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data/files/A003E/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A003E",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2NQD",
|
| 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 |
+
"2NQD"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q966X9",
|
| 31 |
+
"P07711"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EAPRSVDWREKGYVTPVKNQGQCGSAWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV",
|
| 38 |
+
"SHKVTKAHNGATLTVAVGELVEIQLPSNPTTGFAWYFEGGTKESPNESMFTVENKYFPPDSKLLGAGGTEHFHVTVKAAGTHAVNLTYMRPWTGPSHDSERFTVYLKAN"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Chagasin",
|
| 43 |
+
"BC loop",
|
| 44 |
+
"DE loop",
|
| 45 |
+
"FG loop",
|
| 46 |
+
"Cathepsin L",
|
| 47 |
+
"Cathepsin L heavy chain",
|
| 48 |
+
"Cathepsin L light chain",
|
| 49 |
+
"Cleavage; by autolysis"
|
| 50 |
+
],
|
| 51 |
+
"FRAMESTEP": 0.1,
|
| 52 |
+
"TIMESTEP": 2,
|
| 53 |
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"TEMP": 310,
|
| 54 |
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"ENSEMBLE": "NPT",
|
| 55 |
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"FF": [
|
| 56 |
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"CHARMM36m"
|
| 57 |
+
],
|
| 58 |
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"WAT": "TIP3P",
|
| 59 |
+
"BOXTYPE": "Dodecahedron",
|
| 60 |
+
"SYSTATS": 4933,
|
| 61 |
+
"SYSTRES": 330,
|
| 62 |
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"PROTATS": 4933,
|
| 63 |
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"PROTRES": 330,
|
| 64 |
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"NUCLATS": 0,
|
| 65 |
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"NUCLRES": 0,
|
| 66 |
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"LIPIATS": 0,
|
| 67 |
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"LIPIRES": 0,
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| 68 |
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"CARBATS": 0,
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| 69 |
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"CARBRES": 0,
|
| 70 |
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"SOLVATS": 0,
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| 71 |
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"SOLVRES": 0,
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| 72 |
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"COUNCAT": 0,
|
| 73 |
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"COUNANI": 0,
|
| 74 |
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"COUNION": 0,
|
| 75 |
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"INTERACTIONS": [
|
| 76 |
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{
|
| 77 |
+
"name": "chain A-chain B interaction",
|
| 78 |
+
"agent_1": "chain A",
|
| 79 |
+
"agent_2": "chain B",
|
| 80 |
+
"selection_1": "chain A",
|
| 81 |
+
"selection_2": "chain B",
|
| 82 |
+
"type": "protein-protein"
|
| 83 |
+
}
|
| 84 |
+
],
|
| 85 |
+
"PBC_SELECTION": null,
|
| 86 |
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"CHAINNAMES": null,
|
| 87 |
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"MEMBRANES": null,
|
| 88 |
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"CUSTOMS": null,
|
| 89 |
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"ORIENTATION": null,
|
| 90 |
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"PTM": [],
|
| 91 |
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"MULTIMERIC": null,
|
| 92 |
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"COLLECTIONS": "dynarepo",
|
| 93 |
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"WARNINGS": [],
|
| 94 |
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"BOXSIZEX": 9.95686,
|
| 95 |
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"BOXSIZEY": 9.95686,
|
| 96 |
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"BOXSIZEZ": 7.07656,
|
| 97 |
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"mdName": "replica 1",
|
| 98 |
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"mdAtoms": 4933,
|
| 99 |
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"mdFrames": 5001
|
| 100 |
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},
|
| 101 |
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"mds": [
|
| 102 |
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"replica 1",
|
| 103 |
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"replica 2",
|
| 104 |
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"replica 3"
|
| 105 |
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],
|
| 106 |
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"mdref": 0,
|
| 107 |
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"files": [
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| 108 |
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"topology.tpr",
|
| 109 |
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"screenshot.jpg",
|
| 110 |
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"trajectory.bin",
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| 111 |
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"pca_trajectory_01.bin",
|
| 112 |
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"pca_trajectory_02.bin",
|
| 113 |
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"pca_trajectory_03.bin",
|
| 114 |
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"pca_trajectory_04.bin",
|
| 115 |
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"pca_trajectory_05.bin",
|
| 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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"pca_trajectory_13.bin",
|
| 124 |
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"structure.pdb",
|
| 125 |
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"trajectory.xtc",
|
| 126 |
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"clusters_00_screenshot_00.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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|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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"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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|
| 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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"clusters_01_screenshot_17.jpg",
|
| 164 |
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"clusters_01_screenshot_18.jpg",
|
| 165 |
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"pocket_01.pdb",
|
| 166 |
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"pocket_02.pdb",
|
| 167 |
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"pocket_03.pdb",
|
| 168 |
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"pocket_04.pdb",
|
| 169 |
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"pocket_05.pdb",
|
| 170 |
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"pocket_06.pdb",
|
| 171 |
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"pocket_07.pdb",
|
| 172 |
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"pocket_08.pdb",
|
| 173 |
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"pocket_09.pdb",
|
| 174 |
+
"pocket_10.pdb"
|
| 175 |
+
],
|
| 176 |
+
"analyses": [
|
| 177 |
+
"clusters",
|
| 178 |
+
"clusters-00",
|
| 179 |
+
"clusters-01",
|
| 180 |
+
"dist-perres",
|
| 181 |
+
"energies",
|
| 182 |
+
"fluctuation",
|
| 183 |
+
"hbonds",
|
| 184 |
+
"interactions",
|
| 185 |
+
"pca",
|
| 186 |
+
"pockets",
|
| 187 |
+
"rgyr",
|
| 188 |
+
"rmsd-pairwise",
|
| 189 |
+
"rmsd-perres",
|
| 190 |
+
"rmsds",
|
| 191 |
+
"sasa",
|
| 192 |
+
"tmscores"
|
| 193 |
+
],
|
| 194 |
+
"mdIndex": 0,
|
| 195 |
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"mdNumber": 1,
|
| 196 |
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"refframe": 0,
|
| 197 |
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"internalId": "6840630af49fd4972b4ea47e",
|
| 198 |
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"creationDate": "2025-06-04T15:15:22.000Z",
|
| 199 |
+
"identifier": "A003E"
|
| 200 |
+
}
|
data/files/A003G/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A003G",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2O3B",
|
| 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 |
+
"2O3B"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P38446",
|
| 31 |
+
"Q7A260"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GSISVHLLLGNPSGATPTKLTPDNYLMVKNQYALSYNNSKGTANWVAWQLNSSWLGNAERQDNFRPDKTLPAGWVRVTPSMYSGSGYARGHIAPSADRTKTTEDNAATFLMTNMMPQTPDNNRNTWGNLEDYCRELVSQGKELYIVAGPNGSLGKPLKGKVTVPKSTWKIVVVLDSPGSGLEGITANTRVIAVNIPNDPELNNDWRAYKVSVDELESLTGYDFLSNVSPNIQTSIESKVDN",
|
| 38 |
+
"STKTNSEILEQLKQASDGLLFMSESEYPFEVFLWEGSAPPVTHEIVLQQTGHGQDAPFKVVDIDSFFSRATTPQDWYEDEENAVVAKFQKLLEVIKSNLKNPQVYRLGEVELDVYVIGETPAGNLAGISTKVVET"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Nuclease"
|
| 43 |
+
],
|
| 44 |
+
"FRAMESTEP": 0.1,
|
| 45 |
+
"TIMESTEP": 2,
|
| 46 |
+
"TEMP": 310,
|
| 47 |
+
"ENSEMBLE": "NPT",
|
| 48 |
+
"FF": [
|
| 49 |
+
"CHARMM36m"
|
| 50 |
+
],
|
| 51 |
+
"WAT": "TIP3P",
|
| 52 |
+
"BOXTYPE": "Dodecahedron",
|
| 53 |
+
"SYSTATS": 5770,
|
| 54 |
+
"SYSTRES": 376,
|
| 55 |
+
"PROTATS": 5770,
|
| 56 |
+
"PROTRES": 376,
|
| 57 |
+
"NUCLATS": 0,
|
| 58 |
+
"NUCLRES": 0,
|
| 59 |
+
"LIPIATS": 0,
|
| 60 |
+
"LIPIRES": 0,
|
| 61 |
+
"CARBATS": 0,
|
| 62 |
+
"CARBRES": 0,
|
| 63 |
+
"SOLVATS": 0,
|
| 64 |
+
"SOLVRES": 0,
|
| 65 |
+
"COUNCAT": 0,
|
| 66 |
+
"COUNANI": 0,
|
| 67 |
+
"COUNION": 0,
|
| 68 |
+
"INTERACTIONS": [
|
| 69 |
+
{
|
| 70 |
+
"name": "chain A-chain B interaction",
|
| 71 |
+
"agent_1": "chain A",
|
| 72 |
+
"agent_2": "chain B",
|
| 73 |
+
"selection_1": "chain A",
|
| 74 |
+
"selection_2": "chain B",
|
| 75 |
+
"type": "protein-protein"
|
| 76 |
+
}
|
| 77 |
+
],
|
| 78 |
+
"PBC_SELECTION": null,
|
| 79 |
+
"CHAINNAMES": null,
|
| 80 |
+
"MEMBRANES": null,
|
| 81 |
+
"CUSTOMS": null,
|
| 82 |
+
"ORIENTATION": null,
|
| 83 |
+
"PTM": [],
|
| 84 |
+
"MULTIMERIC": null,
|
| 85 |
+
"COLLECTIONS": "dynarepo",
|
| 86 |
+
"WARNINGS": [],
|
| 87 |
+
"BOXSIZEX": 10.6003,
|
| 88 |
+
"BOXSIZEY": 10.6003,
|
| 89 |
+
"BOXSIZEZ": 7.48703,
|
| 90 |
+
"mdName": "replica 1",
|
| 91 |
+
"mdAtoms": 5770,
|
| 92 |
+
"mdFrames": 5001
|
| 93 |
+
},
|
| 94 |
+
"mds": [
|
| 95 |
+
"replica 1",
|
| 96 |
+
"replica 2",
|
| 97 |
+
"replica 3"
|
| 98 |
+
],
|
| 99 |
+
"mdref": 0,
|
| 100 |
+
"files": [
|
| 101 |
+
"topology.tpr",
|
| 102 |
+
"screenshot.jpg",
|
| 103 |
+
"trajectory.bin",
|
| 104 |
+
"pca_trajectory_01.bin",
|
| 105 |
+
"pca_trajectory_02.bin",
|
| 106 |
+
"pca_trajectory_03.bin",
|
| 107 |
+
"pca_trajectory_04.bin",
|
| 108 |
+
"pca_trajectory_05.bin",
|
| 109 |
+
"pca_trajectory_06.bin",
|
| 110 |
+
"pca_trajectory_07.bin",
|
| 111 |
+
"pca_trajectory_08.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_01_screenshot_00.jpg",
|
| 136 |
+
"clusters_01_screenshot_01.jpg",
|
| 137 |
+
"clusters_01_screenshot_02.jpg",
|
| 138 |
+
"clusters_01_screenshot_03.jpg",
|
| 139 |
+
"clusters_01_screenshot_04.jpg",
|
| 140 |
+
"clusters_01_screenshot_05.jpg",
|
| 141 |
+
"clusters_01_screenshot_06.jpg",
|
| 142 |
+
"clusters_01_screenshot_07.jpg",
|
| 143 |
+
"clusters_01_screenshot_08.jpg",
|
| 144 |
+
"clusters_01_screenshot_09.jpg",
|
| 145 |
+
"clusters_01_screenshot_10.jpg",
|
| 146 |
+
"clusters_01_screenshot_11.jpg",
|
| 147 |
+
"clusters_01_screenshot_12.jpg",
|
| 148 |
+
"clusters_01_screenshot_13.jpg",
|
| 149 |
+
"clusters_01_screenshot_14.jpg",
|
| 150 |
+
"clusters_01_screenshot_15.jpg",
|
| 151 |
+
"clusters_01_screenshot_16.jpg",
|
| 152 |
+
"clusters_01_screenshot_17.jpg",
|
| 153 |
+
"clusters_01_screenshot_18.jpg",
|
| 154 |
+
"clusters_01_screenshot_19.jpg",
|
| 155 |
+
"clusters_01_screenshot_20.jpg",
|
| 156 |
+
"clusters_01_screenshot_21.jpg",
|
| 157 |
+
"clusters_01_screenshot_22.jpg",
|
| 158 |
+
"clusters_01_screenshot_23.jpg",
|
| 159 |
+
"pocket_01.pdb",
|
| 160 |
+
"pocket_02.pdb"
|
| 161 |
+
],
|
| 162 |
+
"analyses": [
|
| 163 |
+
"clusters",
|
| 164 |
+
"clusters-00",
|
| 165 |
+
"clusters-01",
|
| 166 |
+
"dist-perres",
|
| 167 |
+
"energies",
|
| 168 |
+
"fluctuation",
|
| 169 |
+
"hbonds",
|
| 170 |
+
"interactions",
|
| 171 |
+
"pca",
|
| 172 |
+
"pockets",
|
| 173 |
+
"rgyr",
|
| 174 |
+
"rmsd-pairwise",
|
| 175 |
+
"rmsd-perres",
|
| 176 |
+
"rmsds",
|
| 177 |
+
"sasa",
|
| 178 |
+
"tmscores"
|
| 179 |
+
],
|
| 180 |
+
"mdIndex": 0,
|
| 181 |
+
"mdNumber": 1,
|
| 182 |
+
"refframe": 0,
|
| 183 |
+
"internalId": "6840698f24e1468e5b2ee158",
|
| 184 |
+
"creationDate": "2025-06-04T15:43:11.000Z",
|
| 185 |
+
"identifier": "A003G"
|
| 186 |
+
}
|
data/files/A003G/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
|
|
|
|
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|
| 1 |
+
{"project_identifier": "A003G", "accession": "A003G", "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 2O3B", "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": ["2O3B"], "FORCED_REFERENCES": null, "REFERENCES": ["P38446", "Q7A260"], 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data/files/A003H/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A003H",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2OIN",
|
| 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": [
|
| 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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"2OIN"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P27958"
|
| 31 |
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],
|
| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
|
| 36 |
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"GSVVIVGRIVLSGKPA",
|
| 37 |
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"VEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPXTXGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLXPAGHAVGLFKAAVCTRGVAKAVDFIPVENLETTM"
|
| 38 |
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],
|
| 39 |
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"NUCLSEQ": [],
|
| 40 |
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"DOMAINS": [
|
| 41 |
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"Genome polyprotein",
|
| 42 |
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"Serine protease/helicase NS3",
|
| 43 |
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"Non-structural protein 4A",
|
| 44 |
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"Peptidase S29",
|
| 45 |
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"Protease NS2-3",
|
| 46 |
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"NS3-binding"
|
| 47 |
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],
|
| 48 |
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"FRAMESTEP": 0.1,
|
| 49 |
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|
| 50 |
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"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
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"FF": [
|
| 53 |
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"CHARMM36m"
|
| 54 |
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],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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"BOXTYPE": "Dodecahedron",
|
| 57 |
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"SYSTATS": 2474,
|
| 58 |
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"SYSTRES": 167,
|
| 59 |
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"PROTATS": 2474,
|
| 60 |
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"PROTRES": 167,
|
| 61 |
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"NUCLATS": 0,
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| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
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| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
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| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
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| 68 |
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"SOLVRES": 0,
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| 69 |
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"COUNCAT": 0,
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| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
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{
|
| 74 |
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"name": "chain A-chain B interaction",
|
| 75 |
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"agent_1": "chain A",
|
| 76 |
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"agent_2": "chain B",
|
| 77 |
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"selection_1": "chain A",
|
| 78 |
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"selection_2": "chain B",
|
| 79 |
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"type": "protein-protein"
|
| 80 |
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}
|
| 81 |
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],
|
| 82 |
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"PBC_SELECTION": null,
|
| 83 |
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"CHAINNAMES": null,
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| 84 |
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| 85 |
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"CUSTOMS": null,
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| 87 |
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"PTM": [],
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| 88 |
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"MULTIMERIC": null,
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| 89 |
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"COLLECTIONS": "dynarepo",
|
| 90 |
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"WARNINGS": [],
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| 91 |
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"BOXSIZEX": 7.70684,
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| 92 |
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"BOXSIZEZ": 5.46323,
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"mdName": "replica 1",
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},
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"mds": [
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| 102 |
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],
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| 135 |
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| 136 |
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| 139 |
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| 147 |
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| 149 |
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| 151 |
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| 152 |
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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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"analyses": [
|
| 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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|
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|
| 174 |
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|
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|
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|
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"internalId": "68406b3f5774bdb707cafecf",
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| 186 |
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"creationDate": "2025-06-04T15:50:23.000Z",
|
| 187 |
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"identifier": "A003H"
|
| 188 |
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}
|
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ADDED
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|
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data/files/A003I/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003I",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2OJE",
|
| 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 |
+
"2OJE"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01903",
|
| 31 |
+
"P01911",
|
| 32 |
+
"Q91LS8",
|
| 33 |
+
"Q48898"
|
| 34 |
+
],
|
| 35 |
+
"INPUT_LIGANDS": null,
|
| 36 |
+
"LIGANDS": [],
|
| 37 |
+
"LIGANDNAMES": null,
|
| 38 |
+
"PROTSEQ": [
|
| 39 |
+
"KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD",
|
| 40 |
+
"PKYVKQNTLKLAT",
|
| 41 |
+
"GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA",
|
| 42 |
+
"SMKLRVENPKKAQKHFVQNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELKTTSDFAKAVFED"
|
| 43 |
+
],
|
| 44 |
+
"NUCLSEQ": [],
|
| 45 |
+
"DOMAINS": [
|
| 46 |
+
"HLA class II histocompatibility antigen, DR alpha chain",
|
| 47 |
+
"Ig-like C1-type",
|
| 48 |
+
"Alpha-1",
|
| 49 |
+
"Alpha-2",
|
| 50 |
+
"Connecting peptide",
|
| 51 |
+
"Self- and pathogen-derived peptide antigen",
|
| 52 |
+
"Self-peptide antigen",
|
| 53 |
+
"Pathogen-derived peptide antigen",
|
| 54 |
+
"HLA class II histocompatibility antigen, DRB1 beta chain",
|
| 55 |
+
"Ig-like C1-type",
|
| 56 |
+
"Beta-1",
|
| 57 |
+
"Beta-2"
