128 |
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"BOXSIZEY": 9.09646,
|
| 129 |
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"BOXSIZEZ": 6.48086,
|
| 130 |
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"mdName": "replica 1",
|
| 131 |
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"mdAtoms": 4389,
|
| 132 |
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"mdFrames": 5001
|
| 133 |
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},
|
| 134 |
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"mds": [
|
| 135 |
+
"replica 1",
|
| 136 |
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"replica 2",
|
| 137 |
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"replica 3"
|
| 138 |
+
],
|
| 139 |
+
"mdref": 0,
|
| 140 |
+
"files": [
|
| 141 |
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|
| 142 |
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"screenshot.jpg",
|
| 143 |
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"trajectory.bin",
|
| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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|
| 157 |
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"structure.pdb",
|
| 158 |
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"trajectory.xtc",
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| 159 |
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data/files/A001J/records.jsonl
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data/files/A001K/project.json
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| 1 |
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{
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| 2 |
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| 3 |
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| 5 |
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| 7 |
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| 8 |
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|
| 9 |
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|
| 10 |
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| 11 |
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| 12 |
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| 16 |
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| 17 |
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| 116 |
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"structure.pdb",
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"trajectory.xtc",
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"clusters_00_screenshot_00.jpg",
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"clusters_01_screenshot_17.jpg",
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"clusters_01_screenshot_18.jpg",
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+
"pocket_01.pdb",
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"pocket_02.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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| 177 |
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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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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 1,
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"internalId": "683f5609ececf955b91e2fb8",
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"creationDate": "2025-06-03T20:07:37.000Z",
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"identifier": "A001K"
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}
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data/files/A001K/records.jsonl
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| 1 |
+
{
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| 2 |
+
"accession": "A001L",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1OP9",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1OP9"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01764",
|
| 31 |
+
"P61626"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"QVQLQESGGGSVQAGGSLRLSCSASGYTYISGWFRQAPGKEREGVAAIRSSDGTTYYADSVKGRFTISQDNAKNTVYLQMNSLKPEDTAMYYCAATEVAGWPLDIGIYDYWGQGTEVTVSS",
|
| 38 |
+
"KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Immunoglobulin heavy variable 3-23",
|
| 43 |
+
"Ig-like",
|
| 44 |
+
"Framework-1",
|
| 45 |
+
"Complementarity-determining-1",
|
| 46 |
+
"Framework-2",
|
| 47 |
+
"Complementarity-determining-2",
|
| 48 |
+
"Framework-3",
|
| 49 |
+
"Complementarity-determining-3",
|
| 50 |
+
"Lysozyme C",
|
| 51 |
+
"C-type lysozyme"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
+
"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 3801,
|
| 63 |
+
"SYSTRES": 251,
|
| 64 |
+
"PROTATS": 3801,
|
| 65 |
+
"PROTRES": 251,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "chain A-chain B interaction",
|
| 80 |
+
"agent_1": "chain A",
|
| 81 |
+
"agent_2": "chain B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
}
|
| 86 |
+
],
|
| 87 |
+
"PBC_SELECTION": null,
|
| 88 |
+
"CHAINNAMES": null,
|
| 89 |
+
"MEMBRANES": null,
|
| 90 |
+
"CUSTOMS": null,
|
| 91 |
+
"ORIENTATION": null,
|
| 92 |
+
"PTM": [],
|
| 93 |
+
"MULTIMERIC": null,
|
| 94 |
+
"COLLECTIONS": "dynarepo",
|
| 95 |
+
"WARNINGS": [],
|
| 96 |
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"BOXSIZEX": 9.53664,
|
| 97 |
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"BOXSIZEY": 9.53664,
|
| 98 |
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"BOXSIZEZ": 6.77299,
|
| 99 |
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"mdName": "replica 1",
|
| 100 |
+
"mdAtoms": 3801,
|
| 101 |
+
"mdFrames": 5001
|
| 102 |
+
},
|
| 103 |
+
"mds": [
|
| 104 |
+
"replica 1",
|
| 105 |
+
"replica 2",
|
| 106 |
+
"replica 3"
|
| 107 |
+
],
|
| 108 |
+
"mdref": 0,
|
| 109 |
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"files": [
|
| 110 |
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"topology.tpr",
|
| 111 |
+
"screenshot.jpg",
|
| 112 |
+
"trajectory.bin",
|
| 113 |
+
"pca_trajectory_01.bin",
|
| 114 |
+
"pca_trajectory_02.bin",
|
| 115 |
+
"pca_trajectory_03.bin",
|
| 116 |
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"pca_trajectory_04.bin",
|
| 117 |
+
"pca_trajectory_05.bin",
|
| 118 |
