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- A000B/project.json +377 -0
- A000B/records.jsonl +0 -0
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- A00AN/project.json +253 -0
- A00AN/records.jsonl +3 -0
- A00CN/project.json +186 -0
A000B/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000B",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1AKJ",
|
| 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 |
+
"1AKJ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P04439",
|
| 31 |
+
"P61769",
|
| 32 |
+
"P01732"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"SQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLPA",
|
| 39 |
+
"QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM",
|
| 40 |
+
"ILKEPVHGV",
|
| 41 |
+
"GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP"
|
| 42 |
+
],
|
| 43 |
+
"NUCLSEQ": [],
|
| 44 |
+
"DOMAINS": [
|
| 45 |
+
"HLA class I histocompatibility antigen, A alpha chain",
|
| 46 |
+
"Ig-like C1-type",
|
| 47 |
+
"Alpha-1",
|
| 48 |
+
"Alpha-2",
|
| 49 |
+
"Alpha-3",
|
| 50 |
+
"Connecting peptide",
|
| 51 |
+
"Beta-2-microglobulin",
|
| 52 |
+
"Beta-2-microglobulin form pI 5.3",
|
| 53 |
+
"Ig-like C1-type",
|
| 54 |
+
"T-cell surface glycoprotein CD8 alpha chain",
|
| 55 |
+
"Ig-like V-type"
|
| 56 |
+
],
|
| 57 |
+
"FRAMESTEP": 0.1,
|
| 58 |
+
"TIMESTEP": 2,
|
| 59 |
+
"TEMP": 310,
|
| 60 |
+
"ENSEMBLE": "NPT",
|
| 61 |
+
"FF": [
|
| 62 |
+
"CHARMM36m"
|
| 63 |
+
],
|
| 64 |
+
"WAT": "TIP3P",
|
| 65 |
+
"BOXTYPE": "Dodecahedron",
|
| 66 |
+
"SYSTATS": 9693,
|
| 67 |
+
"SYSTRES": 611,
|
| 68 |
+
"PROTATS": 9693,
|
| 69 |
+
"PROTRES": 611,
|
| 70 |
+
"NUCLATS": 0,
|
| 71 |
+
"NUCLRES": 0,
|
| 72 |
+
"LIPIATS": 0,
|
| 73 |
+
"LIPIRES": 0,
|
| 74 |
+
"CARBATS": 0,
|
| 75 |
+
"CARBRES": 0,
|
| 76 |
+
"SOLVATS": 0,
|
| 77 |
+
"SOLVRES": 0,
|
| 78 |
+
"COUNCAT": 0,
|
| 79 |
+
"COUNANI": 0,
|
| 80 |
+
"COUNION": 0,
|
| 81 |
+
"INTERACTIONS": [
|
| 82 |
+
{
|
| 83 |
+
"name": "protein-protein interaction E-A",
|
| 84 |
+
"agent_1": "protein E",
|
| 85 |
+
"agent_2": "protein A",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain B",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "protein-protein interaction E-D",
|
| 92 |
+
"agent_1": "protein E",
|
| 93 |
+
"agent_2": "protein D",
|
| 94 |
+
"selection_1": "chain A",
|
| 95 |
+
"selection_2": "chain C",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
},
|
| 98 |
+
{
|
| 99 |
+
"name": "protein-protein interaction E-B",
|
| 100 |
+
"agent_1": "protein E",
|
| 101 |
+
"agent_2": "protein B",
|
| 102 |
+
"selection_1": "chain A",
|
| 103 |
+
"selection_2": "chain D",
|
| 104 |
+
"type": "protein-protein"
|
| 105 |
+
},
|
| 106 |
+
{
|
| 107 |
+
"name": "protein-protein interaction A-C",
|
| 108 |
+
"agent_1": "protein A",
|
| 109 |
+
"agent_2": "protein C",
|
| 110 |
+
"selection_1": "chain A",
|
| 111 |
+
"selection_2": "chain E",
|
| 112 |
+
"type": "protein-protein"
|
| 113 |
+
},
|
| 114 |
+
{
|
| 115 |
+
"name": "protein-protein interaction A-D",
|
| 116 |
+
"agent_1": "protein A",
|
| 117 |
+
"agent_2": "protein D",
|
| 118 |
+
"selection_1": "chain B",
|
| 119 |
+
"selection_2": "chain C",
|
| 120 |
+
"type": "protein-protein"
|
| 121 |
+
},
|
| 122 |
+
{
|
| 123 |
+
"name": "protein-protein interaction A-B",
|
| 124 |
+
"agent_1": "protein A",
|
| 125 |
+
"agent_2": "protein B",
|
| 126 |
+
"selection_1": "chain B",
|
| 127 |
+
"selection_2": "chain D",
|
| 128 |
+
"type": "protein-protein"
|
| 129 |
+
},
|
| 130 |
+
{
|
| 131 |
+
"name": "protein-protein interaction D-B",
|
| 132 |
+
"agent_1": "protein D",
|
| 133 |
+
"agent_2": "protein B",
|
| 134 |
+
"selection_1": "chain B",
|
| 135 |
+
"selection_2": "chain E",
|
| 136 |
+
"type": "protein-protein"
|
| 137 |
+
}
|
| 138 |
+
],
|
| 139 |
+
"PBC_SELECTION": null,
|
| 140 |
+
"CHAINNAMES": null,
|
| 141 |
+
"MEMBRANES": null,
|
| 142 |
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"CUSTOMS": null,
|
| 143 |
+
"ORIENTATION": null,
|
| 144 |
+
"PTM": [],
|
| 145 |
+
"MULTIMERIC": null,
|
| 146 |
+
"COLLECTIONS": "dynarepo",
|
| 147 |
+
"WARNINGS": [],
|
| 148 |
+
"BOXSIZEX": 10.6025,
|
| 149 |
+
"BOXSIZEY": 10.6025,
|
| 150 |
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"BOXSIZEZ": 7.52662,
|
| 151 |
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"mdName": "replica 1",
|
| 152 |
+
"mdAtoms": 9693,
|
| 153 |
+
"mdFrames": 5001
|
| 154 |
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},
|
| 155 |
+
"mds": [
|
| 156 |
+
"replica 1",
|
| 157 |
+
"replica 2",
|
| 158 |
+
"replica 3"
|
| 159 |
+
],
|
| 160 |
+
"mdref": 0,
|
| 161 |
+
"files": [
|
| 162 |
+
"topology.tpr",
|
| 163 |
+
"screenshot.jpg",
|
| 164 |
+
"trajectory.bin",
|
| 165 |
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"pca_trajectory_01.bin",
|
| 166 |
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"pca_trajectory_02.bin",
|
| 167 |
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"pca_trajectory_03.bin",
|
| 168 |
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"pca_trajectory_04.bin",
|
| 169 |
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"pca_trajectory_05.bin",
|
| 170 |
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"pca_trajectory_06.bin",
|
| 171 |
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"pca_trajectory_07.bin",
|
| 172 |
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"pca_trajectory_08.bin",
|
| 173 |
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"pca_trajectory_09.bin",
|
| 174 |
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"pca_trajectory_10.bin",
|
| 175 |
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"pca_trajectory_11.bin",
|
| 176 |
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"structure.pdb",
|
| 177 |
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"trajectory.xtc",
|
| 178 |
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"clusters_00_screenshot_00.jpg",
|
| 179 |
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"clusters_00_screenshot_01.jpg",
|
| 180 |
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"clusters_00_screenshot_02.jpg",
|
| 181 |
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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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"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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"clusters_00_screenshot_19.jpg",
|
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|
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|
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"clusters_01_screenshot_00.jpg",
|
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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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| 312 |
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| 314 |
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| 315 |
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|
| 316 |
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|
| 317 |
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|
| 318 |
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|