|
| 58 |
+
],
|
| 59 |
+
"FRAMESTEP": 0.1,
|
| 60 |
+
"TIMESTEP": 2,
|
| 61 |
+
"TEMP": 310,
|
| 62 |
+
"ENSEMBLE": "NPT",
|
| 63 |
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"FF": [
|
| 64 |
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"CHARMM36m"
|
| 65 |
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],
|
| 66 |
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"WAT": "TIP3P",
|
| 67 |
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"BOXTYPE": "Dodecahedron",
|
| 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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|
| 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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"COUNANI": 0,
|
| 82 |
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"COUNION": 0,
|
| 83 |
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"INTERACTIONS": [
|
| 84 |
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{
|
| 85 |
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"name": "chain A-chain B interaction",
|
| 86 |
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"agent_1": "chain A",
|
| 87 |
+
"agent_2": "chain B",
|
| 88 |
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"selection_1": "chain A",
|
| 89 |
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"selection_2": "chain B",
|
| 90 |
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"type": "protein-protein"
|
| 91 |
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},
|
| 92 |
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{
|
| 93 |
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"name": "chain A-chain C interaction",
|
| 94 |
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"agent_1": "chain A",
|
| 95 |
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"agent_2": "chain C",
|
| 96 |
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"selection_1": "chain A",
|
| 97 |
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"selection_2": "chain C",
|
| 98 |
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"type": "protein-protein"
|
| 99 |
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},
|
| 100 |
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{
|
| 101 |
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"name": "chain A-chain D interaction",
|
| 102 |
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"agent_1": "chain A",
|
| 103 |
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"agent_2": "chain D",
|
| 104 |
+
"selection_1": "chain A",
|
| 105 |
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"selection_2": "chain D",
|
| 106 |
+
"type": "protein-protein"
|
| 107 |
+
},
|
| 108 |
+
{
|
| 109 |
+
"name": "chain B-chain C interaction",
|
| 110 |
+
"agent_1": "chain B",
|
| 111 |
+
"agent_2": "chain C",
|
| 112 |
+
"selection_1": "chain B",
|
| 113 |
+
"selection_2": "chain C",
|
| 114 |
+
"type": "protein-protein"
|
| 115 |
+
},
|
| 116 |
+
{
|
| 117 |
+
"name": "chain B-chain D interaction",
|
| 118 |
+
"agent_1": "chain B",
|
| 119 |
+
"agent_2": "chain D",
|
| 120 |
+
"selection_1": "chain B",
|
| 121 |
+
"selection_2": "chain D",
|
| 122 |
+
"type": "protein-protein"
|
| 123 |
+
},
|
| 124 |
+
{
|
| 125 |
+
"name": "chain C-chain D interaction",
|
| 126 |
+
"agent_1": "chain C",
|
| 127 |
+
"agent_2": "chain D",
|
| 128 |
+
"selection_1": "chain C",
|
| 129 |
+
"selection_2": "chain D",
|
| 130 |
+
"type": "protein-protein"
|
| 131 |
+
}
|
| 132 |
+
],
|
| 133 |
+
"PBC_SELECTION": null,
|
| 134 |
+
"CHAINNAMES": null,
|
| 135 |
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"MEMBRANES": null,
|
| 136 |
+
"CUSTOMS": null,
|
| 137 |
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"ORIENTATION": null,
|
| 138 |
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"PTM": [],
|
| 139 |
+
"MULTIMERIC": null,
|
| 140 |
+
"COLLECTIONS": "dynarepo",
|
| 141 |
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"WARNINGS": [],
|
| 142 |
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"BOXSIZEX": 14.6336,
|
| 143 |
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"BOXSIZEY": 14.6336,
|
| 144 |
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"BOXSIZEZ": 10.33,
|
| 145 |
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"mdName": "replica 1",
|
| 146 |
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"mdAtoms": 9806,
|
| 147 |
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"mdFrames": 5001
|
| 148 |
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},
|
| 149 |
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"mds": [
|
| 150 |
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"replica 1",
|
| 151 |
+
"replica 2",
|
| 152 |
+
"replica 3"
|
| 153 |
+
],
|
| 154 |
+
"mdref": 0,
|
| 155 |
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"files": [
|
| 156 |
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"topology.tpr",
|
| 157 |
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"screenshot.jpg",
|
| 158 |
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"trajectory.bin",
|
| 159 |
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|
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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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"pca_trajectory_09.bin",
|
| 168 |
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"pca_trajectory_10.bin",
|
| 169 |
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"structure.pdb",
|
| 170 |
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"trajectory.xtc",
|
| 171 |
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"clusters_00_screenshot_00.jpg",
|
| 172 |
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| 177 |
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|
| 182 |
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| 183 |
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| 184 |
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| 186 |
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|
| 187 |
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|
| 188 |
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|
| 189 |
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|
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|
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|
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|
| 215 |
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|
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| 223 |
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|
| 224 |
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|
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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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|
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|
| 233 |
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|
| 234 |
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|
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|
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| 237 |
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|
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|
| 239 |
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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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"clusters_04_screenshot_18.jpg",
|
| 269 |
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"clusters_05_screenshot_00.jpg",
|
| 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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|
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|
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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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"clusters_06_screenshot_15.jpg",
|
| 305 |
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|
| 306 |
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|
| 307 |
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"clusters_06_screenshot_18.jpg",
|
| 308 |
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"clusters_06_screenshot_19.jpg",
|
| 309 |
+
"pocket_01.pdb",
|
| 310 |
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"pocket_02.pdb",
|
| 311 |
+
"pocket_03.pdb",
|
| 312 |
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"pocket_04.pdb",
|
| 313 |
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"pocket_05.pdb",
|
| 314 |
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"pocket_06.pdb",
|
| 315 |
+
"pocket_07.pdb",
|
| 316 |
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"pocket_08.pdb",
|
| 317 |
+
"pocket_09.pdb",
|
| 318 |
+
"pocket_10.pdb"
|
| 319 |
+
],
|
| 320 |
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"analyses": [
|
| 321 |
+
"clusters",
|
| 322 |
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"clusters-00",
|
| 323 |
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"clusters-01",
|
| 324 |
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"clusters-02",
|
| 325 |
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"clusters-03",
|
| 326 |
+
"clusters-04",
|
| 327 |
+
"clusters-05",
|
| 328 |
+
"clusters-06",
|
| 329 |
+
"dist-perres",
|
| 330 |
+
"energies",
|
| 331 |
+
"fluctuation",
|
| 332 |
+
"hbonds",
|
| 333 |
+
"interactions",
|
| 334 |
+
"pca",
|
| 335 |
+
"pockets",
|
| 336 |
+
"rgyr",
|
| 337 |
+
"rmsd-pairwise",
|
| 338 |
+
"rmsd-perres",
|
| 339 |
+
"rmsds",
|
| 340 |
+
"sasa",
|
| 341 |
+
"tmscores"
|
| 342 |
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],
|
| 343 |
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"mdIndex": 0,
|
| 344 |
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"mdNumber": 1,
|
| 345 |
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"refframe": 1,
|
| 346 |
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"internalId": "68406d94f344a201096aa952",
|
| 347 |
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"creationDate": "2025-06-04T16:00:20.000Z",
|
| 348 |
+
"identifier": "A003I"
|
| 349 |
+
}
|
data/files/A003I/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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|
data/files/A003J/project.json
ADDED
|
@@ -0,0 +1,196 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A003J",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2OMY",
|
| 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 |
+
"2OMY"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DJM0",
|
| 31 |
+
"P12830"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GPLGSWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQ",
|
| 38 |
+
"ATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLNFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFYNNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKA"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Internalin A",
|
| 43 |
+
"LRRNT",
|
| 44 |
+
"LRRCT",
|
| 45 |
+
"Cadherin-1",
|
| 46 |
+
"Cadherin 1"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 8699,
|
| 58 |
+
"SYSTRES": 566,
|
| 59 |
+
"PROTATS": 8699,
|
| 60 |
+
"PROTRES": 566,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 13.3006,
|
| 92 |
+
"BOXSIZEY": 13.3006,
|
| 93 |
+
"BOXSIZEZ": 9.40102,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 8699,
|
| 96 |
+
"mdFrames": 5001
|
| 97 |
+
},
|
| 98 |
+
"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
+
"mdref": 0,
|
| 104 |
+
"files": [
|
| 105 |
+
"topology.tpr",
|
| 106 |
+
"screenshot.jpg",
|
| 107 |
+
"trajectory.bin",
|
| 108 |
+
"pca_trajectory_01.bin",
|
| 109 |
+
"pca_trajectory_02.bin",
|
| 110 |
+
"pca_trajectory_03.bin",
|
| 111 |
+
"pca_trajectory_04.bin",
|
| 112 |
+
"pca_trajectory_05.bin",
|
| 113 |
+
"pca_trajectory_06.bin",
|
| 114 |
+
"pca_trajectory_07.bin",
|
| 115 |
+
"pca_trajectory_08.bin",
|
| 116 |
+
"pca_trajectory_09.bin",
|
| 117 |
+
"pca_trajectory_10.bin",
|
| 118 |
+
"pca_trajectory_11.bin",
|
| 119 |
+
"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.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 |
+
"pocket_07.pdb",
|
| 170 |
+
"pocket_08.pdb"
|
| 171 |
+
],
|
| 172 |
+
"analyses": [
|
| 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 |
+
"mdIndex": 0,
|
| 191 |
+
"mdNumber": 1,
|
| 192 |
+
"refframe": 0,
|
| 193 |
+
"internalId": "684070eb896faf6305271bea",
|
| 194 |
+
"creationDate": "2025-06-04T16:14:35.000Z",
|
| 195 |
+
"identifier": "A003J"
|
| 196 |
+
}
|
data/files/A003J/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A003J", "accession": "A003J", "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 2OMY", "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": ["2OMY"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DJM0", "P12830"], 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| 1 |
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{
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| 2 |
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"accession": "A003K",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2P4A",
|
| 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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],
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| 15 |
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|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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|
| 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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| 22 |
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
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| 24 |
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"LINKS": null,
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| 25 |
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|
| 26 |
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"2P4A"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P61823",
|
| 31 |
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"A2KD57"
|
| 32 |
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],
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| 33 |
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|
| 34 |
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| 36 |
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| 37 |
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| 39 |
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|
| 40 |
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|
| 41 |
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|
| 42 |
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"Ribonuclease pancreatic",
|
| 43 |
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"Ig-like"
|
| 44 |
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],
|
| 45 |
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|
| 46 |
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|
| 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",
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| 54 |
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|
| 55 |
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| 56 |
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| 57 |
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| 58 |
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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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"COUNION": 0,
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| 69 |
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"INTERACTIONS": [
|
| 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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"agent_2": "chain B",
|
| 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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"PBC_SELECTION": null,
|
| 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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"PTM": [],
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| 85 |
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|
| 86 |
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"COLLECTIONS": "dynarepo",
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| 87 |
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"WARNINGS": [],
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| 88 |
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"BOXSIZEX": 10.0664,
|
| 89 |
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"BOXSIZEY": 10.0664,
|
| 90 |
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"BOXSIZEZ": 7.12226,
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| 91 |
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| 92 |
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| 93 |
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| 94 |
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},
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| 95 |
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"mds": [
|
| 96 |
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"replica 1",
|
| 97 |
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"replica 2",
|
| 98 |
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"replica 3"
|
| 99 |
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],
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| 100 |
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"mdref": 0,
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| 101 |
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"files": [
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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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"pca_trajectory_06.bin",
|
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"structure.pdb",
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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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],
|
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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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| 171 |
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"dist-perres",
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| 172 |
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"energies",
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"fluctuation",
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"hbonds",
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| 175 |
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"interactions",
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| 176 |
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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": "68407338d5c91de75ee4297f",
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"creationDate": "2025-06-04T16:24:24.000Z",
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"identifier": "A003K"
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}
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data/files/A003K/records.jsonl
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| 1 |
+
{
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| 2 |
+
"accession": "A003L",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2PCB",
|
| 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 |
+
"2PCB"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00431",
|
| 31 |
+
"P00004"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL",
|
| 38 |
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"GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Cytochrome c peroxidase, mitochondrial",
|
| 43 |
+
"Transition state stabilizer",
|
| 44 |
+
"Cytochrome c"
|
| 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 |
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"SYSTATS": 6295,
|
| 56 |
+
"SYSTRES": 398,
|
| 57 |
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"PROTATS": 6295,
|
| 58 |
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"PROTRES": 398,
|
| 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 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"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 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 10.2184,
|
| 90 |
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"BOXSIZEY": 10.2184,
|
| 91 |
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"BOXSIZEZ": 7.22271,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 6295,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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"pca_trajectory_01.bin",
|
| 107 |
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"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
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"pca_trajectory_04.bin",
|
| 110 |
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"pca_trajectory_05.bin",
|
| 111 |
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"pca_trajectory_06.bin",
|
| 112 |
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"pca_trajectory_07.bin",
|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
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"pca_trajectory_09.bin",
|
| 115 |