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"pca_trajectory_06.bin",
|
| 119 |
+
"pca_trajectory_07.bin",
|
| 120 |
+
"pca_trajectory_08.bin",
|
| 121 |
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"pca_trajectory_09.bin",
|
| 122 |
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"pca_trajectory_10.bin",
|
| 123 |
+
"pca_trajectory_11.bin",
|
| 124 |
+
"pca_trajectory_12.bin",
|
| 125 |
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"pca_trajectory_13.bin",
|
| 126 |
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"pca_trajectory_14.bin",
|
| 127 |
+
"pca_trajectory_15.bin",
|
| 128 |
+
"pca_trajectory_16.bin",
|
| 129 |
+
"structure.pdb",
|
| 130 |
+
"trajectory.xtc",
|
| 131 |
+
"clusters_00_screenshot_00.jpg",
|
| 132 |
+
"clusters_00_screenshot_01.jpg",
|
| 133 |
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"clusters_00_screenshot_02.jpg",
|
| 134 |
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"clusters_00_screenshot_03.jpg",
|
| 135 |
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"clusters_00_screenshot_04.jpg",
|
| 136 |
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"clusters_00_screenshot_05.jpg",
|
| 137 |
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"clusters_00_screenshot_06.jpg",
|
| 138 |
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"clusters_00_screenshot_07.jpg",
|
| 139 |
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"clusters_00_screenshot_08.jpg",
|
| 140 |
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"clusters_00_screenshot_09.jpg",
|
| 141 |
+
"clusters_00_screenshot_10.jpg",
|
| 142 |
+
"clusters_00_screenshot_11.jpg",
|
| 143 |
+
"clusters_00_screenshot_12.jpg",
|
| 144 |
+
"clusters_00_screenshot_13.jpg",
|
| 145 |
+
"clusters_00_screenshot_14.jpg",
|
| 146 |
+
"clusters_00_screenshot_15.jpg",
|
| 147 |
+
"clusters_00_screenshot_16.jpg",
|
| 148 |
+
"clusters_00_screenshot_17.jpg",
|
| 149 |
+
"clusters_00_screenshot_18.jpg",
|
| 150 |
+
"clusters_00_screenshot_19.jpg",
|
| 151 |
+
"clusters_00_screenshot_20.jpg",
|
| 152 |
+
"clusters_01_screenshot_00.jpg",
|
| 153 |
+
"clusters_01_screenshot_01.jpg",
|
| 154 |
+
"clusters_01_screenshot_02.jpg",
|
| 155 |
+
"clusters_01_screenshot_03.jpg",
|
| 156 |
+
"clusters_01_screenshot_04.jpg",
|
| 157 |
+
"clusters_01_screenshot_05.jpg",
|
| 158 |
+
"clusters_01_screenshot_06.jpg",
|
| 159 |
+
"clusters_01_screenshot_07.jpg",
|
| 160 |
+
"clusters_01_screenshot_08.jpg",
|
| 161 |
+
"clusters_01_screenshot_09.jpg",
|
| 162 |
+
"clusters_01_screenshot_10.jpg",
|
| 163 |
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"clusters_01_screenshot_11.jpg",
|
| 164 |
+
"clusters_01_screenshot_12.jpg",
|
| 165 |
+
"clusters_01_screenshot_13.jpg",
|
| 166 |
+
"clusters_01_screenshot_14.jpg",
|
| 167 |
+
"clusters_01_screenshot_15.jpg",
|
| 168 |
+
"clusters_01_screenshot_16.jpg",
|
| 169 |
+
"clusters_01_screenshot_17.jpg",
|
| 170 |
+
"clusters_01_screenshot_18.jpg",
|
| 171 |
+
"clusters_01_screenshot_19.jpg",
|
| 172 |
+
"pocket_01.pdb",
|
| 173 |
+
"pocket_02.pdb"
|
| 174 |
+
],
|
| 175 |
+
"analyses": [
|
| 176 |
+
"clusters",
|
| 177 |
+
"clusters-00",
|
| 178 |
+
"clusters-01",
|
| 179 |
+
"dist-perres",
|
| 180 |
+
"energies",
|
| 181 |
+
"fluctuation",
|
| 182 |
+
"hbonds",
|
| 183 |
+
"interactions",
|
| 184 |
+
"pca",
|
| 185 |
+
"pockets",
|
| 186 |
+
"rgyr",
|
| 187 |
+
"rmsd-pairwise",
|
| 188 |
+
"rmsd-perres",
|
| 189 |
+
"rmsds",
|
| 190 |
+
"sasa",
|
| 191 |
+
"tmscores"
|
| 192 |
+
],
|
| 193 |
+
"mdIndex": 0,
|
| 194 |
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"mdNumber": 1,
|
| 195 |
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"refframe": 0,
|
| 196 |
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"internalId": "683f573e7765e54ebf3005ea",
|
| 197 |
+
"creationDate": "2025-06-03T20:12:46.000Z",
|
| 198 |
+
"identifier": "A001L"
|
| 199 |
+
}
|
data/files/A001L/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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| 1 |
+
{"project_identifier": "A001L", "accession": "A001L", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1OP9", "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": ["1OP9"], "FORCED_REFERENCES": null, "REFERENCES": ["P01764", "P61626"], 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data/files/A001M/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1OQE",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1OQE"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9Y275",
|
| 31 |
+
"Q96RJ3"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"PTPCVPAECFDLLVRHCVACGLLR",
|
| 38 |
+
"PTPCVPAECFDLLVRHCVACGLLRTPRPKPA",
|
| 39 |
+
"VTQDCLQLIADSETPTIQKGSYTFVPWLLSFKRGSALEEKENKILVKETGYFFIYGQVLYTDKTYAMGHLIQRKKVHVFGDELSLVTLFRCIQNMPETLPNNSCYSAGIAKLEEGDELQLAIPRENAQISLDGDVTFFGALKLL"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Tumor necrosis factor ligand superfamily member 13b, membrane form",
|
| 44 |
+
"Tumor necrosis factor ligand superfamily member 13b, soluble form",
|
| 45 |
+
"THD",
|
| 46 |
+
"Tumor necrosis factor receptor superfamily member 13C",
|
| 47 |
+
"Essential for TNFSF13B/TALL1/BAFF/BLyS binding",
|
| 48 |
+
"Disordered"
|
| 49 |
+
],
|
| 50 |
+
"FRAMESTEP": 0.1,
|
| 51 |
+
"TIMESTEP": 2,
|
| 52 |
+
"TEMP": 310,
|
| 53 |
+
"ENSEMBLE": "NPT",
|
| 54 |
+
"FF": [
|
| 55 |
+
"CHARMM36m"
|
| 56 |
+
],
|
| 57 |
+
"WAT": "TIP3P",
|
| 58 |
+
"BOXTYPE": "Dodecahedron",
|
| 59 |
+
"SYSTATS": 26590,
|
| 60 |
+
"SYSTRES": 1681,
|
| 61 |
+
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| 62 |
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| 63 |
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| 64 |
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| 72 |
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| 74 |
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| 75 |
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|
| 76 |
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| 77 |
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| 78 |
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| 79 |
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| 80 |
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| 81 |