| 319 |
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|
| 320 |
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| 322 |
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|
| 323 |
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|
| 324 |
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|
| 325 |
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|
| 326 |
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|
| 327 |
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|
| 328 |
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|
| 329 |
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|
| 330 |
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|
| 331 |
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|
| 332 |
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|
| 333 |
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|
| 334 |
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"clusters_07_screenshot_18.jpg",
|
| 335 |
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"clusters_07_screenshot_19.jpg",
|
| 336 |
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"pocket_01.pdb",
|
| 337 |
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"pocket_02.pdb",
|
| 338 |
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"pocket_03.pdb",
|
| 339 |
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"pocket_04.pdb",
|
| 340 |
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"pocket_05.pdb",
|
| 341 |
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"pocket_06.pdb",
|
| 342 |
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"pocket_07.pdb",
|
| 343 |
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"pocket_08.pdb",
|
| 344 |
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"pocket_09.pdb",
|
| 345 |
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"pocket_10.pdb"
|
| 346 |
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],
|
| 347 |
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"analyses": [
|
| 348 |
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"clusters",
|
| 349 |
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"clusters-00",
|
| 350 |
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"clusters-01",
|
| 351 |
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"clusters-02",
|
| 352 |
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"clusters-03",
|
| 353 |
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"clusters-04",
|
| 354 |
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"clusters-05",
|
| 355 |
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"clusters-06",
|
| 356 |
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"clusters-07",
|
| 357 |
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"dist-perres",
|
| 358 |
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"energies",
|
| 359 |
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"fluctuation",
|
| 360 |
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"hbonds",
|
| 361 |
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"interactions",
|
| 362 |
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"pca",
|
| 363 |
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"pockets",
|
| 364 |
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"rgyr",
|
| 365 |
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"rmsd-pairwise",
|
| 366 |
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"rmsd-perres",
|
| 367 |
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"rmsds",
|
| 368 |
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"sasa",
|
| 369 |
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"tmscores"
|
| 370 |
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],
|
| 371 |
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"mdIndex": 0,
|
| 372 |
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"mdNumber": 1,
|
| 373 |
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"refframe": 0,
|
| 374 |
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"internalId": "683efd5e2fd085d144cd6bc7",
|
| 375 |
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"creationDate": "2025-06-03T13:49:18.000Z",
|
| 376 |
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"identifier": "A000B"
|
| 377 |
+
}
|
A000B/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A0012/project.json
ADDED
|
@@ -0,0 +1,263 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0012",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1ICF",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"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 |
+
"1ICF"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P07711",
|
| 31 |
+
"P04233"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
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|
| 36 |
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|
| 37 |
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"APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFEST",
|
| 38 |
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"LTKCQEEVSHIPAVHPGSFRPKCDENGNYLPLQCYGSIGYCWCVFPNGTEVPNTRSRGHHNCSES",
|
| 39 |
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"NNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV"
|
| 40 |
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],
|
| 41 |
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"NUCLSEQ": [],
|
| 42 |
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"DOMAINS": [
|
| 43 |
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"Cathepsin L",
|
| 44 |
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"Cathepsin L heavy chain",
|
| 45 |
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"Cathepsin L light chain",
|
| 46 |
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"Cleavage; by autolysis",
|
| 47 |
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"HLA class II histocompatibility antigen gamma chain",
|
| 48 |
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"Thyroglobulin type-1",
|
| 49 |
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"Disordered",
|
| 50 |
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"Required for interaction with CTSL"
|
| 51 |
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|
| 52 |
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|
| 53 |
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|
| 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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|
| 60 |
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|
| 61 |
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|
| 62 |
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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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|
| 75 |
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|
| 76 |
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|
| 77 |
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{
|
| 78 |
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"name": "protein-protein interaction A-B",
|
| 79 |
+
"agent_1": "protein A",
|
| 80 |
+
"agent_2": "protein B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