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"pca_trajectory_10.bin",
|
| 116 |
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"pca_trajectory_11.bin",
|
| 117 |
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"structure.pdb",
|
| 118 |
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"trajectory.xtc",
|
| 119 |
+
"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
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"clusters_00_screenshot_02.jpg",
|
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"clusters_00_screenshot_03.jpg",
|
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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 |
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"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 |
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"clusters_00_screenshot_10.jpg",
|
| 130 |
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"clusters_00_screenshot_11.jpg",
|
| 131 |
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"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_01_screenshot_00.jpg",
|
| 140 |
+
"clusters_01_screenshot_01.jpg",
|
| 141 |
+
"clusters_01_screenshot_02.jpg",
|
| 142 |
+
"clusters_01_screenshot_03.jpg",
|
| 143 |
+
"clusters_01_screenshot_04.jpg",
|
| 144 |
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"clusters_01_screenshot_05.jpg",
|
| 145 |
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"clusters_01_screenshot_06.jpg",
|
| 146 |
+
"clusters_01_screenshot_07.jpg",
|
| 147 |
+
"clusters_01_screenshot_08.jpg",
|
| 148 |
+
"clusters_01_screenshot_09.jpg",
|
| 149 |
+
"clusters_01_screenshot_10.jpg",
|
| 150 |
+
"clusters_01_screenshot_11.jpg",
|
| 151 |
+
"clusters_01_screenshot_12.jpg",
|
| 152 |
+
"clusters_01_screenshot_13.jpg",
|
| 153 |
+
"clusters_01_screenshot_14.jpg",
|
| 154 |
+
"clusters_01_screenshot_15.jpg",
|
| 155 |
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"clusters_01_screenshot_16.jpg",
|
| 156 |
+
"clusters_01_screenshot_17.jpg",
|
| 157 |
+
"clusters_01_screenshot_18.jpg",
|
| 158 |
+
"clusters_01_screenshot_19.jpg",
|
| 159 |
+
"clusters_01_screenshot_20.jpg",
|
| 160 |
+
"pocket_01.pdb",
|
| 161 |
+
"pocket_02.pdb",
|
| 162 |
+
"pocket_03.pdb",
|
| 163 |
+
"pocket_04.pdb",
|
| 164 |
+
"pocket_05.pdb",
|
| 165 |
+
"pocket_06.pdb"
|
| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
+
"clusters",
|
| 169 |
+
"clusters-00",
|
| 170 |
+
"clusters-01",
|
| 171 |
+
"dist-perres",
|
| 172 |
+
"energies",
|
| 173 |
+
"fluctuation",
|
| 174 |
+
"hbonds",
|
| 175 |
+
"interactions",
|
| 176 |
+
"pca",
|
| 177 |
+
"pockets",
|
| 178 |
+
"rgyr",
|
| 179 |
+
"rmsd-pairwise",
|
| 180 |
+
"rmsd-perres",
|
| 181 |
+
"rmsds",
|
| 182 |
+
"sasa",
|
| 183 |
+
"tmscores"
|
| 184 |
+
],
|
| 185 |
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"mdIndex": 0,
|
| 186 |
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"mdNumber": 1,
|
| 187 |
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"refframe": 0,
|
| 188 |
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"internalId": "68407531c16de68ddf4d4a74",
|
| 189 |
+
"creationDate": "2025-06-04T16:32:49.000Z",
|
| 190 |
+
"identifier": "A003L"
|
| 191 |
+
}
|
data/files/A003L/records.jsonl
ADDED
|
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| 1 |
+
{"project_identifier": "A003L", "accession": "A003L", "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 2PCB", "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": ["2PCB"], "FORCED_REFERENCES": null, "REFERENCES": ["P00431", "P00004"], 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data/files/A003M/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2PJY",
|
| 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 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"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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"2PJY"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P10600",
|
| 31 |
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"P37173",
|
| 32 |
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"P36897"
|
| 33 |
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],
|
| 34 |
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"INPUT_LIGANDS": null,
|
| 35 |
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"LIGANDS": [],
|
| 36 |
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"LIGANDNAMES": null,
|
| 37 |
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"PROTSEQ": [
|
| 38 |
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"ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS",
|
| 39 |
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"AGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIF",
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| 40 |
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"ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIEL"
|
| 41 |
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],
|
| 42 |
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"NUCLSEQ": [],
|
| 43 |
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"DOMAINS": [
|
| 44 |
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"Transforming growth factor beta-3",
|
| 45 |
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"TGF-beta receptor type-2",
|
| 46 |
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"TGF-beta receptor type-1"
|
| 47 |
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],
|
| 48 |
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"FRAMESTEP": 0.1,
|
| 49 |
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"TIMESTEP": 2,
|
| 50 |
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"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
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"FF": [
|
| 53 |
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"CHARMM36m"
|
| 54 |
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],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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"BOXTYPE": "Dodecahedron",
|
| 57 |
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"SYSTATS": 4573,
|
| 58 |
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"SYSTRES": 299,
|
| 59 |
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"PROTATS": 4573,
|
| 60 |
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"PROTRES": 299,
|
| 61 |
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"NUCLATS": 0,
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| 62 |
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"NUCLRES": 0,
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| 63 |
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"LIPIATS": 0,
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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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"COUNCAT": 0,
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| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
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{
|
| 74 |
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"name": "chain A-chain B interaction",
|
| 75 |
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"agent_1": "chain A",
|
| 76 |
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"agent_2": "chain B",
|
| 77 |
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"selection_1": "chain A",
|
| 78 |
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"selection_2": "chain B",
|
| 79 |
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"type": "protein-protein"
|
| 80 |
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},
|
| 81 |
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{
|
| 82 |
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"name": "chain A-chain C interaction",
|
| 83 |
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"agent_1": "chain A",
|
| 84 |
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"agent_2": "chain C",
|
| 85 |
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"selection_1": "chain A",
|
| 86 |
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"selection_2": "chain C",
|
| 87 |
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"type": "protein-protein"
|
| 88 |
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},
|
| 89 |
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{
|
| 90 |
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"name": "chain B-chain C interaction",
|
| 91 |
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"agent_1": "chain B",
|
| 92 |
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|
| 93 |
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"selection_1": "chain B",
|
| 94 |
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"selection_2": "chain C",
|
| 95 |
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"type": "protein-protein"
|
| 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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"COLLECTIONS": "dynarepo",
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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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},
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| 114 |
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"mds": [
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| 115 |
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"replica 1",
|
| 116 |
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"replica 2",
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| 117 |
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"replica 3"
|
| 118 |
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],
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| 119 |
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"mdref": 0,
|
| 120 |
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"files": [
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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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"clusters_03_screenshot_20.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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| 218 |
+
],
|
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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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| 223 |
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"clusters-02",
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"clusters-03",
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| 225 |
+
"dist-perres",
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"energies",
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"fluctuation",
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| 228 |
+
"hbonds",
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| 229 |
+
"interactions",
|
| 230 |
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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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| 234 |
+
"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": "684077693a7982f1ea8aa72e",
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"creationDate": "2025-06-04T16:42:17.000Z",
|
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"identifier": "A003M"
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}
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data/files/A003M/records.jsonl
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data/files/A003N/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A003N",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2PSM",
|
| 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",
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| 23 |
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| 24 |
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| 25 |
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"2PSM"
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| 27 |
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],
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| 28 |
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|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P48346",
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| 31 |
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"Q60819"
|
| 32 |
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],
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| 33 |
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| 39 |
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| 40 |
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|
| 41 |
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|
| 42 |
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"Interleukin-15",
|
| 43 |
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"Interleukin-15 receptor subunit alpha",
|
| 44 |
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"Sushi"
|
| 45 |
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],
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| 46 |
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| 47 |
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| 48 |
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|
| 49 |
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|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
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| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
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| 55 |
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"SYSTATS": 2929,
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| 56 |
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| 57 |
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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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"COUNION": 0,
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| 70 |
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| 71 |
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{
|
| 72 |
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"name": "chain A-chain B interaction",
|
| 73 |
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"agent_1": "chain A",
|
| 74 |
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"agent_2": "chain B",
|
| 75 |
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"selection_1": "chain A",
|
| 76 |
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"selection_2": "chain B",
|
| 77 |
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"type": "protein-protein"
|
| 78 |
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}
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| 79 |
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],
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| 80 |
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| 81 |
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| 88 |
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| 89 |
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"BOXSIZEX": 8.30792,
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| 90 |
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| 91 |
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},
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| 99 |
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| 100 |
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| 101 |
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"files": [
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|
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],
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"analyses": [
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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": "684078fe1cc335b8c1f800e1",
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"creationDate": "2025-06-04T16:49:02.000Z",
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"identifier": "A003N"
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}
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|
data/files/A003O/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003O",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2PTT",
|
| 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 |
+
"2PTT"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P18181",
|
| 31 |
+
"Q07763"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"DCPDSSEEVVGVSGKPVQLRPSNIQTKDVSVQWKKTEQGSHRKIEILNWYNDGPSWSNVSFSDIYGFDYGDFALSIKSAKLQDSGHYLLEITNTGGKVCNKNFQLLIL",
|
| 38 |
+
"GSIPDINAYTGSNVTLKIHKDPLGPYRRITWLHTKNQKILEYNYNSTKTIFESEFKGRVYLEENNGALHISNVRKEDKGTYYMRVLRETENELKITLEVFDPV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"CD48 antigen",
|
| 43 |
+
"Ig-like C2-type 1",
|
| 44 |
+
"Natural killer cell receptor 2B4",
|
| 45 |
+
"Ig-like 1"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
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"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
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|
| 57 |
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|
| 58 |
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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 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"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 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"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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"COLLECTIONS": "dynarepo",
|
| 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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"mdFrames": 5001
|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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"topology.tpr",
|
| 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 |
+
"pca_trajectory_03.bin",
|
| 110 |
+
"pca_trajectory_04.bin",
|
| 111 |
+
"pca_trajectory_05.bin",
|
| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
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"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"pca_trajectory_13.bin",
|
| 120 |
+
"pca_trajectory_14.bin",
|
| 121 |
+
"pca_trajectory_15.bin",
|
| 122 |
+
"pca_trajectory_16.bin",
|
| 123 |
+
"pca_trajectory_17.bin",
|
| 124 |
+
"pca_trajectory_18.bin",
|
| 125 |
+
"structure.pdb",
|
| 126 |
+
"trajectory.xtc",
|
| 127 |
+
"clusters_00_screenshot_00.jpg",
|
| 128 |
+
"clusters_00_screenshot_01.jpg",
|
| 129 |
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"clusters_00_screenshot_02.jpg",
|
| 130 |
+
"clusters_00_screenshot_03.jpg",
|
| 131 |
+
"clusters_00_screenshot_04.jpg",
|
| 132 |
+
"clusters_00_screenshot_05.jpg",
|
| 133 |
+
"clusters_00_screenshot_06.jpg",
|
| 134 |
+
"clusters_00_screenshot_07.jpg",
|
| 135 |
+
"clusters_00_screenshot_08.jpg",
|
| 136 |
+
"clusters_00_screenshot_09.jpg",
|
| 137 |
+
"clusters_00_screenshot_10.jpg",
|
| 138 |
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"clusters_00_screenshot_11.jpg",
|
| 139 |
+
"clusters_00_screenshot_12.jpg",
|
| 140 |
+
"clusters_00_screenshot_13.jpg",
|
| 141 |
+
"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_01_screenshot_00.jpg",
|
| 146 |
+
"clusters_01_screenshot_01.jpg",
|
| 147 |
+
"clusters_01_screenshot_02.jpg",
|
| 148 |
+
"clusters_01_screenshot_03.jpg",
|
| 149 |
+
"clusters_01_screenshot_04.jpg",
|
| 150 |
+
"clusters_01_screenshot_05.jpg",
|
| 151 |
+
"clusters_01_screenshot_06.jpg",
|
| 152 |
+
"clusters_01_screenshot_07.jpg",
|
| 153 |
+
"clusters_01_screenshot_08.jpg",
|
| 154 |
+
"clusters_01_screenshot_09.jpg",
|
| 155 |
+
"clusters_01_screenshot_10.jpg",
|
| 156 |
+
"clusters_01_screenshot_11.jpg",
|
| 157 |
+
"clusters_01_screenshot_12.jpg",
|
| 158 |
+
"clusters_01_screenshot_13.jpg",
|
| 159 |
+
"clusters_01_screenshot_14.jpg",
|
| 160 |
+
"clusters_01_screenshot_15.jpg",
|
| 161 |
+
"clusters_01_screenshot_16.jpg",
|
| 162 |
+
"clusters_01_screenshot_17.jpg",
|
| 163 |
+
"clusters_01_screenshot_18.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 |
+
],
|
| 172 |
+
"analyses": [
|
| 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 |
+
"mdIndex": 0,
|
| 191 |
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"mdNumber": 1,
|
| 192 |
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"refframe": 0,
|
| 193 |
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"internalId": "68407a6eb314550fea852822",
|
| 194 |
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"creationDate": "2025-06-04T16:55:10.000Z",
|
| 195 |
+
"identifier": "A003O"
|
| 196 |
+
}
|
data/files/A003O/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
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|
|
|
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|
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|
| 1 |
+
{"project_identifier": "A003O", "accession": "A003O", "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 2PTT", "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": ["2PTT"], "FORCED_REFERENCES": null, "REFERENCES": ["P18181", "Q07763"], 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data/files/A003P/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003P",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2Q0O",