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| 82 |
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| 83 |
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| 84 |
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| 85 |
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| 86 |
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| 87 |
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| 88 |
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| 89 |
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| 90 |
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| 91 |
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| 92 |
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| 93 |
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| 94 |
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| 95 |
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| 96 |
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| 97 |
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| 98 |
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| 99 |
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| 100 |
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| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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| 108 |
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| 109 |
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| 110 |
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| 111 |
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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| 117 |
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| 118 |
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| 119 |
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| 120 |
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| 121 |
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| 122 |
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| 123 |
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| 124 |
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| 125 |
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| 126 |
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| 127 |
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| 128 |
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| 129 |
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| 130 |
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| 131 |
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| 132 |
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| 133 |
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| 134 |
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| 135 |
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| 136 |
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| 137 |
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| 138 |
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| 139 |
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| 140 |
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| 141 |
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| 142 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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| 157 |
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| 158 |
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| 159 |
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| 160 |
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| 161 |
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| 162 |
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| 163 |
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| 164 |
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| 165 |
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| 166 |
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| 167 |
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| 168 |
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| 169 |
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| 170 |
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| 171 |
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| 172 |
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| 173 |
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| 174 |
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| 175 |
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| 176 |
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| 177 |
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| 178 |
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| 179 |
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| 180 |
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| 181 |
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| 182 |
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| 183 |
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| 184 |
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| 185 |
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| 186 |
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| 187 |
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| 188 |
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| 189 |
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| 190 |
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| 191 |
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| 192 |
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| 193 |
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| 194 |
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| 195 |
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| 196 |
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| 197 |
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| 198 |
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| 199 |
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| 200 |
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| 201 |
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| 202 |
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| 203 |
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| 204 |
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| 205 |
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| 206 |