},
|
| 85 |
+
{
|
| 86 |
+
"name": "protein-protein interaction A-C",
|
| 87 |
+
"agent_1": "protein A",
|
| 88 |
+
"agent_2": "protein C",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain C",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "protein-protein interaction B-C",
|
| 95 |
+
"agent_1": "protein B",
|
| 96 |
+
"agent_2": "protein C",
|
| 97 |
+
"selection_1": "chain B",
|
| 98 |
+
"selection_2": "chain C",
|
| 99 |
+
"type": "protein-protein"
|
| 100 |
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}
|
| 101 |
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],
|
| 102 |
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"PBC_SELECTION": null,
|
| 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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"COLLECTIONS": "dynarepo",
|
| 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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"mds": [
|
| 119 |
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"replica 1",
|
| 120 |
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"replica 2",
|
| 121 |
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"replica 3"
|
| 122 |
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],
|
| 123 |
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"mdref": 0,
|
| 124 |
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|
| 125 |
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|
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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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|
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|
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|
| 138 |
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|
| 139 |
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|
| 140 |
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"pca_trajectory_13.bin",
|
| 141 |
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"structure.pdb",
|
| 142 |
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|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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|
| 163 |
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"clusters_01_screenshot_00.jpg",
|
| 164 |
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"clusters_01_screenshot_01.jpg",
|
| 165 |
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|
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"clusters_01_screenshot_03.jpg",
|
| 167 |
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"clusters_01_screenshot_04.jpg",
|
| 168 |
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|
| 169 |
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|
| 170 |
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|
| 171 |
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|
| 172 |
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|
| 173 |
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"clusters_01_screenshot_10.jpg",
|
| 174 |
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|
| 175 |
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|
| 176 |
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"clusters_01_screenshot_13.jpg",
|
| 177 |
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"clusters_01_screenshot_14.jpg",
|
| 178 |
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"clusters_01_screenshot_15.jpg",
|
| 179 |
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|
| 180 |
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"clusters_01_screenshot_17.jpg",
|
| 181 |
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"clusters_01_screenshot_18.jpg",
|
| 182 |
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|
| 183 |
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"clusters_01_screenshot_20.jpg",
|
| 184 |
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"clusters_01_screenshot_21.jpg",
|
| 185 |
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"clusters_01_screenshot_22.jpg",
|
| 186 |
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"clusters_02_screenshot_00.jpg",
|
| 187 |
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"clusters_02_screenshot_01.jpg",
|
| 188 |
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|
| 189 |
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|
| 190 |
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|
| 191 |
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"clusters_02_screenshot_05.jpg",
|
| 192 |
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|
| 193 |
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|
| 194 |
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|
| 195 |
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|
| 196 |
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|
| 197 |
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|
| 198 |
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|
| 199 |
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|
| 200 |
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|
| 201 |
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|
| 202 |
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"clusters_02_screenshot_16.jpg",
|
| 203 |
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|
| 204 |
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"clusters_02_screenshot_18.jpg",
|
| 205 |
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"clusters_02_screenshot_19.jpg",
|
| 206 |
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"clusters_03_screenshot_00.jpg",
|
| 207 |
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"clusters_03_screenshot_01.jpg",
|
| 208 |
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"clusters_03_screenshot_02.jpg",
|
| 209 |
+
"clusters_03_screenshot_03.jpg",
|
| 210 |
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"clusters_03_screenshot_04.jpg",
|
| 211 |
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"clusters_03_screenshot_05.jpg",
|
| 212 |
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"clusters_03_screenshot_06.jpg",
|
| 213 |
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"clusters_03_screenshot_07.jpg",
|
| 214 |
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"clusters_03_screenshot_08.jpg",
|
| 215 |
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"clusters_03_screenshot_09.jpg",
|
| 216 |
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"clusters_03_screenshot_10.jpg",
|
| 217 |
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"clusters_03_screenshot_11.jpg",
|
| 218 |
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"clusters_03_screenshot_12.jpg",
|
| 219 |
+
"clusters_03_screenshot_13.jpg",
|
| 220 |
+
"clusters_03_screenshot_14.jpg",
|
| 221 |
+
"clusters_03_screenshot_15.jpg",
|
| 222 |
+
"clusters_03_screenshot_16.jpg",
|
| 223 |
+
"clusters_03_screenshot_17.jpg",
|
| 224 |
+
"clusters_03_screenshot_18.jpg",
|
| 225 |
+
"clusters_03_screenshot_19.jpg",
|
| 226 |
+
"clusters_03_screenshot_20.jpg",
|
| 227 |
+
"pocket_01.pdb",
|
| 228 |
+
"pocket_02.pdb",
|
| 229 |
+
"pocket_03.pdb",
|
| 230 |
+
"pocket_04.pdb",