|
| 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 |
+
"2Q0O"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P55407",
|
| 31 |
+
"P55408"
|
| 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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"SVNGNLRSLIDMLEAAQDGHMIKIALRSFAHSCGYDRFAYLQKDGTQVRTFHSYPGPWESIYLGSDYFNIDPVLAEAKRRRDVFFWTADAWPARGSSPLRRFRDEAISHGIRCGVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIAAKTVLNPKQMLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRGLV",
|
| 38 |
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"EARYSVMTKSELEALAVSAIREHRRLLWADQAVYEEWLRASDDPSISGPVLQTLQDEYVARQKRSEAQQEELSDILDALGFVPDVPF",
|
| 39 |
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"EARYSVMTKSELEALAVSAIREHRRLLWADQAVYEEWLRASDDPSISGPVLQTLQDEYVARQKRSEAQQEELSDILDALGFVPDVP"
|
| 40 |
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],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Probable transcriptional activator protein TraR",
|
| 44 |
+
"HTH luxR-type",
|
| 45 |
+
"Probable transcriptional repressor TraM",
|
| 46 |
+
"Disordered"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
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"SYSTATS": 10154,
|
| 58 |
+
"SYSTRES": 643,
|
| 59 |
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"PROTATS": 10154,
|
| 60 |
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"PROTRES": 643,
|
| 61 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
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"COUNCAT": 0,
|
| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
},
|
| 81 |
+
{
|
| 82 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain A-chain D interaction",
|
| 91 |
+
"agent_1": "chain A",
|
| 92 |
+
"agent_2": "chain D",
|
| 93 |
+
"selection_1": "chain A",
|
| 94 |
+
"selection_2": "chain D",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
},
|
| 97 |
+
{
|
| 98 |
+
"name": "chain B-chain C interaction",
|
| 99 |
+
"agent_1": "chain B",
|
| 100 |
+
"agent_2": "chain C",
|
| 101 |
+
"selection_1": "chain B",
|
| 102 |
+
"selection_2": "chain C",
|
| 103 |
+
"type": "protein-protein"
|
| 104 |
+
},
|
| 105 |
+
{
|
| 106 |
+
"name": "chain B-chain D interaction",
|
| 107 |
+
"agent_1": "chain B",
|
| 108 |
+
"agent_2": "chain D",
|
| 109 |
+
"selection_1": "chain B",
|
| 110 |
+
"selection_2": "chain D",
|
| 111 |
+
"type": "protein-protein"
|
| 112 |
+
}
|
| 113 |
+
],
|
| 114 |
+
"PBC_SELECTION": null,
|
| 115 |
+
"CHAINNAMES": null,
|
| 116 |
+
"MEMBRANES": null,
|
| 117 |
+
"CUSTOMS": null,
|
| 118 |
+
"ORIENTATION": null,
|
| 119 |
+
"PTM": [],
|
| 120 |
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"MULTIMERIC": null,
|
| 121 |
+
"COLLECTIONS": "dynarepo",
|
| 122 |
+
"WARNINGS": [],
|
| 123 |
+
"BOXSIZEX": 13.6469,
|
| 124 |
+
"BOXSIZEY": 13.6469,
|
| 125 |
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"BOXSIZEZ": 9.69602,
|
| 126 |
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"mdName": "replica 1",
|
| 127 |
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"mdAtoms": 10154,
|
| 128 |
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"mdFrames": 5001
|
| 129 |
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},
|
| 130 |
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"mds": [
|
| 131 |
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"replica 1",
|
| 132 |
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"replica 2",
|
| 133 |
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"replica 3"
|
| 134 |
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],
|
| 135 |
+
"mdref": 0,
|
| 136 |
+
"files": [
|
| 137 |
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"topology.tpr",
|
| 138 |
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"screenshot.jpg",
|
| 139 |
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"trajectory.bin",
|
| 140 |
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"pca_trajectory_01.bin",
|
| 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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| 147 |
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|
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|
| 270 |
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|
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|
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|
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|
| 274 |
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|
| 275 |
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|
| 276 |
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|
| 277 |
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"pocket_08.pdb",
|
| 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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|
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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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|
| 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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|
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|
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|
| 302 |
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| 308 |
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"identifier": "A003P"
|
| 309 |
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}
|
data/files/A003P/records.jsonl
ADDED
|
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|
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|
data/files/A003Q/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
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"accession": "A003Q",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2QEJ",
|
| 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 |
+
"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 |
+
"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": [
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| 26 |
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"2QEJ"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P01876",
|
| 31 |
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"A0A0H3K6Z8"
|
| 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": [
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| 37 |
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| 39 |
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"YDIKDLHRYYSSESFEFSNISGKVENYNGSNVVRFNQEKQNHQLFLLGEDKAKYKQGLQGQDVFVVKELIDPNGRLSTVGGVTKKNNQSSETNIHLLVNKLDGGNLDATNDSFLINKEEVSLKELDFKIRKQLVEKYGLYQGTSKYGKITIILNGGKKQEIDLGDKLQFERMGDVLNSKDINKIEVTLKQI",
|
| 40 |
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"CHPRLSLHRPALEDLLLGSEANLTCTLTGLRDASGVTFTWTPSSGKSAVQGPPERDLCGCYSVSSVLPGCAEPWNHGKTFTCTAAYPESKTPLTATLSKSGNTFRPEVHLLPPPSEELALNELVTLTCLARGFSPKDVLVRWLQGSQELPREKYLTWASRQEPSQGTTTFAVTSILRVAAEDWKKGDTFSCMVGHEALPLAFTQKTIDR"
|
| 41 |
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],
|
| 42 |
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"NUCLSEQ": [],
|
| 43 |
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|
| 44 |
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"Immunoglobulin heavy constant alpha 1",
|
| 45 |
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"Ig-like 2",
|
| 46 |
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"Ig-like 3",
|
| 47 |
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"Disordered",
|
| 48 |
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|
| 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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|
| 56 |
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],
|
| 57 |
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|
| 58 |
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|
| 59 |
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| 75 |
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{
|
| 76 |
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"name": "chain A-chain B interaction",
|
| 77 |
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|
| 78 |
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|
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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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"name": "chain A-chain C interaction",
|
| 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": "chain A-chain D interaction",
|
| 93 |
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"agent_1": "chain A",
|
| 94 |
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|
| 95 |
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"selection_1": "chain A",
|
| 96 |
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"selection_2": "chain D",
|
| 97 |
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"type": "protein-protein"
|
| 98 |
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},
|
| 99 |
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{
|
| 100 |
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"name": "chain B-chain C interaction",
|
| 101 |
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"agent_1": "chain B",
|
| 102 |
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"agent_2": "chain C",
|
| 103 |
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"selection_1": "chain B",
|
| 104 |
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"selection_2": "chain C",
|
| 105 |
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"type": "protein-protein"
|
| 106 |
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},
|
| 107 |
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{
|
| 108 |
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"name": "chain B-chain D interaction",
|
| 109 |
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"agent_1": "chain B",
|
| 110 |
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"agent_2": "chain D",
|
| 111 |
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"selection_1": "chain B",
|
| 112 |
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"selection_2": "chain D",
|
| 113 |
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"type": "protein-protein"
|
| 114 |
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}
|
| 115 |
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],
|
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|
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"COLLECTIONS": "dynarepo",
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},
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|
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| 197 |
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|
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| 203 |
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| 207 |
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|
| 208 |
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| 211 |
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| 212 |
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|
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|
| 217 |
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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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| 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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|
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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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"clusters_05_screenshot_10.jpg",
|
| 265 |
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|
| 266 |
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|
| 267 |
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"clusters_05_screenshot_13.jpg",
|
| 268 |
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"clusters_05_screenshot_14.jpg",
|
| 269 |
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|
| 270 |
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|
| 271 |
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|
| 272 |
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"clusters_05_screenshot_18.jpg",
|
| 273 |
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"clusters_05_screenshot_19.jpg",
|
| 274 |
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"pocket_01.pdb",
|
| 275 |
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"pocket_02.pdb",
|
| 276 |
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"pocket_03.pdb",
|
| 277 |
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"pocket_04.pdb",
|
| 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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"pocket_08.pdb",
|
| 282 |
+
"pocket_09.pdb",
|
| 283 |
+
"pocket_10.pdb"
|
| 284 |
+
],
|
| 285 |
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"analyses": [
|
| 286 |
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"clusters",
|
| 287 |
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"clusters-00",
|
| 288 |
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"clusters-01",
|
| 289 |
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"clusters-02",
|
| 290 |
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"clusters-03",
|
| 291 |
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"clusters-04",
|
| 292 |
+
"clusters-05",
|
| 293 |
+
"dist-perres",
|
| 294 |
+
"energies",
|
| 295 |
+
"fluctuation",
|
| 296 |
+
"hbonds",
|
| 297 |
+
"interactions",
|
| 298 |
+
"pca",
|
| 299 |
+
"pockets",
|
| 300 |
+
"rgyr",
|
| 301 |
+
"rmsd-pairwise",
|
| 302 |
+
"rmsd-perres",
|
| 303 |
+
"rmsds",
|
| 304 |
+
"sasa",
|
| 305 |
+
"tmscores"
|
| 306 |
+
],
|
| 307 |
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"mdIndex": 0,
|
| 308 |
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"mdNumber": 1,
|
| 309 |
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"refframe": 0,
|
| 310 |
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"internalId": "684080fc6fc23624d4a7ba84",
|
| 311 |
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"creationDate": "2025-06-04T17:23:08.000Z",
|
| 312 |
+
"identifier": "A003Q"
|
| 313 |
+
}
|
data/files/A003Q/records.jsonl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
data/files/A003R/project.json
ADDED
|
@@ -0,0 +1,183 @@
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| 1 |
+
{
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| 2 |
+
"accession": "A003R",
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| 3 |
+
"published": true,
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| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2QHO",
|
| 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": [
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| 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 |
+
"2QHO"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0CH28",
|
| 31 |
+
"O95071"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SIPASVIPEELISQAQVVLQGKSRSVIIRELQRTNLDVNLAVNNLLS",
|
| 38 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ubiquitin",
|
| 43 |
+
"Ubiquitin-like 2",
|
| 44 |
+
"E3 ubiquitin-protein ligase UBR5",
|
| 45 |
+
"UBA"
|
| 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": 1921,
|
| 57 |
+
"SYSTRES": 119,
|
| 58 |
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"PROTATS": 1921,
|
| 59 |
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"PROTRES": 119,
|
| 60 |
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"NUCLATS": 0,
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| 61 |
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"NUCLRES": 0,
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| 62 |
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"LIPIATS": 0,
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| 63 |
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| 64 |
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"CARBATS": 0,
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| 65 |
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"CARBRES": 0,
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| 66 |
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"SOLVATS": 0,
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| 67 |
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"SOLVRES": 0,
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| 68 |
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"COUNCAT": 0,
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| 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 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
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"CHAINNAMES": null,
|
| 83 |
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"MEMBRANES": null,
|
| 84 |
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|
| 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": 7.43242,
|
| 91 |
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"BOXSIZEY": 7.43242,
|
| 92 |
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| 93 |
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"mdName": "replica 1",
|
| 94 |
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|
| 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 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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"topology.tpr",
|
| 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",
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| 109 |
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"pca_trajectory_03.bin",
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| 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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"structure.pdb",
|
| 117 |
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"trajectory.xtc",
|
| 118 |
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"clusters_00_screenshot_00.jpg",
|
| 119 |
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"clusters_00_screenshot_01.jpg",
|
| 120 |
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"clusters_00_screenshot_02.jpg",
|
| 121 |
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"clusters_00_screenshot_03.jpg",
|
| 122 |
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"clusters_00_screenshot_04.jpg",
|
| 123 |
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"clusters_00_screenshot_05.jpg",
|
| 124 |
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"clusters_00_screenshot_06.jpg",
|
| 125 |
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"clusters_00_screenshot_07.jpg",
|
| 126 |
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"clusters_00_screenshot_08.jpg",
|
| 127 |
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"clusters_00_screenshot_09.jpg",
|
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"clusters_00_screenshot_10.jpg",
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"clusters_00_screenshot_11.jpg",
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"clusters_00_screenshot_12.jpg",
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"clusters_00_screenshot_13.jpg",
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"clusters_00_screenshot_14.jpg",
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"clusters_00_screenshot_15.jpg",
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"clusters_00_screenshot_16.jpg",
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"clusters_00_screenshot_17.jpg",
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"clusters_00_screenshot_18.jpg",
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| 137 |
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"clusters_00_screenshot_19.jpg",
|
| 138 |
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"clusters_01_screenshot_00.jpg",
|
| 139 |
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"clusters_01_screenshot_01.jpg",
|
| 140 |
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"clusters_01_screenshot_02.jpg",
|
| 141 |
+
"clusters_01_screenshot_03.jpg",
|
| 142 |
+
"clusters_01_screenshot_04.jpg",
|
| 143 |
+
"clusters_01_screenshot_05.jpg",
|
| 144 |
+
"clusters_01_screenshot_06.jpg",
|
| 145 |
+
"clusters_01_screenshot_07.jpg",
|
| 146 |
+
"clusters_01_screenshot_08.jpg",
|
| 147 |
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"clusters_01_screenshot_09.jpg",
|
| 148 |
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"clusters_01_screenshot_10.jpg",
|
| 149 |
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"clusters_01_screenshot_11.jpg",
|
| 150 |
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"clusters_01_screenshot_12.jpg",
|
| 151 |
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"clusters_01_screenshot_13.jpg",
|
| 152 |
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"clusters_01_screenshot_14.jpg",
|
| 153 |
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"clusters_01_screenshot_15.jpg",
|
| 154 |
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"clusters_01_screenshot_16.jpg",
|
| 155 |
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"clusters_01_screenshot_17.jpg",
|
| 156 |
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"clusters_01_screenshot_18.jpg",
|
| 157 |
+
"clusters_01_screenshot_19.jpg",
|
| 158 |
+