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| 207 |
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| 208 |
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| 209 |
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| 210 |
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| 211 |
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| 212 |
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| 213 |
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| 214 |
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| 215 |
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| 216 |
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| 217 |
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| 218 |
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| 219 |
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| 220 |
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| 221 |
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| 222 |
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| 223 |
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| 224 |
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| 225 |
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| 226 |
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| 227 |
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| 228 |
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| 229 |
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| 230 |
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| 231 |
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| 232 |
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| 233 |
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| 234 |
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| 235 |
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| 236 |
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| 237 |
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| 238 |
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| 239 |
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| 240 |
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| 241 |
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| 242 |
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| 243 |
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| 244 |
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| 245 |
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| 246 |
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| 247 |
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| 248 |
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| 249 |
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| 250 |
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| 251 |
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| 252 |
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| 253 |
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| 254 |
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| 255 |
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| 256 |
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| 257 |
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| 258 |
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| 259 |
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| 260 |
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| 261 |
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| 262 |
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| 263 |
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| 264 |
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| 265 |
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| 266 |
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| 267 |
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| 268 |
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| 269 |
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| 270 |
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| 271 |
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| 272 |
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| 273 |
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| 274 |
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| 275 |
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| 276 |
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| 277 |
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| 278 |
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| 279 |
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| 280 |
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| 281 |
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| 282 |
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| 283 |
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| 284 |
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| 285 |
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| 286 |
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| 287 |
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| 288 |
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| 289 |
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| 290 |
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| 291 |
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| 292 |
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| 293 |
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| 294 |
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| 295 |
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| 296 |
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| 297 |
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| 298 |
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| 299 |
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| 300 |
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| 301 |
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| 302 |
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| 303 |
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| 304 |
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| 305 |
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| 306 |
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| 307 |
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| 308 |