|
| 231 |
+
"pocket_05.pdb",
|
| 232 |
+
"pocket_06.pdb",
|
| 233 |
+
"pocket_07.pdb",
|
| 234 |
+
"pocket_08.pdb",
|
| 235 |
+
"pocket_09.pdb"
|
| 236 |
+
],
|
| 237 |
+
"analyses": [
|
| 238 |
+
"clusters",
|
| 239 |
+
"clusters-00",
|
| 240 |
+
"clusters-01",
|
| 241 |
+
"clusters-02",
|
| 242 |
+
"clusters-03",
|
| 243 |
+
"dist-perres",
|
| 244 |
+
"energies",
|
| 245 |
+
"fluctuation",
|
| 246 |
+
"hbonds",
|
| 247 |
+
"interactions",
|
| 248 |
+
"pca",
|
| 249 |
+
"pockets",
|
| 250 |
+
"rgyr",
|
| 251 |
+
"rmsd-pairwise",
|
| 252 |
+
"rmsd-perres",
|
| 253 |
+
"rmsds",
|
| 254 |
+
"sasa",
|
| 255 |
+
"tmscores"
|
| 256 |
+
],
|
| 257 |
+
"mdIndex": 0,
|
| 258 |
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"mdNumber": 1,
|
| 259 |
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"refframe": 0,
|
| 260 |
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"internalId": "683f383a614edc1219cdccf7",
|
| 261 |
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"creationDate": "2025-06-03T18:00:26.000Z",
|
| 262 |
+
"identifier": "A0012"
|
| 263 |
+
}
|
A0012/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0012", "accession": "A0012", "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 1ICF", "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": ["1ICF"], "FORCED_REFERENCES": null, "REFERENCES": 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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1LX5",
|
| 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 |
+
"1LX5"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P18075",
|
| 31 |
+
"P27038"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPE",
|
| 38 |
+
"QACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Bone morphogenetic protein 7",
|
| 43 |
+
"Activin receptor type-2A"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
"SYSTATS": 3094,
|
| 55 |
+
"SYSTRES": 198,
|
| 56 |
+
"PROTATS": 3094,
|
| 57 |
+
"PROTRES": 198,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
+
"SOLVRES": 0,
|
| 66 |
+
"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
+
"MEMBRANES": null,
|
| 82 |
+
"CUSTOMS": null,
|
| 83 |
+
"ORIENTATION": null,
|
| 84 |
+
"PTM": [],
|
| 85 |
+
"MULTIMERIC": null,
|
| 86 |
+
"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
+
"BOXSIZEX": 9.97602,
|
| 89 |
+
"BOXSIZEY": 9.97602,
|
| 90 |
+
"BOXSIZEZ": 7.07223,
|
| 91 |
+
"mdName": "replica 1",
|
| 92 |
+
"mdAtoms": 3094,
|
| 93 |
+
"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
+
"mdref": 0,
|
| 101 |
+
"files": [
|
| 102 |
+
"topology.tpr",
|
| 103 |
+
"screenshot.jpg",
|
| 104 |
+
"trajectory.bin",
|
| 105 |
+
"pca_trajectory_01.bin",
|
| 106 |
+
"pca_trajectory_02.bin",
|
| 107 |
+
"pca_trajectory_03.bin",
|
| 108 |
+
"pca_trajectory_04.bin",
|
| 109 |
+
"pca_trajectory_05.bin",
|
| 110 |
+
"pca_trajectory_06.bin",
|
| 111 |
+
"pca_trajectory_07.bin",
|
| 112 |
+
"pca_trajectory_08.bin",
|
| 113 |
+
"pca_trajectory_09.bin",
|
| 114 |
+
"pca_trajectory_10.bin",
|
| 115 |
+
"structure.pdb",
|
| 116 |
+
"trajectory.xtc",
|
| 117 |
+
"clusters_00_screenshot_00.jpg",
|
| 118 |
+
"clusters_00_screenshot_01.jpg",
|
| 119 |
+
"clusters_00_screenshot_02.jpg",
|
| 120 |
+
"clusters_00_screenshot_03.jpg",
|
| 121 |
+
"clusters_00_screenshot_04.jpg",
|
| 122 |
+
"clusters_00_screenshot_05.jpg",
|
| 123 |
+
"clusters_00_screenshot_06.jpg",
|
| 124 |
+
"clusters_00_screenshot_07.jpg",
|
| 125 |
+
"clusters_00_screenshot_08.jpg",
|
| 126 |
+
"clusters_00_screenshot_09.jpg",
|
| 127 |
+
"clusters_00_screenshot_10.jpg",
|
| 128 |
+
"clusters_00_screenshot_11.jpg",
|
| 129 |
+
"clusters_00_screenshot_12.jpg",
|
| 130 |
+
"clusters_00_screenshot_13.jpg",
|
| 131 |
+
"clusters_00_screenshot_14.jpg",
|
| 132 |
+
"clusters_00_screenshot_15.jpg",
|
| 133 |
+
"clusters_00_screenshot_16.jpg",
|
| 134 |
+
"clusters_00_screenshot_17.jpg",
|
| 135 |
+
"clusters_00_screenshot_18.jpg",
|
| 136 |
+
"clusters_00_screenshot_19.jpg",
|
| 137 |
+
"clusters_00_screenshot_20.jpg",
|
| 138 |
+
"clusters_01_screenshot_00.jpg",
|
| 139 |
+
"clusters_01_screenshot_01.jpg",
|
| 140 |
+
"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 |
+
"clusters_01_screenshot_09.jpg",
|
| 148 |
+
"clusters_01_screenshot_10.jpg",
|
| 149 |
+
"clusters_01_screenshot_11.jpg",
|
| 150 |
+
"clusters_01_screenshot_12.jpg",
|
| 151 |
+
"clusters_01_screenshot_13.jpg",
|
| 152 |
+
"clusters_01_screenshot_14.jpg",
|
| 153 |
+
"clusters_01_screenshot_15.jpg",
|
| 154 |
+
"clusters_01_screenshot_16.jpg",
|
| 155 |
+
"clusters_01_screenshot_17.jpg",
|
| 156 |
+
"clusters_01_screenshot_18.jpg",
|
| 157 |
+
"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 |
+
],
|
| 165 |
+
"analyses": [
|
| 166 |
+
"clusters",
|
| 167 |
+
"clusters-00",
|
| 168 |
+
"clusters-01",
|
| 169 |
+
"dist-perres",
|
| 170 |
+
"energies",
|
| 171 |
+
"fluctuation",
|
| 172 |
+
"hbonds",
|
| 173 |
+
"interactions",
|
| 174 |
+
"pca",
|
| 175 |
+
"pockets",
|
| 176 |
+
"rgyr",
|
| 177 |
+
"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
+
"rmsds",
|
| 180 |
+
"sasa",
|
| 181 |
+
"tmscores"
|
| 182 |
+
],
|
| 183 |
+
"mdIndex": 0,
|
| 184 |
+
"mdNumber": 1,
|
| 185 |
+
"refframe": 0,
|
| 186 |
+
"internalId": "683f4f8aec8949a2ae628ec9",
|
| 187 |
+
"creationDate": "2025-06-03T19:39:54.000Z",
|
| 188 |
+
"identifier": "A001F"
|
| 189 |
+
}
|
A001F/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A001F", "accession": "A001F", "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 1LX5", "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": ["1LX5"], "FORCED_REFERENCES": null, "REFERENCES": ["P18075", "P27038"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPE", "QACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH"], "NUCLSEQ": [], "DOMAINS": ["Bone morphogenetic protein 7", "Activin receptor type-2A"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3094, "SYSTRES": 198, "PROTATS": 3094, "PROTRES": 198, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.97602, "BOXSIZEY": 9.97602, "BOXSIZEZ": 7.07223, "mdName": "replica 1", "mdAtoms": 3094, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001F/files/topology.tpr", "length": 1191700, "contentType": "application/octet-stream", "metadata": {"project": "683f4f8aec8949a2ae628ec9", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001F/files/screenshot.jpg", "length": 17879, "contentType": "application/octet-stream", "metadata": {"project": "683f4f8aec8949a2ae628ec9", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001F/files/trajectory.bin", "length": 185677128, "contentType": "application/octet-stream", "metadata": {"project": "683f4f8aec8949a2ae628ec9", "md": 0, "frames": 5001, "atoms": 3094}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001F/files/pca_trajectory_01.bin", "length": 142560, "contentType": 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|
A001Y/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001Y",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1T63",
|
| 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 |
+
"1T63"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P10275",
|
| 31 |
+