"clusters_01_screenshot_20.jpg"
|
| 159 |
+
],
|
| 160 |
+
"analyses": [
|
| 161 |
+
"clusters",
|
| 162 |
+
"clusters-00",
|
| 163 |
+
"clusters-01",
|
| 164 |
+
"dist-perres",
|
| 165 |
+
"energies",
|
| 166 |
+
"fluctuation",
|
| 167 |
+
"hbonds",
|
| 168 |
+
"interactions",
|
| 169 |
+
"pca",
|
| 170 |
+
"rgyr",
|
| 171 |
+
"rmsd-pairwise",
|
| 172 |
+
"rmsd-perres",
|
| 173 |
+
"rmsds",
|
| 174 |
+
"sasa",
|
| 175 |
+
"tmscores"
|
| 176 |
+
],
|
| 177 |
+
"mdIndex": 0,
|
| 178 |
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"mdNumber": 1,
|
| 179 |
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"refframe": 0,
|
| 180 |
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"internalId": "684083b264c87b9af9dce9d4",
|
| 181 |
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"creationDate": "2025-06-04T17:34:42.000Z",
|
| 182 |
+
"identifier": "A003R"
|
| 183 |
+
}
|
data/files/A003R/records.jsonl
ADDED
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+
{"project_identifier": "A003R", "accession": "A003R", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2QHO", "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": ["2QHO"], "FORCED_REFERENCES": null, "REFERENCES": ["P0CH28", "O95071"], "INPUT_LIGANDS": null, 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| 3 |
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| 1 |
+
{
|
| 2 |
+
"accession": "A003S",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2QXV",
|
| 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 |
+
"2QXV"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q921E6",
|
| 31 |
+
"Q61188"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TMFSSNRQKILERTETLNQEWKQRRIQPV",
|
| 38 |
+
"FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Polycomb protein EED",
|
| 43 |
+
"Interaction with EZH2",
|
| 44 |
+
"Histone-lysine N-methyltransferase EZH2",
|
| 45 |
+
"Interaction with DNMT1, DNMT3A and DNMT3B",
|
| 46 |
+
"Interaction with EED"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 6132,
|
| 58 |
+
"SYSTRES": 381,
|
| 59 |
+
"PROTATS": 6132,
|
| 60 |
+
"PROTRES": 381,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 8.49332,
|
| 92 |
+
"BOXSIZEY": 8.49332,
|
| 93 |
+
"BOXSIZEZ": 6.0081,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 6132,
|
| 96 |
+
"mdFrames": 5001
|
| 97 |
+
},
|
| 98 |
+
"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
+
"mdref": 0,
|
| 104 |
+
"files": [
|
| 105 |
+
"topology.tpr",
|
| 106 |
+
"screenshot.jpg",
|
| 107 |
+
"trajectory.bin",
|
| 108 |
+
"pca_trajectory_01.bin",
|
| 109 |
+
"pca_trajectory_02.bin",
|
| 110 |
+
"pca_trajectory_03.bin",
|
| 111 |
+
"pca_trajectory_04.bin",
|
| 112 |
+
"pca_trajectory_05.bin",
|
| 113 |
+
"pca_trajectory_06.bin",
|
| 114 |
+
"pca_trajectory_07.bin",
|
| 115 |
+
"pca_trajectory_08.bin",
|
| 116 |
+
"pca_trajectory_09.bin",
|
| 117 |
+
"pca_trajectory_10.bin",
|
| 118 |
+
"pca_trajectory_11.bin",
|
| 119 |
+
"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.bin",
|
| 121 |
+
"pca_trajectory_14.bin",
|
| 122 |
+
"pca_trajectory_15.bin",
|
| 123 |
+
"pca_trajectory_16.bin",
|
| 124 |
+
"pca_trajectory_17.bin",
|
| 125 |
+
"pca_trajectory_18.bin",
|
| 126 |
+
"pca_trajectory_19.bin",
|
| 127 |
+
"structure.pdb",
|
| 128 |
+
"trajectory.xtc",
|
| 129 |
+
"clusters_00_screenshot_00.jpg",
|
| 130 |
+
"clusters_00_screenshot_01.jpg",
|
| 131 |
+
"clusters_00_screenshot_02.jpg",
|
| 132 |
+
"clusters_00_screenshot_03.jpg",
|
| 133 |
+
"clusters_00_screenshot_04.jpg",
|
| 134 |
+
"clusters_00_screenshot_05.jpg",
|
| 135 |
+
"clusters_00_screenshot_06.jpg",
|
| 136 |
+
"clusters_00_screenshot_07.jpg",
|
| 137 |
+
"clusters_00_screenshot_08.jpg",
|
| 138 |
+
"clusters_00_screenshot_09.jpg",
|
| 139 |
+
"clusters_00_screenshot_10.jpg",
|
| 140 |
+
"clusters_00_screenshot_11.jpg",
|
| 141 |
+
"clusters_00_screenshot_12.jpg",
|
| 142 |
+
"clusters_00_screenshot_13.jpg",
|
| 143 |
+
"clusters_00_screenshot_14.jpg",
|
| 144 |
+
"clusters_00_screenshot_15.jpg",
|
| 145 |
+
"clusters_00_screenshot_16.jpg",
|
| 146 |
+
"clusters_00_screenshot_17.jpg",
|
| 147 |
+
"clusters_00_screenshot_18.jpg",
|
| 148 |
+
"clusters_00_screenshot_19.jpg",
|
| 149 |
+
"clusters_01_screenshot_00.jpg",
|
| 150 |
+
"clusters_01_screenshot_01.jpg",
|
| 151 |
+
"clusters_01_screenshot_02.jpg",
|
| 152 |
+
"clusters_01_screenshot_03.jpg",
|
| 153 |
+
"clusters_01_screenshot_04.jpg",
|
| 154 |
+
"clusters_01_screenshot_05.jpg",
|
| 155 |
+
"clusters_01_screenshot_06.jpg",
|
| 156 |
+
"clusters_01_screenshot_07.jpg",
|
| 157 |
+
"clusters_01_screenshot_08.jpg",
|
| 158 |
+
"clusters_01_screenshot_09.jpg",
|
| 159 |
+
"clusters_01_screenshot_10.jpg",
|
| 160 |
+
"clusters_01_screenshot_11.jpg",
|
| 161 |
+
"clusters_01_screenshot_12.jpg",
|
| 162 |
+
"clusters_01_screenshot_13.jpg",
|
| 163 |
+
"clusters_01_screenshot_14.jpg",
|
| 164 |
+
"clusters_01_screenshot_15.jpg",
|
| 165 |
+
"clusters_01_screenshot_16.jpg",
|
| 166 |
+
"clusters_01_screenshot_17.jpg",
|
| 167 |
+
"clusters_01_screenshot_18.jpg",
|
| 168 |
+
"clusters_01_screenshot_19.jpg",
|
| 169 |
+
"pocket_01.pdb",
|
| 170 |
+
"pocket_02.pdb",
|
| 171 |
+
"pocket_03.pdb",
|
| 172 |
+
"pocket_04.pdb",
|
| 173 |
+
"pocket_05.pdb",
|
| 174 |
+
"pocket_06.pdb",
|
| 175 |
+
"pocket_07.pdb",
|
| 176 |
+
"pocket_08.pdb"
|
| 177 |
+
],
|
| 178 |
+
"analyses": [
|
| 179 |
+
"clusters",
|
| 180 |
+
"clusters-00",
|
| 181 |
+
"clusters-01",
|
| 182 |
+
"dist-perres",
|
| 183 |
+
"energies",
|
| 184 |
+
"fluctuation",
|
| 185 |
+
"hbonds",
|
| 186 |
+
"interactions",
|
| 187 |
+
"pca",
|
| 188 |
+
"pockets",
|
| 189 |
+
"rgyr",
|
| 190 |
+
"rmsd-pairwise",
|
| 191 |
+
"rmsd-perres",
|
| 192 |
+
"rmsds",
|
| 193 |
+
"sasa",
|
| 194 |
+
"tmscores"
|
| 195 |
+
],
|
| 196 |
+
"mdIndex": 0,
|
| 197 |
+
"mdNumber": 1,
|
| 198 |
+
"refframe": 0,
|
| 199 |
+
"internalId": "6840856ec90c3a181a98ed1a",
|
| 200 |
+
"creationDate": "2025-06-04T17:42:06.000Z",
|
| 201 |
+
"identifier": "A003S"
|
| 202 |
+
}
|
data/files/A003S/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A003S", "accession": "A003S", "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 2QXV", "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": ["2QXV"], "FORCED_REFERENCES": null, "REFERENCES": ["Q921E6", "Q61188"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TMFSSNRQKILERTETLNQEWKQRRIQPV", "FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"], "NUCLSEQ": [], "DOMAINS": ["Polycomb protein EED", "Interaction with EZH2", "Histone-lysine N-methyltransferase EZH2", "Interaction with DNMT1, DNMT3A and DNMT3B", "Interaction with EED"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6132, "SYSTRES": 381, "PROTATS": 6132, "PROTRES": 381, "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": 8.49332, "BOXSIZEY": 8.49332, "BOXSIZEZ": 6.0081, "mdName": "replica 1", "mdAtoms": 6132, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003S/files/topology.tpr", "length": 1904752, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003S/files/screenshot.jpg", "length": 25037, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003S/files/trajectory.bin", "length": 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| 1 |
+
{
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| 2 |
+
"accession": "A003T",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2SNI",
|
| 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 |
+
"2SNI"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P00782",
|
| 31 |
+
"P01053"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG",
|
| 38 |
+
"AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLQNTTTKLGDSFYYGKGLINVQAAAQ"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Subtilisin BPN'",
|
| 43 |
+
"Peptidase S8",
|
| 44 |
+
"Subtilisin-chymotrypsin inhibitor-2A",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Reactive bond"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 4901,
|
| 58 |
+
"SYSTRES": 339,
|
| 59 |
+
"PROTATS": 4901,
|
| 60 |
+
"PROTRES": 339,
|
| 61 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
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"MEMBRANES": null,
|
| 85 |
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"CUSTOMS": null,
|
| 86 |
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"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 8.76713,
|
| 92 |
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"BOXSIZEY": 8.76713,
|
| 93 |
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"BOXSIZEZ": 6.24666,
|
| 94 |
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"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 4901,
|
| 96 |
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"mdFrames": 5001
|
| 97 |
+
},
|
| 98 |
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"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
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"mdref": 0,
|
| 104 |
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"files": [
|
| 105 |
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"topology.tpr",
|
| 106 |
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"screenshot.jpg",
|
| 107 |
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"trajectory.bin",
|
| 108 |
+
"pca_trajectory_01.bin",
|
| 109 |
+
"pca_trajectory_02.bin",
|
| 110 |
+
"pca_trajectory_03.bin",
|
| 111 |
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"pca_trajectory_04.bin",
|
| 112 |
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"pca_trajectory_05.bin",
|
| 113 |
+
"pca_trajectory_06.bin",
|
| 114 |
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"pca_trajectory_07.bin",
|
| 115 |
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"pca_trajectory_08.bin",
|
| 116 |
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"pca_trajectory_09.bin",
|
| 117 |
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"pca_trajectory_10.bin",
|
| 118 |
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"pca_trajectory_11.bin",
|
| 119 |
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"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.bin",
|
| 121 |
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"structure.pdb",
|
| 122 |
+
"trajectory.xtc",
|
| 123 |
+
"clusters_00_screenshot_00.jpg",
|
| 124 |
+
"clusters_00_screenshot_01.jpg",
|
| 125 |
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"clusters_00_screenshot_02.jpg",
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| 126 |
+
"clusters_00_screenshot_03.jpg",
|
| 127 |
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"clusters_00_screenshot_04.jpg",
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| 128 |
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"clusters_00_screenshot_05.jpg",
|
| 129 |
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"clusters_00_screenshot_06.jpg",
|
| 130 |
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"clusters_00_screenshot_07.jpg",
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| 131 |
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"clusters_00_screenshot_08.jpg",
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| 132 |
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"clusters_00_screenshot_09.jpg",
|
| 133 |
+
"clusters_00_screenshot_10.jpg",
|
| 134 |
+
"clusters_00_screenshot_11.jpg",
|
| 135 |
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"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 |
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"clusters_01_screenshot_15.jpg",
|
| 159 |
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"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 |
+
"pocket_07.pdb"
|
| 170 |
+
],
|
| 171 |
+
"analyses": [
|
| 172 |
+
"clusters",
|
| 173 |
+
"clusters-00",
|
| 174 |
+
"clusters-01",
|
| 175 |
+
"dist-perres",
|
| 176 |
+
"energies",
|
| 177 |
+
"fluctuation",
|
| 178 |
+
"hbonds",
|
| 179 |
+
"interactions",
|
| 180 |
+
"pca",
|
| 181 |
+
"pockets",
|
| 182 |
+
"rgyr",
|
| 183 |
+
"rmsd-pairwise",
|
| 184 |
+
"rmsd-perres",
|
| 185 |
+
"rmsds",
|
| 186 |
+
"sasa",
|
| 187 |
+
"tmscores"
|
| 188 |
+
],
|
| 189 |
+
"mdIndex": 0,
|
| 190 |
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"mdNumber": 1,
|
| 191 |
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"refframe": 0,
|
| 192 |
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"internalId": "6840878bcbe8a3cd5b0dede8",
|
| 193 |
+
"creationDate": "2025-06-04T17:51:07.000Z",
|
| 194 |
+
"identifier": "A003T"
|
| 195 |
+
}
|
data/files/A003T/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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+
{"project_identifier": "A003T", "accession": "A003T", "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 2SNI", "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": ["2SNI"], "FORCED_REFERENCES": null, "REFERENCES": ["P00782", "P01053"], 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data/files/A003U/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003U",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2UUY",
|
| 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 |
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"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 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"2UUY"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"P00760",
|
| 31 |
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"Q1EG59"
|
| 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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"CTVPIGWSEPVKGLCKARFTRYYCMGNCCKVYEGCYTGGYSRMGECARNCPA",
|
| 38 |
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"IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Serine protease 1",
|
| 43 |
+
"Alpha-trypsin chain 1",
|
| 44 |
+
"Alpha-trypsin chain 2",
|
| 45 |
+
"Peptidase S1",
|
| 46 |
+
""
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
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"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
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],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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"BOXTYPE": "Dodecahedron",
|
| 57 |
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"SYSTATS": 3992,
|
| 58 |
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"SYSTRES": 275,
|
| 59 |
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"PROTATS": 3992,
|
| 60 |
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"PROTRES": 275,
|
| 61 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
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"COUNCAT": 0,
|
| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
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{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
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"CHAINNAMES": null,
|
| 84 |
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"MEMBRANES": null,
|
| 85 |
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"CUSTOMS": null,
|
| 86 |
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"ORIENTATION": null,
|
| 87 |
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"PTM": [],
|
| 88 |
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"MULTIMERIC": null,
|
| 89 |
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"COLLECTIONS": "dynarepo",
|
| 90 |
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"WARNINGS": [],
|
| 91 |
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"BOXSIZEX": 8.48024,
|
| 92 |
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"BOXSIZEY": 8.48024,
|
| 93 |
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"BOXSIZEZ": 6.00964,
|
| 94 |
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"mdName": "replica 1",
|
| 95 |
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"mdAtoms": 3992,
|
| 96 |
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"mdFrames": 5001
|
| 97 |
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},
|
| 98 |
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"mds": [
|
| 99 |
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"replica 1",
|
| 100 |
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"replica 2",
|
| 101 |
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"replica 3"
|
| 102 |
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],
|
| 103 |
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"mdref": 0,
|
| 104 |
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"files": [
|
| 105 |
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"topology.tpr",
|
| 106 |
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"screenshot.jpg",
|
| 107 |
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"trajectory.bin",
|
| 108 |
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"pca_trajectory_01.bin",
|
| 109 |
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"pca_trajectory_02.bin",
|
| 110 |
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"pca_trajectory_03.bin",
|
| 111 |
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"pca_trajectory_04.bin",
|
| 112 |
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"pca_trajectory_05.bin",
|
| 113 |
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|
| 114 |
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"pca_trajectory_07.bin",
|
| 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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"pca_trajectory_12.bin",
|
| 120 |
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|
| 121 |
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"pca_trajectory_14.bin",
|
| 122 |
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"pca_trajectory_15.bin",
|
| 123 |
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"structure.pdb",
|
| 124 |
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"clusters_01_screenshot_13.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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"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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],
|
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+
"analyses": [
|
| 174 |
+
"clusters",
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| 175 |
+
"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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| 181 |
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"interactions",
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| 182 |
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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": "68408967612886fa3a11dc2e",
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"creationDate": "2025-06-04T17:59:03.000Z",
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+
"identifier": "A003U"
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}
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data/files/A003U/records.jsonl
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| 1 |
+
{
|
| 2 |
+
"accession": "A003V",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2V1D",
|
| 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 |
+
"2V1D"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O60341",
|
| 31 |
+
"Q9UKL0",
|
| 32 |
+
"Q16695"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
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"ARTMQTARKSTGGKAP",
|
| 39 |
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"RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE",
|
| 40 |
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"PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Lysine-specific histone demethylase 1A",
|
| 45 |
+
"SWIRM",
|
| 46 |
+
"Disordered",
|
| 47 |
+
"Demethylase activity",
|
| 48 |
+
"REST corepressor 1",
|
| 49 |
+
"SANT 2",
|
| 50 |
+
"Disordered",
|
| 51 |
+
"Interaction with KDM1A",
|
| 52 |
+
"Histone H3.1t",
|
| 53 |
+
"Disordered"
|
| 54 |
+
],
|
| 55 |
+
"FRAMESTEP": 0.1,
|
| 56 |
+
"TIMESTEP": 2,
|
| 57 |
+
"TEMP": 310,
|
| 58 |
+
"ENSEMBLE": "NPT",
|
| 59 |
+
"FF": [
|
| 60 |
+
"CHARMM36m"
|
| 61 |
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],
|
| 62 |
+
"WAT": "TIP3P",
|
| 63 |
+
"BOXTYPE": "Dodecahedron",
|
| 64 |
+
"SYSTATS": 12883,
|
| 65 |
+
"SYSTRES": 815,
|
| 66 |
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"PROTATS": 12883,
|
| 67 |
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"PROTRES": 815,
|
| 68 |
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"NUCLATS": 0,
|
| 69 |
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"NUCLRES": 0,
|
| 70 |
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"LIPIATS": 0,
|
| 71 |
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"LIPIRES": 0,
|
| 72 |
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"CARBATS": 0,
|
| 73 |
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"CARBRES": 0,
|
| 74 |
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"SOLVATS": 0,
|
| 75 |
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"SOLVRES": 0,
|
| 76 |
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"COUNCAT": 0,
|
| 77 |
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"COUNANI": 0,
|
| 78 |
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"COUNION": 0,