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| 309 |
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| 310 |
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| 311 |
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| 312 |
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| 313 |
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| 314 |
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| 315 |
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| 316 |
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| 317 |
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| 318 |
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| 320 |
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| 321 |
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| 322 |
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| 323 |
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| 324 |
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| 325 |
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| 326 |
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| 327 |
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| 328 |
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| 330 |
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| 332 |
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| 334 |
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| 335 |
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| 336 |
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| 337 |
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| 338 |
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| 339 |
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| 340 |
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| 341 |
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| 342 |
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| 343 |
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| 344 |
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| 345 |
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| 346 |
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| 347 |
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| 348 |
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| 349 |
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| 350 |
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| 351 |
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| 352 |
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| 353 |
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| 354 |
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| 355 |
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| 356 |
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| 359 |
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| 360 |
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| 361 |
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| 362 |
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| 364 |
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| 369 |
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| 370 |
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| 371 |
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| 372 |
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| 373 |
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| 374 |
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| 375 |
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| 378 |
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| 379 |
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| 380 |
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| 381 |
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| 382 |
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| 384 |
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| 385 |
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| 386 |
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| 388 |
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| 396 |
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| 410 |
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| 411 |
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"clusters-22",
|
| 1354 |
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"clusters-23",
|
| 1355 |
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"clusters-24",
|
| 1356 |
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"clusters-25",
|
| 1357 |
+
"clusters-26",
|
| 1358 |
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"clusters-27",
|
| 1359 |
+
"clusters-28",
|
| 1360 |
+
"clusters-29",
|
| 1361 |
+
"clusters-30",
|
| 1362 |
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"clusters-31",
|
| 1363 |
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"clusters-32",
|
| 1364 |
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"clusters-33",
|
| 1365 |
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"clusters-34",
|
| 1366 |
+
"clusters-35",
|
| 1367 |
+
"clusters-36",
|
| 1368 |
+
"clusters-37",
|
| 1369 |
+
"clusters-38",
|
| 1370 |
+
"clusters-39",
|
| 1371 |
+
"clusters-40",
|
| 1372 |
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"clusters-41",
|
| 1373 |
+
"clusters-42",
|
| 1374 |
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"dist-perres",
|
| 1375 |
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"energies",
|
| 1376 |
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"fluctuation",
|
| 1377 |
+
"hbonds",
|
| 1378 |
+
"interactions",
|
| 1379 |
+
"pca",
|
| 1380 |
+
"pockets",
|
| 1381 |
+
"rgyr"
|
| 1382 |
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|
| 1383 |
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|
| 1384 |
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| 1385 |
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| 1386 |
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|
| 1387 |
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"creationDate": "2025-06-03T20:27:20.000Z",
|
| 1388 |
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"identifier": "A001M"
|
| 1389 |
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}
|
data/files/A001M/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