"Q15596"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"CQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGKVKPIYFHT",
|
| 38 |
+
"KENALLRYLLDKDD"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Androgen receptor",
|
| 43 |
+
"NR LBD",
|
| 44 |
+
"Interaction with LPXN",
|
| 45 |
+
"Interaction with CCAR1",
|
| 46 |
+
"Interaction with KAT7",
|
| 47 |
+
"Interaction with coactivator LXXL and FXXFY motifs",
|
| 48 |
+
"Interaction with coactivator FXXLF and FXXFY motifs",
|
| 49 |
+
"Nuclear receptor coactivator 2",
|
| 50 |
+
"CASP8AP2-binding",
|
| 51 |
+
"Interaction with BMAL1",
|
| 52 |
+
"LXXLL motif 3"
|
| 53 |
+
],
|
| 54 |
+
"FRAMESTEP": 0.1,
|
| 55 |
+
"TIMESTEP": 2,
|
| 56 |
+
"TEMP": 310,
|
| 57 |
+
"ENSEMBLE": "NPT",
|
| 58 |
+
"FF": [
|
| 59 |
+
"CHARMM36m"
|
| 60 |
+
],
|
| 61 |
+
"WAT": "TIP3P",
|
| 62 |
+
"BOXTYPE": "Dodecahedron",
|
| 63 |
+
"SYSTATS": 4353,
|
| 64 |
+
"SYSTRES": 264,
|
| 65 |
+
"PROTATS": 4353,
|
| 66 |
+
"PROTRES": 264,
|
| 67 |
+
"NUCLATS": 0,
|
| 68 |
+
"NUCLRES": 0,
|
| 69 |
+
"LIPIATS": 0,
|
| 70 |
+
"LIPIRES": 0,
|
| 71 |
+
"CARBATS": 0,
|
| 72 |
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"CARBRES": 0,
|
| 73 |
+
"SOLVATS": 0,
|
| 74 |
+
"SOLVRES": 0,
|
| 75 |
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"COUNCAT": 0,
|
| 76 |
+
"COUNANI": 0,
|
| 77 |
+
"COUNION": 0,
|
| 78 |
+
"INTERACTIONS": [
|
| 79 |
+
{
|
| 80 |
+
"name": "chain A-chain B interaction",
|
| 81 |
+
"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain B",
|
| 83 |
+
"selection_1": "chain A",
|
| 84 |
+
"selection_2": "chain B",
|
| 85 |
+
"type": "protein-protein"
|
| 86 |
+
}
|
| 87 |
+
],
|
| 88 |
+
"PBC_SELECTION": null,
|
| 89 |
+
"CHAINNAMES": null,
|
| 90 |
+
"MEMBRANES": null,
|
| 91 |
+
"CUSTOMS": null,
|
| 92 |
+
"ORIENTATION": null,
|
| 93 |
+
"PTM": [],
|
| 94 |
+
"MULTIMERIC": null,
|
| 95 |
+
"COLLECTIONS": "dynarepo",
|
| 96 |
+
"WARNINGS": [],
|
| 97 |
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"BOXSIZEX": 9.2576,
|
| 98 |
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"BOXSIZEY": 9.2576,
|
| 99 |
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"BOXSIZEZ": 6.55557,
|
| 100 |
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"mdName": "replica 1",
|
| 101 |
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"mdAtoms": 4353,
|
| 102 |
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"mdFrames": 5001
|
| 103 |
+
},
|
| 104 |
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"mds": [
|
| 105 |
+
"replica 1",
|
| 106 |
+
"replica 2",
|
| 107 |
+
"replica 3"
|
| 108 |
+
],
|
| 109 |
+
"mdref": 0,
|
| 110 |
+
"files": [
|
| 111 |
+
"topology.tpr",
|
| 112 |
+
"screenshot.jpg",
|
| 113 |
+
"trajectory.bin",
|
| 114 |
+
"pca_trajectory_01.bin",
|
| 115 |
+
"pca_trajectory_02.bin",
|
| 116 |
+
"pca_trajectory_03.bin",
|
| 117 |
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"pca_trajectory_04.bin",
|
| 118 |
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"pca_trajectory_05.bin",
|
| 119 |
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"pca_trajectory_06.bin",
|
| 120 |
+
"pca_trajectory_07.bin",
|
| 121 |
+
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"clusters_01_screenshot_16.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": [
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"clusters",
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"clusters-00",
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"clusters-01",
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| 185 |
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f6d15b204f2a7930d4272",
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"creationDate": "2025-06-03T21:45:57.000Z",
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"identifier": "A001Y"
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}
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A001Y/records.jsonl
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|
A0022/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0022",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1U0S",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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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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"1U0S"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q56312",
|
| 31 |
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"Q56310"
|
| 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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"GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS",
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| 38 |
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|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Chemotaxis protein CheY",
|
| 43 |
+
"Response regulatory",
|
| 44 |
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"Chemotaxis protein CheA"
|
| 45 |
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],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 3294,
|
| 56 |
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"SYSTRES": 204,
|
| 57 |
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"PROTATS": 3294,
|
| 58 |
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"PROTRES": 204,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 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 |
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"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
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"PBC_SELECTION": null,
|
| 81 |
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"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 8.14965,
|
| 90 |
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"BOXSIZEY": 8.14965,
|
| 91 |
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"BOXSIZEZ": 5.76276,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 3294,
|
| 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 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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"pca_trajectory_01.bin",
|
| 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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"structure.pdb",
|
| 119 |
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"trajectory.xtc",
|
| 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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"clusters_00_screenshot_15.jpg",
|
| 136 |
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"clusters_00_screenshot_16.jpg",
|
| 137 |
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"clusters_00_screenshot_17.jpg",
|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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|
| 143 |
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| 144 |
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|
| 145 |
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| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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"pocket_01.pdb",
|
| 163 |
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"pocket_02.pdb",
|
| 164 |