|
| 79 |
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"INTERACTIONS": [
|
| 80 |
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{
|
| 81 |
+
"name": "chain A-chain B interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain B",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain B",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "chain A-chain C interaction",
|
| 90 |
+
"agent_1": "chain A",
|
| 91 |
+
"agent_2": "chain C",
|
| 92 |
+
"selection_1": "chain A",
|
| 93 |
+
"selection_2": "chain C",
|
| 94 |
+
"type": "protein-protein"
|
| 95 |
+
},
|
| 96 |
+
{
|
| 97 |
+
"name": "chain B-chain C interaction",
|
| 98 |
+
"agent_1": "chain B",
|
| 99 |
+
"agent_2": "chain C",
|
| 100 |
+
"selection_1": "chain B",
|
| 101 |
+
"selection_2": "chain C",
|
| 102 |
+
"type": "protein-protein"
|
| 103 |
+
}
|
| 104 |
+
],
|
| 105 |
+
"PBC_SELECTION": null,
|
| 106 |
+
"CHAINNAMES": null,
|
| 107 |
+
"MEMBRANES": null,
|
| 108 |
+
"CUSTOMS": null,
|
| 109 |
+
"ORIENTATION": null,
|
| 110 |
+
"PTM": [],
|
| 111 |
+
"MULTIMERIC": null,
|
| 112 |
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"COLLECTIONS": "dynarepo",
|
| 113 |
+
"WARNINGS": [],
|
| 114 |
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"BOXSIZEX": 17.8707,
|
| 115 |
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"BOXSIZEY": 17.8707,
|
| 116 |
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"BOXSIZEZ": 12.6256,
|
| 117 |
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"mdName": "replica 1",
|
| 118 |
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"mdAtoms": 12883,
|
| 119 |
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"mdFrames": 5001
|
| 120 |
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},
|
| 121 |
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"mds": [
|
| 122 |
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"replica 1",
|
| 123 |
+
"replica 2",
|
| 124 |
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"replica 3"
|
| 125 |
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],
|
| 126 |
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"mdref": 0,
|
| 127 |
+
"files": [
|
| 128 |
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"topology.tpr",
|
| 129 |
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"screenshot.jpg",
|
| 130 |
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"trajectory.bin",
|
| 131 |
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"pca_trajectory_01.bin",
|
| 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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|
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|
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|
| 163 |
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|
| 164 |
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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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|
| 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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"clusters_03_screenshot_20.jpg",
|
| 224 |
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"pocket_01.pdb",
|
| 225 |
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"pocket_02.pdb",
|
| 226 |
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"pocket_03.pdb",
|
| 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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"pocket_09.pdb",
|
| 233 |
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"pocket_10.pdb"
|
| 234 |
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],
|
| 235 |
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"analyses": [
|
| 236 |
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"clusters",
|
| 237 |
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"clusters-00",
|
| 238 |
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|
| 239 |
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|
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|
| 241 |
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|
| 242 |
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|
| 243 |
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"fluctuation",
|
| 244 |
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"hbonds",
|
| 245 |
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"interactions",
|
| 246 |
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"pca",
|
| 247 |
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"pockets",
|
| 248 |
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"rgyr",
|
| 249 |
+
"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": "68408c8d6fac002ae3a0ae09",
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"creationDate": "2025-06-04T18:12:29.000Z",
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"identifier": "A003V"
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}
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data/files/A003V/records.jsonl
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data/files/A003W/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003W",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2V5Q",
|
| 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 |
+
"2V5Q"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P53350",
|
| 31 |
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"Q00420"
|
| 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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"EIPEVLVDPRSRRRYVRGRFLGKGGFAKCFEISDADTKEVFAGKIVPKSLLLKPHQREKMSMEISIHRSLAHQHVVGFHGFFEDNDFVFVVLELCRRRSLLELHKRRKALTEPEARYYLRQIVLGCQYLHRNRVIHRDLKLGNLFLNEDLEVKIGDFGLATKVEYDGERKKTLCGTPNYIAPEVLSKKGHSFEVDVWSIGCIMYTLLVGKPPFETSCLKETYLRIKKNEYSIPKHINPVAASLIQKMLQTDPTARPTINELLNDEFFTSGYIPARLPITCLTIPP",
|
| 38 |
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"DLGKKLLEAARAGQDDEVRILIANGADVNAVDNTGLTPLHLAAVSGHLEIVEVLLKHGADVDAADVYGFTPLHLAAMTGHLEIVEVLLKYGADVNAFDMTGSTPLHLAADEGHLEIVEVLLKYGADVNA"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Serine/threonine-protein kinase PLK1",
|
| 43 |
+
"Protein kinase",
|
| 44 |
+
"Activation loop",
|
| 45 |
+
"GA-binding protein subunit beta-1"
|
| 46 |
+
],
|
| 47 |
+
"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 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 6589,
|
| 57 |
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"SYSTRES": 414,
|
| 58 |
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"PROTATS": 6589,
|
| 59 |
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"PROTRES": 414,
|
| 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 |
+
"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 |
+
],
|
| 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": 9.91447,
|
| 91 |
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"BOXSIZEY": 9.91447,
|
| 92 |
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"BOXSIZEZ": 7.00414,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 6589,
|
| 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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],
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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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|
| 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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"pca_trajectory_13.bin",
|
| 120 |
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"structure.pdb",
|
| 121 |
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"trajectory.xtc",
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| 122 |
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|
| 123 |
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| 124 |
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| 125 |
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| 128 |
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| 129 |
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"clusters_01_screenshot_12.jpg",
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"clusters_01_screenshot_13.jpg",
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"clusters_01_screenshot_14.jpg",
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"clusters_01_screenshot_15.jpg",
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"clusters_01_screenshot_16.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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"pocket_03.pdb",
|
| 167 |
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"pocket_04.pdb",
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| 168 |
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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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| 172 |
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"pocket_09.pdb",
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| 173 |
+
"pocket_10.pdb"
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| 174 |
+
],
|
| 175 |
+
"analyses": [
|
| 176 |
+
"clusters",
|
| 177 |
+
"clusters-00",
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| 178 |
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"clusters-01",
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| 179 |
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"dist-perres",
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| 180 |
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"energies",
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| 181 |
+
"fluctuation",
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| 182 |
+
"hbonds",
|
| 183 |
+
"interactions",
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| 184 |
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"pca",
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| 185 |
+
"pockets",
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| 186 |
+
"rgyr",
|
| 187 |
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"rmsd-pairwise",
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| 188 |
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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": "6840903adbf083adda95e302",
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| 197 |
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"creationDate": "2025-06-04T18:28:10.000Z",
|
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+
"identifier": "A003W"
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+
}
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data/files/A003W/records.jsonl
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A003X",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2V8S",
|
| 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 |
+
"2V8S"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q14677",
|
| 31 |
+
"Q9UEU0"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ASSAASSEHFEKLHEIFRGLLEDLQGVPERLLGTAGTEEKKKLVRDFDEKQQEANETLAEMEEELRYAPLTFRNPMMSKLRNYRKDLAKLHRE",
|
| 38 |
+
"SEIESKVREATNDDPWGPSGQLMGEIAKATFMYEQFPELMNMLWSRMLKDNKKNWRRVYKSLLLLAYLIRNGSERVVTSAREHIYDLRSLENYHFVDEHGKDQGINIRQKVKELVEFAQDDDRLREERKKAKKNKDK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Clathrin interactor 1",
|
| 43 |
+
"ENTH",
|
| 44 |
+
"Interaction with VTI1B",
|
| 45 |
+
"Vesicle transport through interaction with t-SNAREs homolog 1B",
|
| 46 |
+
"Interaction with CLINT1"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 3818,
|
| 58 |
+
"SYSTRES": 230,
|
| 59 |
+
"PROTATS": 3818,
|
| 60 |
+
"PROTRES": 230,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 10.0218,
|
| 92 |
+
"BOXSIZEY": 10.0218,
|
| 93 |
+
"BOXSIZEZ": 7.09248,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 3818,
|
| 96 |
+
"mdFrames": 5001
|
| 97 |
+
},
|
| 98 |
+
"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
+
"mdref": 0,
|
| 104 |
+
"files": [
|
| 105 |
+
"topology.tpr",
|
| 106 |
+
"screenshot.jpg",
|
| 107 |
+
"trajectory.bin",
|
| 108 |
+
"pca_trajectory_01.bin",
|
| 109 |
+
"pca_trajectory_02.bin",
|
| 110 |
+
"pca_trajectory_03.bin",
|
| 111 |
+
"pca_trajectory_04.bin",
|
| 112 |
+
"pca_trajectory_05.bin",
|
| 113 |
+
"pca_trajectory_06.bin",
|
| 114 |
+
"pca_trajectory_07.bin",
|
| 115 |
+
"pca_trajectory_08.bin",
|
| 116 |
+
"pca_trajectory_09.bin",
|
| 117 |
+
"pca_trajectory_10.bin",
|
| 118 |
+
"pca_trajectory_11.bin",
|
| 119 |
+
"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.bin",
|
| 121 |
+
"pca_trajectory_14.bin",
|
| 122 |
+
"structure.pdb",
|
| 123 |
+
"trajectory.xtc",
|
| 124 |
+
"clusters_00_screenshot_00.jpg",
|
| 125 |
+
"clusters_00_screenshot_01.jpg",
|
| 126 |
+
"clusters_00_screenshot_02.jpg",
|
| 127 |
+
"clusters_00_screenshot_03.jpg",
|
| 128 |
+
"clusters_00_screenshot_04.jpg",
|
| 129 |
+
"clusters_00_screenshot_05.jpg",
|
| 130 |
+
"clusters_00_screenshot_06.jpg",
|
| 131 |
+
"clusters_00_screenshot_07.jpg",
|
| 132 |
+
"clusters_00_screenshot_08.jpg",
|
| 133 |
+
"clusters_00_screenshot_09.jpg",
|
| 134 |
+
"clusters_00_screenshot_10.jpg",
|
| 135 |
+
"clusters_00_screenshot_11.jpg",
|
| 136 |
+
"clusters_00_screenshot_12.jpg",
|
| 137 |
+
"clusters_00_screenshot_13.jpg",
|
| 138 |
+
"clusters_00_screenshot_14.jpg",
|
| 139 |
+
"clusters_00_screenshot_15.jpg",
|
| 140 |
+
"clusters_00_screenshot_16.jpg",
|
| 141 |
+
"clusters_00_screenshot_17.jpg",
|
| 142 |
+
"clusters_00_screenshot_18.jpg",
|
| 143 |
+
"clusters_00_screenshot_19.jpg",
|
| 144 |
+
"clusters_01_screenshot_00.jpg",
|
| 145 |
+
"clusters_01_screenshot_01.jpg",
|
| 146 |
+
"clusters_01_screenshot_02.jpg",
|
| 147 |
+
"clusters_01_screenshot_03.jpg",
|
| 148 |
+
"clusters_01_screenshot_04.jpg",
|
| 149 |
+
"clusters_01_screenshot_05.jpg",
|
| 150 |
+
"clusters_01_screenshot_06.jpg",
|
| 151 |
+
"clusters_01_screenshot_07.jpg",
|
| 152 |
+
"clusters_01_screenshot_08.jpg",
|
| 153 |
+
"clusters_01_screenshot_09.jpg",
|
| 154 |
+
"clusters_01_screenshot_10.jpg",
|
| 155 |
+
"clusters_01_screenshot_11.jpg",
|
| 156 |
+
"clusters_01_screenshot_12.jpg",
|
| 157 |
+
"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
+
"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"clusters_01_screenshot_17.jpg",
|
| 162 |
+
"clusters_01_screenshot_18.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": "684092691d3a1d0a3e7d78e5",
|
| 192 |
+
"creationDate": "2025-06-04T18:37:29.000Z",
|
| 193 |
+
"identifier": "A003X"
|
| 194 |
+
}
|
data/files/A003X/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A003X", "accession": "A003X", "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 2V8S", "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": ["2V8S"], "FORCED_REFERENCES": null, "REFERENCES": ["Q14677", "Q9UEU0"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ASSAASSEHFEKLHEIFRGLLEDLQGVPERLLGTAGTEEKKKLVRDFDEKQQEANETLAEMEEELRYAPLTFRNPMMSKLRNYRKDLAKLHRE", "SEIESKVREATNDDPWGPSGQLMGEIAKATFMYEQFPELMNMLWSRMLKDNKKNWRRVYKSLLLLAYLIRNGSERVVTSAREHIYDLRSLENYHFVDEHGKDQGINIRQKVKELVEFAQDDDRLREERKKAKKNKDK"], "NUCLSEQ": [], "DOMAINS": ["Clathrin interactor 1", "ENTH", "Interaction with VTI1B", "Vesicle transport through interaction with t-SNAREs homolog 1B", "Interaction with CLINT1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3818, "SYSTRES": 230, "PROTATS": 3818, "PROTRES": 230, "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": 10.0218, "BOXSIZEY": 10.0218, "BOXSIZEZ": 7.09248, "mdName": "replica 1", "mdAtoms": 3818, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003X/files/topology.tpr", "length": 1368300, "contentType": "application/octet-stream", "metadata": {"project": "684092691d3a1d0a3e7d78e5", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003X/files/screenshot.jpg", "length": 20335, "contentType": "application/octet-stream", "metadata": {"project": "684092691d3a1d0a3e7d78e5", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003X/files/trajectory.bin", "length": 229125816, "contentType": "application/octet-stream", "metadata": {"project": "684092691d3a1d0a3e7d78e5", "md": 0, "frames": 5001, "atoms": 3818}}, {"name": 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data/files/A003Y/project.json
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|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A003Y",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2VYR",
|
| 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 |
+
"2VYR"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O15151",
|
| 31 |
+
"P01764"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EVQLLESGGGLVQPGGSLRLSCAASGFTFEEYAMLWVRQAPGKGLEWVSGINARGYTTYYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCAKPWYPFMASKGSEFDYWGQGTLVTVSS",
|
| 38 |
+
"NQVRPKLPLLKILHAAGAQGEMFTVKEVMHYLGQYIMVKQLYDQQEQHMVYCGGDLLGELLGRQSFSVKDPSPLYDMLRKNLVTLA",
|
| 39 |
+
"EVQLLESGGGLVQPGGSLRLSCAASGFTFEEYAMLWVRQAPGKGLEWVSGINARGYTTYYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCAKPWYPFMASKGSEFDYWGQGTLVTVS",
|
| 40 |
+
"EVQLLESGGGLVQPGGSLRLSCAASGFTFEEYAMLWVRQAPGKGLEWVSGINARGYTTYYADSVKGRFTISRDNSKNTLYLQMNSLRTEDTAVYYCAKPWYPFMASKGSEFDYWGQGTLVTVSSA"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Protein Mdm4",
|
| 45 |
+
"SWIB/MDM2",
|
| 46 |
+
"Immunoglobulin heavy variable 3-23",
|
| 47 |
+
"Ig-like",
|
| 48 |
+
"Framework-1",
|
| 49 |
+
"Complementarity-determining-1",
|
| 50 |
+
"Framework-2",
|
| 51 |
+
"Complementarity-determining-2",
|
| 52 |
+
"Framework-3",
|
| 53 |
+
"Complementarity-determining-3"
|
| 54 |
+
],
|
| 55 |
+
"FRAMESTEP": 0.1,
|
| 56 |
+
"TIMESTEP": 2,
|
| 57 |
+
"TEMP": 310,
|
| 58 |
+
"ENSEMBLE": "NPT",
|
| 59 |
+
"FF": [
|
| 60 |
+
"CHARMM36m"
|
| 61 |
+
],
|
| 62 |
+
"WAT": "TIP3P",
|
| 63 |
+
"BOXTYPE": "Dodecahedron",
|
| 64 |
+
"SYSTATS": 20731,
|
| 65 |
+
"SYSTRES": 1336,
|
| 66 |
+
"PROTATS": 20731,
|
| 67 |
+
"PROTRES": 1336,
|
| 68 |
+
"NUCLATS": 0,
|
| 69 |
+
"NUCLRES": 0,
|
| 70 |
+
"LIPIATS": 0,
|
| 71 |
+
"LIPIRES": 0,
|
| 72 |
+
"CARBATS": 0,
|
| 73 |
+
"CARBRES": 0,
|
| 74 |
+
"SOLVATS": 0,
|
| 75 |
+
"SOLVRES": 0,
|
| 76 |
+
"COUNCAT": 0,
|
| 77 |
+
"COUNANI": 0,
|
| 78 |
+
"COUNION": 0,
|
| 79 |
+
"INTERACTIONS": [
|
| 80 |
+
{
|
| 81 |
+
"name": "chain A-chain D interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain D",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain B",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "chain A-chain E interaction",
|
| 90 |
+
"agent_1": "chain A",
|
| 91 |
+
"agent_2": "chain E",
|
| 92 |
+
"selection_1": "chain A",
|
| 93 |
+
"selection_2": "chain C",
|
| 94 |
+
"type": "protein-protein"
|
| 95 |
+
},
|
| 96 |
+
{
|
| 97 |
+
"name": "chain A-chain F interaction",
|
| 98 |
+
"agent_1": "chain A",
|
| 99 |
+
"agent_2": "chain F",
|
| 100 |
+
"selection_1": "chain A",
|
| 101 |
+
"selection_2": "chain D",
|
| 102 |
+
"type": "protein-protein"
|
| 103 |
+
},
|
| 104 |
+
{
|
| 105 |
+
"name": "chain A-chain H interaction",
|
| 106 |
+
"agent_1": "chain A",
|
| 107 |
+
"agent_2": "chain H",
|
| 108 |
+
"selection_1": "chain A",
|
| 109 |
+
"selection_2": "chain E",
|
| 110 |
+
"type": "protein-protein"
|
| 111 |
+
},
|
| 112 |
+
{
|
| 113 |
+
"name": "chain A-chain J interaction",
|
| 114 |
+
"agent_1": "chain A",
|
| 115 |
+
"agent_2": "chain J",
|
| 116 |
+
"selection_1": "chain A",
|
| 117 |
+
"selection_2": "chain F",
|
| 118 |
+
"type": "protein-protein"
|
| 119 |
+
},
|
| 120 |
+
{
|
| 121 |
+
"name": "chain A-chain L interaction",
|
| 122 |
+
"agent_1": "chain A",
|
| 123 |
+
"agent_2": "chain L",
|
| 124 |
+
"selection_1": "chain A",
|
| 125 |
+
"selection_2": "chain G",
|
| 126 |
+
"type": "protein-protein"
|
| 127 |
+
},
|
| 128 |
+
{
|
| 129 |
+
"name": "chain B-chain C interaction",
|
| 130 |
+
"agent_1": "chain B",
|
| 131 |
+
"agent_2": "chain C",
|
| 132 |
+
"selection_1": "chain A",
|
| 133 |
+
"selection_2": "chain H",
|
| 134 |
+
"type": "protein-protein"
|
| 135 |
+
},
|
| 136 |
+
{
|
| 137 |
+
"name": "chain B-chain F interaction",
|
| 138 |
+
"agent_1": "chain B",
|
| 139 |
+
"agent_2": "chain F",
|
| 140 |
+
"selection_1": "chain A",
|
| 141 |
+
"selection_2": "chain I",
|
| 142 |
+
"type": "protein-protein"
|
| 143 |
+
},
|
| 144 |
+
{
|
| 145 |
+
"name": "chain B-chain G interaction",
|
| 146 |
+
"agent_1": "chain B",
|
| 147 |
+
"agent_2": "chain G",
|
| 148 |
+
"selection_1": "chain A",
|
| 149 |
+
"selection_2": "chain J",
|
| 150 |
+
"type": "protein-protein"
|
| 151 |
+
},
|
| 152 |
+
{
|
| 153 |
+
"name": "chain B-chain I interaction",
|
| 154 |
+
"agent_1": "chain B",
|
| 155 |
+
"agent_2": "chain I",
|
| 156 |
+
"selection_1": "chain A",
|
| 157 |
+
"selection_2": "chain K",
|
| 158 |
+
"type": "protein-protein"
|
| 159 |
+
},
|
| 160 |
+
{
|
| 161 |
+
"name": "chain C-chain G interaction",
|
| 162 |
+
"agent_1": "chain C",
|
| 163 |
+
"agent_2": "chain G",
|
| 164 |
+
"selection_1": "chain A",
|
| 165 |
+
"selection_2": "chain L",
|
| 166 |
+
"type": "protein-protein"
|
| 167 |
+
},
|
| 168 |
+
{
|
| 169 |
+
"name": "chain D-chain H interaction",
|
| 170 |
+
"agent_1": "chain D",
|
| 171 |
+
"agent_2": "chain H",
|
| 172 |
+
"selection_1": "chain B",
|
| 173 |
+
"selection_2": "chain C",
|
| 174 |
+
"type": "protein-protein"
|
| 175 |
+
},
|
| 176 |
+
{
|
| 177 |
+
"name": "chain D-chain J interaction",
|
| 178 |
+
"agent_1": "chain D",
|
| 179 |
+
"agent_2": "chain J",
|
| 180 |
+
"selection_1": "chain B",
|