data/files/A001N/project.json
ADDED
|
@@ -0,0 +1,321 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001N",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1P27",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"1P27"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P61326",
|
| 31 |
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"Q9Y5S9"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP",
|
| 38 |
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"ESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKP"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Protein mago nashi homolog",
|
| 43 |
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"RNA-binding protein 8A",
|
| 44 |
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"RRM",
|
| 45 |
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"Disordered"
|
| 46 |
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],
|
| 47 |
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"FRAMESTEP": 0.1,
|
| 48 |
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"TIMESTEP": 2,
|
| 49 |
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"TEMP": 310,
|
| 50 |
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"ENSEMBLE": "NPT",
|
| 51 |
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"FF": [
|
| 52 |
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"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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"WAT": "TIP3P",
|
| 55 |
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"BOXTYPE": "Dodecahedron",
|
| 56 |
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"SYSTATS": 7628,
|
| 57 |
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"SYSTRES": 472,
|
| 58 |
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"PROTATS": 7628,
|
| 59 |
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"PROTRES": 472,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
|
| 63 |
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|
| 64 |
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"CARBATS": 0,
|
| 65 |
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"CARBRES": 0,
|
| 66 |
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"SOLVATS": 0,
|
| 67 |
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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
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"COUNANI": 0,
|
| 70 |
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"COUNION": 0,
|
| 71 |
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"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
},
|
| 80 |
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{
|
| 81 |
+
"name": "chain A-chain C interaction",
|
| 82 |
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"agent_1": "chain A",
|
| 83 |
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"agent_2": "chain C",
|
| 84 |
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"selection_1": "chain A",
|
| 85 |
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"selection_2": "chain C",
|
| 86 |
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"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
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{
|
| 89 |
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"name": "chain A-chain D interaction",
|
| 90 |
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"agent_1": "chain A",
|
| 91 |
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"agent_2": "chain D",
|
| 92 |
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"selection_1": "chain A",
|
| 93 |
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"selection_2": "chain D",
|
| 94 |
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"type": "protein-protein"
|
| 95 |
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},
|
| 96 |
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{
|
| 97 |
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"name": "chain B-chain C interaction",
|
| 98 |
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"agent_1": "chain B",
|
| 99 |
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"agent_2": "chain C",
|
| 100 |
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"selection_1": "chain B",
|
| 101 |
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"selection_2": "chain C",
|
| 102 |
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"type": "protein-protein"
|
| 103 |
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},
|
| 104 |
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{
|
| 105 |
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"name": "chain C-chain D interaction",
|
| 106 |
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"agent_1": "chain C",
|
| 107 |
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"agent_2": "chain D",
|
| 108 |
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"selection_1": "chain B",
|
| 109 |
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"selection_2": "chain D",
|
| 110 |
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"type": "protein-protein"
|
| 111 |
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}
|
| 112 |
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],
|
| 113 |
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"PBC_SELECTION": null,
|
| 114 |
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"CHAINNAMES": null,
|
| 115 |
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"MEMBRANES": null,
|
| 116 |
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"CUSTOMS": null,
|
| 117 |
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"ORIENTATION": null,
|
| 118 |
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"PTM": [],
|
| 119 |
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"MULTIMERIC": null,
|
| 120 |
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"COLLECTIONS": "dynarepo",
|
| 121 |
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"WARNINGS": [],
|
| 122 |
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"BOXSIZEX": 11.1136,
|
| 123 |
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"BOXSIZEY": 11.1136,
|
| 124 |