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"pocket_03.pdb",
|
| 165 |
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"pocket_04.pdb",
|
| 166 |
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"pocket_05.pdb",
|
| 167 |
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"pocket_06.pdb",
|
| 168 |
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"pocket_07.pdb"
|
| 169 |
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],
|
| 170 |
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"analyses": [
|
| 171 |
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"clusters",
|
| 172 |
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"clusters-00",
|
| 173 |
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|
| 174 |
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|
| 175 |
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|
| 176 |
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|
| 177 |
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|
| 178 |
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|
| 179 |
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|
| 180 |
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"pockets",
|
| 181 |
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"rgyr",
|
| 182 |
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"rmsd-pairwise",
|
| 183 |
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|
| 184 |
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|
| 185 |
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|
| 186 |
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|
| 187 |
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],
|
| 188 |
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"mdIndex": 0,
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"mdNumber": 1,
|
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}
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|
A002Q/project.json
ADDED
|
@@ -0,0 +1,190 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A002Q",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2BYK",
|
| 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 |
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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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"2BYK"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"Q9V452",
|
| 31 |
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"Q9V444"
|
| 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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"MKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKI",
|
| 38 |
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"PNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEK"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
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"Chromatin accessibility complex 16kD protein",
|
| 43 |
+
"DNA polymerase epsilon subunit 3",
|
| 44 |
+
"Disordered"
|
| 45 |
+
],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 2568,
|
| 56 |
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"SYSTRES": 161,
|
| 57 |
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"PROTATS": 2568,
|
| 58 |
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"PROTRES": 161,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 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 |
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}
|
| 79 |
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],
|
| 80 |
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"PBC_SELECTION": null,
|
| 81 |
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"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 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 8.95696,
|
| 90 |
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"BOXSIZEY": 8.95696,
|
| 91 |
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"BOXSIZEZ": 6.37334,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 2568,
|
| 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 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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"pca_trajectory_01.bin",
|
| 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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"structure.pdb",
|
| 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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"clusters_00_screenshot_10.jpg",
|
| 131 |
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|
| 132 |
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|
| 133 |
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"clusters_00_screenshot_13.jpg",
|
| 134 |
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"clusters_00_screenshot_14.jpg",
|
| 135 |
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"clusters_00_screenshot_15.jpg",
|
| 136 |
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"clusters_00_screenshot_16.jpg",
|
| 137 |
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"clusters_00_screenshot_17.jpg",
|
| 138 |
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"clusters_00_screenshot_18.jpg",
|
| 139 |
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"clusters_00_screenshot_19.jpg",
|
| 140 |
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"clusters_00_screenshot_20.jpg",
|
| 141 |
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|
| 142 |
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"clusters_00_screenshot_22.jpg",
|
| 143 |
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"clusters_00_screenshot_23.jpg",
|
| 144 |
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"clusters_01_screenshot_00.jpg",
|
| 145 |
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"clusters_01_screenshot_01.jpg",
|
| 146 |
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"clusters_01_screenshot_02.jpg",
|
| 147 |
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|
| 148 |
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"clusters_01_screenshot_04.jpg",
|
| 149 |
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"clusters_01_screenshot_05.jpg",
|
| 150 |
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"clusters_01_screenshot_06.jpg",
|
| 151 |
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"clusters_01_screenshot_07.jpg",
|
| 152 |
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"clusters_01_screenshot_08.jpg",
|
| 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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"clusters_01_screenshot_13.jpg",
|
| 158 |
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"clusters_01_screenshot_14.jpg",
|
| 159 |
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"clusters_01_screenshot_15.jpg",
|
| 160 |
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"clusters_01_screenshot_16.jpg",
|
| 161 |
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|
| 162 |
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"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"clusters_01_screenshot_19.jpg",
|
| 164 |
+
"pocket_01.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 |
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"rgyr",