| 181 |
+
"selection_2": "chain D",
|
| 182 |
+
"type": "protein-protein"
|
| 183 |
+
},
|
| 184 |
+
{
|
| 185 |
+
"name": "chain E-chain J interaction",
|
| 186 |
+
"agent_1": "chain E",
|
| 187 |
+
"agent_2": "chain J",
|
| 188 |
+
"selection_1": "chain B",
|
| 189 |
+
"selection_2": "chain E",
|
| 190 |
+
"type": "protein-protein"
|
| 191 |
+
},
|
| 192 |
+
{
|
| 193 |
+
"name": "chain E-chain L interaction",
|
| 194 |
+
"agent_1": "chain E",
|
| 195 |
+
"agent_2": "chain L",
|
| 196 |
+
"selection_1": "chain B",
|
| 197 |
+
"selection_2": "chain F",
|
| 198 |
+
"type": "protein-protein"
|
| 199 |
+
},
|
| 200 |
+
{
|
| 201 |
+
"name": "chain F-chain H interaction",
|
| 202 |
+
"agent_1": "chain F",
|
| 203 |
+
"agent_2": "chain H",
|
| 204 |
+
"selection_1": "chain B",
|
| 205 |
+
"selection_2": "chain G",
|
| 206 |
+
"type": "protein-protein"
|
| 207 |
+
},
|
| 208 |
+
{
|
| 209 |
+
"name": "chain F-chain I interaction",
|
| 210 |
+
"agent_1": "chain F",
|
| 211 |
+
"agent_2": "chain I",
|
| 212 |
+
"selection_1": "chain B",
|
| 213 |
+
"selection_2": "chain H",
|
| 214 |
+
"type": "protein-protein"
|
| 215 |
+
},
|
| 216 |
+
{
|
| 217 |
+
"name": "chain J-chain K interaction",
|
| 218 |
+
"agent_1": "chain J",
|
| 219 |
+
"agent_2": "chain K",
|
| 220 |
+
"selection_1": "chain B",
|
| 221 |
+
"selection_2": "chain I",
|
| 222 |
+
"type": "protein-protein"
|
| 223 |
+
},
|
| 224 |
+
{
|
| 225 |
+
"name": "chain J-chain L interaction",
|
| 226 |
+
"agent_1": "chain J",
|
| 227 |
+
"agent_2": "chain L",
|
| 228 |
+
"selection_1": "chain B",
|
| 229 |
+
"selection_2": "chain J",
|
| 230 |
+
"type": "protein-protein"
|
| 231 |
+
}
|
| 232 |
+
],
|
| 233 |
+
"PBC_SELECTION": null,
|
| 234 |
+
"CHAINNAMES": null,
|
| 235 |
+
"MEMBRANES": null,
|
| 236 |
+
"CUSTOMS": null,
|
| 237 |
+
"ORIENTATION": null,
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|
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|
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| 714 |
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data/files/A003Y/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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|
data/files/A003Z/project.json
ADDED
|
@@ -0,0 +1,202 @@
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|
| 1 |
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{
|
| 2 |
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"accession": "A003Z",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2W80",
|
| 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 |
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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",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
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| 25 |
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"PDBIDS": [
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| 26 |
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"2W80"
|
| 27 |
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],
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| 28 |
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|
| 29 |
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| 30 |
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|
| 31 |
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|
| 32 |
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| 33 |
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| 34 |
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| 35 |
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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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|
| 42 |
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"Complement factor H",
|
| 43 |
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|
| 44 |
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"Sushi 6",
|
| 45 |
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"Sushi 7",
|
| 46 |
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"Factor H binding protein",
|
| 47 |
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"Domain A",
|
| 48 |
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"Domain B",
|
| 49 |
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"Domain C",
|
| 50 |
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"Important for antibody recognition"
|
| 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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|
| 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",
|
| 61 |
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"SYSTATS": 5608,
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| 62 |
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| 63 |
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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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"name": "chain A-chain B interaction",
|
| 79 |
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|
| 80 |
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|
| 81 |
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"selection_1": "chain A",
|
| 82 |
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|
| 83 |
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"type": "protein-protein"
|
| 84 |
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}
|
| 85 |
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],
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| 86 |
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|
| 87 |
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|
| 94 |
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"mds": [
|
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"replica 1",
|
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"replica 2",
|
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|
| 106 |
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| 107 |
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|
| 108 |
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| 112 |
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"pca_trajectory_01.bin",
|
| 113 |
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"pca_trajectory_02.bin",
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| 114 |
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"pca_trajectory_03.bin",
|
| 115 |
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"pca_trajectory_04.bin",
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"pca_trajectory_05.bin",
|
| 117 |
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"pca_trajectory_06.bin",
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"pca_trajectory_07.bin",
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"pca_trajectory_08.bin",
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| 120 |
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"pca_trajectory_09.bin",
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| 121 |
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"pca_trajectory_10.bin",
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| 122 |
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"pca_trajectory_11.bin",
|
| 123 |
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"pca_trajectory_12.bin",
|
| 124 |
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"pca_trajectory_13.bin",
|
| 125 |
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"pca_trajectory_14.bin",
|
| 126 |
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"pca_trajectory_15.bin",
|
| 127 |
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"structure.pdb",
|
| 128 |
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"trajectory.xtc",
|
| 129 |
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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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"clusters_00_screenshot_15.jpg",
|
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"clusters_00_screenshot_17.jpg",
|
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"clusters_00_screenshot_18.jpg",
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"clusters_01_screenshot_00.jpg",
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"clusters_01_screenshot_01.jpg",
|
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"clusters_01_screenshot_02.jpg",
|
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"clusters_01_screenshot_03.jpg",
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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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"clusters_01_screenshot_10.jpg",
|
| 159 |
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"clusters_01_screenshot_11.jpg",
|
| 160 |
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"clusters_01_screenshot_12.jpg",
|
| 161 |
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"clusters_01_screenshot_13.jpg",
|
| 162 |
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"clusters_01_screenshot_14.jpg",
|
| 163 |
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|
| 164 |
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"clusters_01_screenshot_16.jpg",
|
| 165 |
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"clusters_01_screenshot_17.jpg",
|
| 166 |
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"clusters_01_screenshot_18.jpg",
|
| 167 |
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"pocket_01.pdb",
|
| 168 |
+
"pocket_02.pdb",
|
| 169 |
+
"pocket_03.pdb",
|
| 170 |
+
"pocket_04.pdb",
|
| 171 |
+
"pocket_05.pdb",
|
| 172 |
+
"pocket_06.pdb",
|
| 173 |
+
"pocket_07.pdb",
|
| 174 |
+
"pocket_08.pdb",
|
| 175 |
+
"pocket_09.pdb",
|
| 176 |
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"pocket_10.pdb"
|
| 177 |
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],
|
| 178 |
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|
| 179 |
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"clusters",
|
| 180 |
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|
| 181 |
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"clusters-01",
|
| 182 |
+
"dist-perres",
|
| 183 |
+
"energies",
|
| 184 |
+
"fluctuation",
|
| 185 |
+
"hbonds",
|
| 186 |
+
"interactions",
|
| 187 |
+
"pca",
|
| 188 |
+
"pockets",
|
| 189 |
+
"rgyr",
|
| 190 |
+
"rmsd-pairwise",
|
| 191 |
+
"rmsd-perres",
|
| 192 |
+
"rmsds",
|
| 193 |
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"sasa",
|
| 194 |
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"tmscores"
|
| 195 |
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|
| 196 |
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"mdIndex": 0,
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|
| 200 |
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"creationDate": "2025-06-04T19:15:44.000Z",
|
| 201 |
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"identifier": "A003Z"
|
| 202 |
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}
|
data/files/A003Z/records.jsonl
ADDED
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data/files/A0040/project.json
ADDED
|
@@ -0,0 +1,194 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0040",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2W8B",
|
| 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 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"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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"2W8B"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"P0A855",
|
| 31 |
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"P0A912"
|
| 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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"QNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYL",
|
| 38 |
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"EVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVLYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYL"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
+
"Tol-Pal system protein TolB",
|
| 43 |
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"TolA box",
|
| 44 |
+
"Peptidoglycan-associated lipoprotein",
|
| 45 |
+
"OmpA-like"
|
| 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": 7767,
|
| 57 |
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"SYSTRES": 517,
|
| 58 |
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"PROTATS": 7767,
|
| 59 |
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"PROTRES": 517,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
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| 63 |
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|
| 64 |
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"CARBATS": 0,
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| 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 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"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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"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": 11.7628,
|
| 91 |
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|
| 92 |
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"BOXSIZEZ": 8.31858,
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| 93 |
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"mdName": "replica 1",
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| 94 |
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| 95 |
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| 96 |
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},
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| 97 |
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"mds": [
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| 98 |
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"replica 1",
|
| 99 |
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| 100 |
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|
| 101 |
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],
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| 102 |
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| 103 |
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| 104 |
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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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"clusters_01_screenshot_00.jpg",
|
| 140 |
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"clusters_01_screenshot_01.jpg",
|
| 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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"clusters_01_screenshot_19.jpg",
|
| 159 |
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"pocket_01.pdb",
|
| 160 |
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|
| 161 |
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"pocket_03.pdb",
|
| 162 |
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"pocket_04.pdb",
|
| 163 |
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"pocket_05.pdb",
|
| 164 |
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"pocket_06.pdb",
|
| 165 |
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"pocket_07.pdb",
|
| 166 |
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"pocket_08.pdb",
|
| 167 |
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"pocket_09.pdb",
|
| 168 |
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"pocket_10.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
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"clusters",
|
| 172 |
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"clusters-00",
|
| 173 |
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"clusters-01",
|
| 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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"rmsd-pairwise",
|
| 183 |
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"rmsd-perres",
|
| 184 |
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|
| 185 |
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"sasa",
|
| 186 |
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"tmscores"
|
| 187 |
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],
|
| 188 |
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"mdIndex": 0,
|
| 189 |
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| 190 |
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| 191 |
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"internalId": "68409dcb8a2553024048ca37",
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| 192 |
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"creationDate": "2025-06-04T19:26:03.000Z",
|
| 193 |
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"identifier": "A0040"
|
| 194 |
+
}
|
data/files/A0040/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
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|
|
|
|
|
|
|
|
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data/files/A0041/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A0041",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2WD5",
|
| 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 |
+
"2WD5"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9CU62",
|
| 31 |
+
"Q9CW03"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"KQQLLRAATGKAILNGIDSINKVLEHFRRKGINQHVQNGYHGIVMNNFECEPAFYTCVEVTAGNRLFYHIVDSDEVSTKILMEFNKMNLPGEVTFLPLNKLDVRDTAYPETNDAIPMISKLRYNPRFDKAFKHVFGKTLICRSMEVSTQLARAFTMDCITLEGDQVSHRGALTGGYYDTRKSRLELQKDVRKAE",
|
| 38 |
+
"RKAEIMESIKRLYPGSVYGRLIDLCQPTQKKYQIAVTKVLGKNMDAIIVDSEKTGRDCIQYIKEQRGEPETFLPLDYLEVKPTDEKLRELKGAKLVIDVIRYEPPHIKKALQYACGNALVCDNVEDARRIAFGGHQRHKTVALDGTLFQKSGVISGGASDLKAKARRWDEKAVDKLK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Structural maintenance of chromosomes protein 1A",
|
| 43 |
+
"SMC hinge",
|
| 44 |
+
"Structural maintenance of chromosomes protein 3",
|
| 45 |
+
"SMC hinge"
|
| 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": 5978,
|
| 57 |
+
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|
| 58 |
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|
| 59 |
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"PROTRES": 371,
|
| 60 |
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"NUCLATS": 0,
|
| 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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"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"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 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
+
"CHAINNAMES": null,
|
| 83 |
+
"MEMBRANES": null,
|
| 84 |
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|
| 85 |
+
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|
| 86 |
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"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
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"COLLECTIONS": "dynarepo",
|
| 89 |
+
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|
| 90 |
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"BOXSIZEX": 8.98797,
|
| 91 |
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"BOXSIZEY": 8.98797,
|
| 92 |
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"BOXSIZEZ": 6.37143,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 5978,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
+
"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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"topology.tpr",
|
| 105 |
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"screenshot.jpg",
|
| 106 |
+
"trajectory.bin",
|
| 107 |
+
"pca_trajectory_01.bin",
|
| 108 |
+
"pca_trajectory_02.bin",
|
| 109 |
+
"pca_trajectory_03.bin",
|
| 110 |
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"pca_trajectory_04.bin",
|
| 111 |
+
"pca_trajectory_05.bin",
|
| 112 |
+
"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
+
"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"pca_trajectory_13.bin",
|
| 120 |
+
"pca_trajectory_14.bin",
|
| 121 |
+
"pca_trajectory_15.bin",
|
| 122 |
+
"pca_trajectory_16.bin",
|
| 123 |
+
"pca_trajectory_17.bin",
|
| 124 |
+
"structure.pdb",
|
| 125 |
+
"trajectory.xtc",
|
| 126 |
+
"clusters_00_screenshot_00.jpg",
|
| 127 |
+
"clusters_00_screenshot_01.jpg",
|
| 128 |
+
"clusters_00_screenshot_02.jpg",
|
| 129 |
+
"clusters_00_screenshot_03.jpg",
|
| 130 |
+
"clusters_00_screenshot_04.jpg",
|
| 131 |
+
"clusters_00_screenshot_05.jpg",
|
| 132 |
+
"clusters_00_screenshot_06.jpg",
|
| 133 |
+
"clusters_00_screenshot_07.jpg",
|
| 134 |
+
"clusters_00_screenshot_08.jpg",
|
| 135 |
+
"clusters_00_screenshot_09.jpg",
|
| 136 |
+
"clusters_00_screenshot_10.jpg",
|
| 137 |
+
"clusters_00_screenshot_11.jpg",
|
| 138 |
+
"clusters_00_screenshot_12.jpg",
|
| 139 |
+
"clusters_00_screenshot_13.jpg",
|
| 140 |
+
"clusters_00_screenshot_14.jpg",
|
| 141 |
+
"clusters_00_screenshot_15.jpg",
|
| 142 |
+
"clusters_00_screenshot_16.jpg",
|
| 143 |
+
"clusters_00_screenshot_17.jpg",
|
| 144 |
+
"clusters_00_screenshot_18.jpg",
|
| 145 |
+
"clusters_00_screenshot_19.jpg",
|
| 146 |
+
"clusters_01_screenshot_00.jpg",
|
| 147 |
+
"clusters_01_screenshot_01.jpg",
|
| 148 |
+
"clusters_01_screenshot_02.jpg",
|
| 149 |
+
"clusters_01_screenshot_03.jpg",
|
| 150 |
+
"clusters_01_screenshot_04.jpg",
|
| 151 |
+
"clusters_01_screenshot_05.jpg",
|
| 152 |
+