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"BOXSIZEZ": 7.80571,
|
| 125 |
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"mdName": "replica 1",
|
| 126 |
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|
| 127 |
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|
| 128 |
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},
|
| 129 |
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"mds": [
|
| 130 |
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"replica 1",
|
| 131 |
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"replica 2",
|
| 132 |
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"replica 3"
|
| 133 |
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],
|
| 134 |
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"mdref": 0,
|
| 135 |
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"files": [
|
| 136 |
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|
| 137 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
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|
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|
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|
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|
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"clusters_01_screenshot_17.jpg",
|
| 198 |
+
"clusters_01_screenshot_18.jpg",
|
| 199 |
+
"clusters_02_screenshot_00.jpg",
|
| 200 |
+
"clusters_02_screenshot_01.jpg",
|
| 201 |
+
"clusters_02_screenshot_02.jpg",
|
| 202 |
+
"clusters_02_screenshot_03.jpg",
|
| 203 |
+
"clusters_02_screenshot_04.jpg",
|
| 204 |
+
"clusters_02_screenshot_05.jpg",
|
| 205 |
+
"clusters_02_screenshot_06.jpg",
|
| 206 |
+
"clusters_02_screenshot_07.jpg",
|
| 207 |
+
"clusters_02_screenshot_08.jpg",
|
| 208 |
+
"clusters_02_screenshot_09.jpg",
|
| 209 |
+
"clusters_02_screenshot_10.jpg",
|
| 210 |
+
"clusters_02_screenshot_11.jpg",
|
| 211 |
+
"clusters_02_screenshot_12.jpg",
|
| 212 |
+
"clusters_02_screenshot_13.jpg",
|
| 213 |
+
"clusters_02_screenshot_14.jpg",
|
| 214 |
+
"clusters_02_screenshot_15.jpg",
|
| 215 |
+
"clusters_02_screenshot_16.jpg",
|
| 216 |
+
"clusters_02_screenshot_17.jpg",
|
| 217 |
+
"clusters_03_screenshot_00.jpg",
|
| 218 |
+
"clusters_03_screenshot_01.jpg",
|
| 219 |
+
"clusters_03_screenshot_02.jpg",
|
| 220 |
+
"clusters_03_screenshot_03.jpg",
|
| 221 |
+
"clusters_03_screenshot_04.jpg",
|
| 222 |
+
"clusters_03_screenshot_05.jpg",
|
| 223 |
+
"clusters_03_screenshot_06.jpg",
|
| 224 |
+
"clusters_03_screenshot_07.jpg",
|
| 225 |
+
"clusters_03_screenshot_08.jpg",
|
| 226 |
+
"clusters_03_screenshot_09.jpg",
|
| 227 |
+
"clusters_03_screenshot_10.jpg",
|
| 228 |
+
"clusters_03_screenshot_11.jpg",
|
| 229 |
+
"clusters_03_screenshot_12.jpg",
|
| 230 |
+
"clusters_03_screenshot_13.jpg",
|
| 231 |
+
"clusters_03_screenshot_14.jpg",
|
| 232 |
+
"clusters_03_screenshot_15.jpg",
|
| 233 |
+
"clusters_03_screenshot_16.jpg",
|
| 234 |
+
"clusters_03_screenshot_17.jpg",
|
| 235 |
+
"clusters_03_screenshot_18.jpg",
|
| 236 |
+
"clusters_03_screenshot_19.jpg",
|
| 237 |
+
"clusters_04_screenshot_00.jpg",
|
| 238 |
+
"clusters_04_screenshot_01.jpg",
|
| 239 |
+
"clusters_04_screenshot_02.jpg",
|
| 240 |
+
"clusters_04_screenshot_03.jpg",
|
| 241 |
+
"clusters_04_screenshot_04.jpg",
|
| 242 |
+
"clusters_04_screenshot_05.jpg",
|
| 243 |
+
"clusters_04_screenshot_06.jpg",
|
| 244 |
+
"clusters_04_screenshot_07.jpg",
|
| 245 |
+
"clusters_04_screenshot_08.jpg",
|
| 246 |
+
"clusters_04_screenshot_09.jpg",
|
| 247 |
+
"clusters_04_screenshot_10.jpg",
|
| 248 |
+
"clusters_04_screenshot_11.jpg",
|
| 249 |
+
"clusters_04_screenshot_12.jpg",
|
| 250 |
+
"clusters_04_screenshot_13.jpg",
|
| 251 |
+
"clusters_04_screenshot_14.jpg",
|
| 252 |
+
"clusters_04_screenshot_15.jpg",
|
| 253 |
+
"clusters_04_screenshot_16.jpg",
|
| 254 |
+
"clusters_04_screenshot_17.jpg",
|
| 255 |
+
"clusters_04_screenshot_18.jpg",
|
| 256 |
+
"clusters_04_screenshot_19.jpg",
|
| 257 |
+
"clusters_04_screenshot_20.jpg",
|
| 258 |
+
"clusters_04_screenshot_21.jpg",
|
| 259 |
+
"clusters_05_screenshot_00.jpg",
|
| 260 |
+
"clusters_05_screenshot_01.jpg",
|
| 261 |
+
"clusters_05_screenshot_02.jpg",
|
| 262 |
+
"clusters_05_screenshot_03.jpg",
|
| 263 |
+
"clusters_05_screenshot_04.jpg",
|
| 264 |
+
"clusters_05_screenshot_05.jpg",
|
| 265 |
+
"clusters_05_screenshot_06.jpg",
|
| 266 |
+
"clusters_05_screenshot_07.jpg",
|
| 267 |
+
"clusters_05_screenshot_08.jpg",
|
| 268 |
+
"clusters_05_screenshot_09.jpg",
|
| 269 |
+
"clusters_05_screenshot_10.jpg",
|
| 270 |
+
"clusters_05_screenshot_11.jpg",
|
| 271 |
+
"clusters_05_screenshot_12.jpg",
|
| 272 |
+
"clusters_05_screenshot_13.jpg",
|
| 273 |
+
"clusters_05_screenshot_14.jpg",
|
| 274 |
+
"clusters_05_screenshot_15.jpg",
|
| 275 |
+
"clusters_05_screenshot_16.jpg",
|
| 276 |
+
"clusters_05_screenshot_17.jpg",
|
| 277 |
+
"clusters_05_screenshot_18.jpg",
|
| 278 |
+
"clusters_05_screenshot_19.jpg",
|
| 279 |
+
"clusters_05_screenshot_20.jpg",
|
| 280 |
+
"clusters_05_screenshot_21.jpg",
|
| 281 |
+
"clusters_05_screenshot_22.jpg",
|
| 282 |
+
"pocket_01.pdb",
|
| 283 |
+
"pocket_02.pdb",
|
| 284 |
+
"pocket_03.pdb",
|
| 285 |
+
"pocket_04.pdb",
|
| 286 |
+
"pocket_05.pdb",
|
| 287 |
+
"pocket_06.pdb",
|
| 288 |
+
"pocket_07.pdb",
|
| 289 |
+
"pocket_08.pdb",
|
| 290 |
+
"pocket_09.pdb",
|
| 291 |
+
"pocket_10.pdb"
|
| 292 |
+
],
|
| 293 |
+
"analyses": [
|
| 294 |
+
"clusters",
|
| 295 |
+
"clusters-00",
|
| 296 |
+
"clusters-01",
|
| 297 |
+
"clusters-02",
|
| 298 |
+
"clusters-03",
|
| 299 |
+
"clusters-04",
|
| 300 |
+
"clusters-05",
|
| 301 |
+
"dist-perres",
|
| 302 |
+
"energies",
|
| 303 |
+
"fluctuation",
|
| 304 |
+
"hbonds",
|
| 305 |
+
"interactions",
|
| 306 |
+
"pca",
|
| 307 |
+
"pockets",
|
| 308 |
+
"rgyr",
|
| 309 |
+
"rmsd-pairwise",
|
| 310 |
+
"rmsd-perres",
|
| 311 |
+
"rmsds",
|
| 312 |
+
"sasa",
|
| 313 |
+
"tmscores"
|
| 314 |
+
],
|
| 315 |
+
"mdIndex": 0,
|
| 316 |
+
"mdNumber": 1,
|
| 317 |
+
"refframe": 0,
|
| 318 |
+
"internalId": "683f5caf846726452676d0d5",
|
| 319 |
+
"creationDate": "2025-06-03T20:35:59.000Z",
|
| 320 |
+
"identifier": "A001N"
|
| 321 |
+
}
|
data/files/A001N/records.jsonl
ADDED
|
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|