|
| 178 |
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"rmsd-pairwise",
|
| 179 |
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"rmsd-perres",
|
| 180 |
+
"rmsds",
|
| 181 |
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"sasa",
|
| 182 |
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"tmscores"
|
| 183 |
+
],
|
| 184 |
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"mdIndex": 0,
|
| 185 |
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"mdNumber": 1,
|
| 186 |
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"refframe": 0,
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| 187 |
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"internalId": "684025f0317ca4e20d47d73f",
|
| 188 |
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"creationDate": "2025-06-04T10:54:40.000Z",
|
| 189 |
+
"identifier": "A002Q"
|
| 190 |
+
}
|
A002Q/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
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|
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| 1 |
+
{
|
| 2 |
+
"accession": "A003F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2NYZ",
|
| 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 |
+
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|
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|
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|
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|
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|
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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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|
| 290 |
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|
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|
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|
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|
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|
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|
| 296 |
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|
| 297 |
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|
| 298 |
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|
| 299 |
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"rmsd-pairwise",
|
| 300 |
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"rmsd-perres",
|
| 301 |
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"rmsds",
|
| 302 |
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"sasa",
|
| 303 |
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|
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"creationDate": "2025-06-04T15:28:41.000Z",
|
| 310 |
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"identifier": "A003F"
|
| 311 |
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}
|
A003F/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A003X/project.json
ADDED
|
@@ -0,0 +1,194 @@
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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 |
+
}
|
A003X/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
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|
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| 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"], 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|
A0044/project.json
ADDED
|
@@ -0,0 +1,190 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0044",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2WUS",
|
| 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 |
+
"2WUS"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9WZ57",
|
| 31 |
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"Q9X2H8"
|
| 32 |
+
],
|
| 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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"LRKDIGIDLGTANTLVFLRGKGIVVNEPSVIAIDSTTGEILKVGLEAKNMIGKTPATIKAIRPMRDGVIADYTVALVMLRYFINKAKGGMNLFKPRVVIGVPIGITDVERRAILDAGLEAGASKVFLIEEPMAAAIGSNLNVEEPSGNMVVDIGGGTTEVAVISLGSIVTWESIRIAGDEMDEAIVQYVRETYRVAIGERTAERVKIEIGNVFPSKENDELETTVSGIDLSTGLPRKLTLKGGEVREALRSVVVAIVESVRTTLEKTPPELVSDIIERGIFLTGGGSLLRGLDTLLQKETGISVIRSEEPLTAVAKGAGMVLDKVNILKKLQGAG",
|
| 38 |
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"SEKWKELGETFRKKREERRITLLDASLFTNINPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFLELSPDEMLKLYEEGKEEVAEEVE"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [],
|
| 42 |
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"FRAMESTEP": 0.1,
|
| 43 |
+
"TIMESTEP": 2,
|
| 44 |
+
"TEMP": 310,
|
| 45 |
+
"ENSEMBLE": "NPT",
|
| 46 |
+
"FF": [
|
| 47 |
+
"CHARMM36m"
|
| 48 |
+
],
|
| 49 |
+
"WAT": "TIP3P",
|
| 50 |
+
"BOXTYPE": "Dodecahedron",
|
| 51 |
+
"SYSTATS": 6613,
|
| 52 |
+
"SYSTRES": 422,
|
| 53 |
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"PROTATS": 6613,
|
| 54 |
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"PROTRES": 422,
|
| 55 |
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"NUCLATS": 0,
|
| 56 |
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"NUCLRES": 0,
|
| 57 |
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"LIPIATS": 0,
|
| 58 |
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"LIPIRES": 0,
|
| 59 |
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"CARBATS": 0,
|
| 60 |
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"CARBRES": 0,
|
| 61 |
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"SOLVATS": 0,
|
| 62 |
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"SOLVRES": 0,
|
| 63 |
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"COUNCAT": 0,
|
| 64 |
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"COUNANI": 0,
|
| 65 |
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"COUNION": 0,
|
| 66 |
+
"INTERACTIONS": [
|
| 67 |
+
{
|
| 68 |
+
"name": "chain A-chain B interaction",
|
| 69 |
+
"agent_1": "chain A",
|
| 70 |
+
"agent_2": "chain B",
|
| 71 |
+
"selection_1": "chain A",
|
| 72 |
+
"selection_2": "chain B",
|
| 73 |
+
"type": "protein-protein"
|
| 74 |
+
}
|
| 75 |
+
],
|
| 76 |
+
"PBC_SELECTION": null,
|
| 77 |
+
"CHAINNAMES": null,
|
| 78 |
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"MEMBRANES": null,
|
| 79 |
+
"CUSTOMS": null,
|
| 80 |
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"ORIENTATION": null,
|
| 81 |
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"PTM": [],
|
| 82 |
+
"MULTIMERIC": null,
|
| 83 |
+
"COLLECTIONS": "dynarepo",
|
| 84 |
+
"WARNINGS": [],
|
| 85 |
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"BOXSIZEX": 10.6396,
|
| 86 |
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"BOXSIZEY": 10.6396,
|
| 87 |
+
"BOXSIZEZ": 7.50241,
|
| 88 |
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"mdName": "replica 1",
|
| 89 |
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"mdAtoms": 6613,
|
| 90 |
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"mdFrames": 5001
|
| 91 |
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},
|
| 92 |
+
"mds": [
|
| 93 |
+
"replica 1",
|
| 94 |
+
"replica 2",
|
| 95 |
+
"replica 3"
|
| 96 |
+
],
|
| 97 |
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"mdref": 0,
|
| 98 |
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"files": [
|
| 99 |