"clusters_01_screenshot_06.jpg",
|
| 153 |
+
"clusters_01_screenshot_07.jpg",
|
| 154 |
+
"clusters_01_screenshot_08.jpg",
|
| 155 |
+
"clusters_01_screenshot_09.jpg",
|
| 156 |
+
"clusters_01_screenshot_10.jpg",
|
| 157 |
+
"clusters_01_screenshot_11.jpg",
|
| 158 |
+
"clusters_01_screenshot_12.jpg",
|
| 159 |
+
"clusters_01_screenshot_13.jpg",
|
| 160 |
+
"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 |
+
"clusters_01_screenshot_19.jpg",
|
| 166 |
+
"pocket_01.pdb",
|
| 167 |
+
"pocket_02.pdb",
|
| 168 |
+
"pocket_03.pdb",
|
| 169 |
+
"pocket_04.pdb",
|
| 170 |
+
"pocket_05.pdb",
|
| 171 |
+
"pocket_06.pdb",
|
| 172 |
+
"pocket_07.pdb",
|
| 173 |
+
"pocket_08.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 |
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"refframe": 0,
|
| 196 |
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"internalId": "6840a0436a0bb976bc04a30b",
|
| 197 |
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"creationDate": "2025-06-04T19:36:35.000Z",
|
| 198 |
+
"identifier": "A0041"
|
| 199 |
+
}
|
data/files/A0041/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0041", "accession": "A0041", "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 2WD5", "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": ["2WD5"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9CU62", "Q9CW03"], 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| 1 |
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{
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| 2 |
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"accession": "A0042",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2WO3",
|
| 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 |
+
"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",
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| 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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"2WO3"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P54764",
|
| 31 |
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"O43921"
|
| 32 |
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],
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| 33 |
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"INPUT_LIGANDS": null,
|
| 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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| 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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"Ephrin type-A receptor 4",
|
| 43 |
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"Eph LBD",
|
| 44 |
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"Ephrin-A2",
|
| 45 |
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"Ephrin RBD"
|
| 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": 5040,
|
| 57 |
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"SYSTRES": 318,
|
| 58 |
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"PROTATS": 5040,
|
| 59 |
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"PROTRES": 318,
|
| 60 |
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"NUCLATS": 0,
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| 61 |
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"NUCLRES": 0,
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| 62 |
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"LIPIATS": 0,
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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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"COUNCAT": 0,
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| 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 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"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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"CUSTOMS": null,
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| 85 |
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| 86 |
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"PTM": [],
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| 87 |
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"MULTIMERIC": null,
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| 88 |
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"COLLECTIONS": "dynarepo",
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| 89 |
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"WARNINGS": [],
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| 90 |
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"BOXSIZEX": 9.54765,
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| 91 |
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"BOXSIZEY": 9.54765,
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| 92 |
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"BOXSIZEZ": 6.72566,
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| 93 |
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"mdName": "replica 1",
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| 94 |
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| 95 |
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| 96 |
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},
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| 97 |
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"mds": [
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| 98 |
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"replica 1",
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| 99 |
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| 100 |
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| 101 |
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| 102 |
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"screenshot.jpg",
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"structure.pdb",
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"trajectory.xtc",
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"clusters_01_screenshot_13.jpg",
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"clusters_01_screenshot_14.jpg",
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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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| 167 |
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],
|
| 168 |
+
"analyses": [
|
| 169 |
+
"clusters",
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| 170 |
+
"clusters-00",
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"clusters-01",
|
| 172 |
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"dist-perres",
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| 173 |
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"energies",
|
| 174 |
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"fluctuation",
|
| 175 |
+
"hbonds",
|
| 176 |
+
"interactions",
|
| 177 |
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"pca",
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| 178 |
+
"pockets",
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| 179 |
+
"rgyr",
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| 180 |
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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": "6840a260ba0364e14d82393b",
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"creationDate": "2025-06-04T19:45:36.000Z",
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+
"identifier": "A0042"
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}
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data/files/A0042/records.jsonl
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0043",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2WP0",
|
| 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 |
+
"2WP0"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O25828",
|
| 31 |
+
"O26057"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"NIEKEILALVKQNPKVSLIEYENYFSQLKYNPNASKSDIAFFYAPNQVLCTTITAKYGALLKEILSQNKVGMHLAHSVDVRIEVAP",
|
| 38 |
+
"NNNIEKEILALVKQNPKVSLIEYENYFSQLKYNPNASKSDIAFFYAPNQVLCTTITAKYGALLKEILSQNKVGMHLAHSVDVRIEVAP",
|
| 39 |
+
"MKNFYDWIKEFIRDQGEFIAQQSGWLELERSSYAKLIAQTISHVLNGGSLLVSADSSRHWFLNYILSNLNPKDLKERPLLSVIDFNASSFYPKNDANLSLATIEMTYQNPMFWHVGKIENEGLKTILLSKIPSFLWLFEELKEDCLLLKEHDSLLDYKLLQLFKLFENALFSVLYNKVTL"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"DNA replication regulator protein HobA",
|
| 44 |
+
"Chromosomal replication initiator protein DnaA",
|
| 45 |
+
"Domain I, interacts with DnaA modulators",
|
| 46 |
+
"Domain II"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 8754,
|
| 58 |
+
"SYSTRES": 534,
|
| 59 |
+
"PROTATS": 8754,
|
| 60 |
+
"PROTRES": 534,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
},
|
| 81 |
+
{
|
| 82 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain B-chain D interaction",
|
| 91 |
+
"agent_1": "chain B",
|
| 92 |
+
"agent_2": "chain D",
|
| 93 |
+
"selection_1": "chain A",
|
| 94 |
+
"selection_2": "chain D",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
}
|
| 97 |
+
],
|
| 98 |
+
"PBC_SELECTION": null,
|
| 99 |
+
"CHAINNAMES": null,
|
| 100 |
+
"MEMBRANES": null,
|
| 101 |
+
"CUSTOMS": null,
|
| 102 |
+
"ORIENTATION": null,
|
| 103 |
+
"PTM": [],
|
| 104 |
+
"MULTIMERIC": null,
|
| 105 |
+
"COLLECTIONS": "dynarepo",
|
| 106 |
+
"WARNINGS": [],
|
| 107 |
+
"BOXSIZEX": 14.0121,
|
| 108 |
+
"BOXSIZEY": 14.0121,
|
| 109 |
+
"BOXSIZEZ": 9.87066,
|
| 110 |
+
"mdName": "replica 1",
|
| 111 |
+
"mdAtoms": 8754,
|
| 112 |
+
"mdFrames": 5001
|
| 113 |
+
},
|
| 114 |
+
"mds": [
|
| 115 |
+
"replica 1",
|
| 116 |
+
"replica 2",
|
| 117 |
+
"replica 3"
|
| 118 |
+
],
|
| 119 |
+
"mdref": 0,
|
| 120 |
+
"files": [
|
| 121 |
+
"topology.tpr",
|
| 122 |
+
"screenshot.jpg",
|
| 123 |
+
"trajectory.bin",
|
| 124 |
+
"pca_trajectory_01.bin",
|
| 125 |
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"pca_trajectory_02.bin",
|
| 126 |
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"pca_trajectory_03.bin",
|
| 127 |
+
"pca_trajectory_04.bin",
|
| 128 |
+
"pca_trajectory_05.bin",
|
| 129 |
+
"pca_trajectory_06.bin",
|
| 130 |
+
"pca_trajectory_07.bin",
|
| 131 |
+
"pca_trajectory_08.bin",
|
| 132 |
+
"pca_trajectory_09.bin",
|
| 133 |
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"pca_trajectory_10.bin",
|
| 134 |
+
"pca_trajectory_11.bin",
|
| 135 |
+
"pca_trajectory_12.bin",
|
| 136 |
+
"structure.pdb",
|
| 137 |
+
"trajectory.xtc",
|
| 138 |
+
"clusters_00_screenshot_00.jpg",
|
| 139 |
+
"clusters_00_screenshot_01.jpg",
|
| 140 |
+
"clusters_00_screenshot_02.jpg",
|
| 141 |
+
"clusters_00_screenshot_03.jpg",
|
| 142 |
+
"clusters_00_screenshot_04.jpg",
|
| 143 |
+
"clusters_00_screenshot_05.jpg",
|
| 144 |
+
"clusters_00_screenshot_06.jpg",
|
| 145 |
+
"clusters_00_screenshot_07.jpg",
|
| 146 |
+
"clusters_00_screenshot_08.jpg",
|
| 147 |
+
"clusters_00_screenshot_09.jpg",
|
| 148 |
+
"clusters_00_screenshot_10.jpg",
|
| 149 |
+
"clusters_00_screenshot_11.jpg",
|
| 150 |
+
"clusters_00_screenshot_12.jpg",
|
| 151 |
+
"clusters_00_screenshot_13.jpg",
|
| 152 |
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"clusters_00_screenshot_14.jpg",
|
| 153 |
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"clusters_00_screenshot_15.jpg",
|
| 154 |
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"clusters_00_screenshot_16.jpg",
|
| 155 |
+
"clusters_00_screenshot_17.jpg",
|
| 156 |
+
"clusters_00_screenshot_18.jpg",
|
| 157 |
+
"clusters_00_screenshot_19.jpg",
|
| 158 |
+
"clusters_01_screenshot_00.jpg",
|
| 159 |
+
"clusters_01_screenshot_01.jpg",
|
| 160 |
+
"clusters_01_screenshot_02.jpg",
|
| 161 |
+
"clusters_01_screenshot_03.jpg",
|
| 162 |
+
"clusters_01_screenshot_04.jpg",
|
| 163 |
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"clusters_01_screenshot_05.jpg",
|
| 164 |
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"clusters_01_screenshot_06.jpg",
|
| 165 |
+
"clusters_01_screenshot_07.jpg",
|
| 166 |
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"clusters_01_screenshot_08.jpg",
|
| 167 |
+
"clusters_01_screenshot_09.jpg",
|
| 168 |
+
"clusters_01_screenshot_10.jpg",
|
| 169 |
+
"clusters_01_screenshot_11.jpg",
|
| 170 |
+
"clusters_01_screenshot_12.jpg",
|
| 171 |
+
"clusters_01_screenshot_13.jpg",
|
| 172 |
+
"clusters_01_screenshot_14.jpg",
|
| 173 |
+
"clusters_01_screenshot_15.jpg",
|
| 174 |
+
"clusters_01_screenshot_16.jpg",
|
| 175 |
+
"clusters_01_screenshot_17.jpg",
|
| 176 |
+
"clusters_01_screenshot_18.jpg",
|
| 177 |
+
"clusters_02_screenshot_00.jpg",
|
| 178 |
+
"clusters_02_screenshot_01.jpg",
|
| 179 |
+
"clusters_02_screenshot_02.jpg",
|
| 180 |
+
"clusters_02_screenshot_03.jpg",
|
| 181 |
+
"clusters_02_screenshot_04.jpg",
|
| 182 |
+
"clusters_02_screenshot_05.jpg",
|
| 183 |
+
"clusters_02_screenshot_06.jpg",
|
| 184 |
+
"clusters_02_screenshot_07.jpg",
|
| 185 |
+
"clusters_02_screenshot_08.jpg",
|
| 186 |
+
"clusters_02_screenshot_09.jpg",
|
| 187 |
+
"clusters_02_screenshot_10.jpg",
|
| 188 |
+
"clusters_02_screenshot_11.jpg",
|
| 189 |
+
"clusters_02_screenshot_12.jpg",
|
| 190 |
+
"clusters_02_screenshot_13.jpg",
|
| 191 |
+
"clusters_02_screenshot_14.jpg",
|
| 192 |
+
"clusters_02_screenshot_15.jpg",
|
| 193 |
+
"clusters_02_screenshot_16.jpg",
|
| 194 |
+
"clusters_02_screenshot_17.jpg",
|
| 195 |
+
"clusters_02_screenshot_18.jpg",
|
| 196 |
+
"clusters_03_screenshot_00.jpg",
|
| 197 |
+
"clusters_03_screenshot_01.jpg",
|
| 198 |
+
"clusters_03_screenshot_02.jpg",
|
| 199 |
+
"clusters_03_screenshot_03.jpg",
|
| 200 |
+
"clusters_03_screenshot_04.jpg",
|
| 201 |
+
"clusters_03_screenshot_05.jpg",
|
| 202 |
+
"clusters_03_screenshot_06.jpg",
|
| 203 |
+
"clusters_03_screenshot_07.jpg",
|
| 204 |
+
"clusters_03_screenshot_08.jpg",
|
| 205 |
+
"clusters_03_screenshot_09.jpg",
|
| 206 |
+
"clusters_03_screenshot_10.jpg",
|
| 207 |
+
"clusters_03_screenshot_11.jpg",
|
| 208 |
+
"clusters_03_screenshot_12.jpg",
|
| 209 |
+
"clusters_03_screenshot_13.jpg",
|
| 210 |
+
"clusters_03_screenshot_14.jpg",
|
| 211 |
+
"clusters_03_screenshot_15.jpg",
|
| 212 |
+
"clusters_03_screenshot_16.jpg",
|
| 213 |
+
"clusters_03_screenshot_17.jpg",
|
| 214 |
+
"clusters_03_screenshot_18.jpg",
|
| 215 |
+
"clusters_03_screenshot_19.jpg",
|
| 216 |
+
"clusters_03_screenshot_20.jpg",
|
| 217 |
+
"clusters_03_screenshot_21.jpg",
|
| 218 |
+
"clusters_03_screenshot_22.jpg",
|
| 219 |
+
"pocket_01.pdb",
|
| 220 |
+
"pocket_02.pdb",
|
| 221 |
+
"pocket_03.pdb",
|
| 222 |
+
"pocket_04.pdb",
|
| 223 |
+
"pocket_05.pdb",
|
| 224 |
+
"pocket_06.pdb",
|
| 225 |
+
"pocket_07.pdb",
|
| 226 |
+
"pocket_08.pdb",
|
| 227 |
+
"pocket_09.pdb",
|
| 228 |
+
"pocket_10.pdb"
|
| 229 |
+
],
|
| 230 |
+
"analyses": [
|
| 231 |
+
"clusters",
|
| 232 |
+
"clusters-00",
|
| 233 |
+
"clusters-01",
|
| 234 |
+
"clusters-02",
|
| 235 |
+
"clusters-03",
|
| 236 |
+
"dist-perres",
|
| 237 |
+
"energies",
|
| 238 |
+
"fluctuation",
|
| 239 |
+
"hbonds",
|
| 240 |
+
"interactions",
|
| 241 |
+
"pca",
|
| 242 |
+
"pockets",
|
| 243 |
+
"rgyr",
|
| 244 |
+
"rmsd-pairwise",
|
| 245 |
+
"rmsd-perres",
|
| 246 |
+
"rmsds",
|
| 247 |
+
"sasa",
|
| 248 |
+
"tmscores"
|
| 249 |
+
],
|
| 250 |
+
"mdIndex": 0,
|
| 251 |
+
"mdNumber": 1,
|
| 252 |
+
"refframe": 0,
|
| 253 |
+
"internalId": "6840a4f66170ec54e465dd9b",
|
| 254 |
+
"creationDate": "2025-06-04T19:56:38.000Z",
|
| 255 |
+
"identifier": "A0043"
|
| 256 |
+
}
|
data/files/A0043/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0043", "accession": "A0043", "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 2WP0", "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": ["2WP0"], "FORCED_REFERENCES": null, "REFERENCES": 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data/files/A0044/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A0044",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2WUS",
|
| 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",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
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| 25 |
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"PDBIDS": [
|
| 26 |
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"2WUS"
|
| 27 |
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],
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| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q9WZ57",
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| 31 |
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"Q9X2H8"
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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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| 35 |
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| 36 |
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"PROTSEQ": [
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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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| 42 |
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| 43 |
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"TIMESTEP": 2,
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| 44 |
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"TEMP": 310,
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| 45 |
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"ENSEMBLE": "NPT",
|
| 46 |
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"FF": [
|
| 47 |
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"CHARMM36m"
|
| 48 |
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],
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| 49 |
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"WAT": "TIP3P",
|
| 50 |
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"BOXTYPE": "Dodecahedron",
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| 51 |
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"SYSTATS": 6613,
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| 52 |
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"SYSTRES": 422,
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| 53 |
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| 54 |
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| 55 |
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| 56 |
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| 57 |
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| 58 |
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| 59 |
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| 60 |
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| 61 |
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| 64 |
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"COUNANI": 0,
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| 65 |
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"COUNION": 0,
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| 66 |
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"INTERACTIONS": [
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| 67 |
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{
|
| 68 |
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"name": "chain A-chain B interaction",
|
| 69 |
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"agent_1": "chain A",
|
| 70 |
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"agent_2": "chain B",
|
| 71 |
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"selection_1": "chain A",
|
| 72 |
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"selection_2": "chain B",
|
| 73 |
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"type": "protein-protein"
|
| 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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| 83 |
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"COLLECTIONS": "dynarepo",
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| 84 |
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"WARNINGS": [],
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| 85 |
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"BOXSIZEX": 10.6396,
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| 86 |
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| 87 |
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| 89 |
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| 91 |
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},
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| 92 |
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"mds": [
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| 93 |
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"replica 1",
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| 94 |
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| 95 |
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| 96 |
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| 97 |
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"clusters_01_screenshot_19.jpg",
|
| 158 |
+
"pocket_01.pdb",
|
| 159 |
+
"pocket_02.pdb",
|
| 160 |
+
"pocket_03.pdb",
|
| 161 |
+
"pocket_04.pdb",
|
| 162 |
+
"pocket_05.pdb",
|
| 163 |
+
"pocket_06.pdb",
|
| 164 |
+
"pocket_07.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": 1,
|
| 187 |
+
"internalId": "6840a7b743f7debe157a59d1",
|
| 188 |
+
"creationDate": "2025-06-04T20:08:23.000Z",
|
| 189 |
+
"identifier": "A0044"
|
| 190 |
+
}
|