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"topology.tpr",
|
| 100 |
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"screenshot.jpg",
|
| 101 |
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"trajectory.bin",
|
| 102 |
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"pca_trajectory_01.bin",
|
| 103 |
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"pca_trajectory_02.bin",
|
| 104 |
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"pca_trajectory_03.bin",
|
| 105 |
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"pca_trajectory_04.bin",
|
| 106 |
+
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"structure.pdb",
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"clusters_01_screenshot_18.jpg",
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"clusters_01_screenshot_19.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb"
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],
|
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"analyses": [
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| 167 |
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"clusters",
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| 168 |
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"clusters-00",
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"clusters-01",
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| 170 |
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"dist-perres",
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| 171 |
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"energies",
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| 172 |
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"fluctuation",
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| 173 |
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"hbonds",
|
| 174 |
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"interactions",
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| 175 |
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"pca",
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"pockets",
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| 177 |
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 1,
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"internalId": "6840a7b743f7debe157a59d1",
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"creationDate": "2025-06-04T20:08:23.000Z",
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"identifier": "A0044"
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}
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A0044/records.jsonl
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|
A005F/project.json
ADDED
|
@@ -0,0 +1,194 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3K75",
|
| 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 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"3K75"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
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"P18887",
|
| 31 |
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"P06766"
|
| 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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"PEIRLRHVVSCSSQDSTHCAENLLKADTYRKWRAAKAGEKTISVVLQLEKEEQIHSVDIGNDGSAFVEVLVGSSAGGAGEQDYEVLLVTSSFMSPSESRSGSNPNRVRMFGPDKLVRAAAEKRWDRVKIVCSQPYSKDSPFGLSFVRFHSPP",
|
| 38 |
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"DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSEHHH"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"DNA repair protein XRCC1",
|
| 43 |
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"DNA polymerase beta",
|
| 44 |
+
"DNA-binding"
|
| 45 |
+
],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 6349,
|
| 56 |
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"SYSTRES": 400,
|
| 57 |
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"PROTATS": 6349,
|
| 58 |
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"PROTRES": 400,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
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"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 |
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"PBC_SELECTION": null,
|
| 81 |
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"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 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 11.7561,
|
| 90 |
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"BOXSIZEY": 11.7561,
|
| 91 |
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"BOXSIZEZ": 8.31625,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 6349,
|
| 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 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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"pca_trajectory_01.bin",
|
| 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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"structure.pdb",
|
| 119 |
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"trajectory.xtc",
|
| 120 |
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"clusters_00_screenshot_00.jpg",
|
| 121 |
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"clusters_00_screenshot_01.jpg",
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| 122 |
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"clusters_00_screenshot_02.jpg",
|
| 123 |
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| 124 |
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|
| 125 |
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"clusters_00_screenshot_05.jpg",
|
| 126 |
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"clusters_00_screenshot_06.jpg",
|
| 127 |
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"clusters_00_screenshot_07.jpg",
|
| 128 |
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"clusters_00_screenshot_08.jpg",
|
| 129 |
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"clusters_00_screenshot_09.jpg",
|
| 130 |
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"clusters_00_screenshot_10.jpg",
|
| 131 |
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"clusters_00_screenshot_11.jpg",
|
| 132 |
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"clusters_00_screenshot_12.jpg",
|
| 133 |
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"clusters_00_screenshot_13.jpg",
|
| 134 |
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"clusters_00_screenshot_14.jpg",
|
| 135 |
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"clusters_00_screenshot_15.jpg",
|
| 136 |
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"clusters_00_screenshot_16.jpg",
|
| 137 |
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"clusters_00_screenshot_17.jpg",
|
| 138 |
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"clusters_00_screenshot_18.jpg",
|
| 139 |
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"clusters_00_screenshot_19.jpg",
|
| 140 |
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"clusters_00_screenshot_20.jpg",
|
| 141 |
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"clusters_00_screenshot_21.jpg",
|
| 142 |
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"clusters_00_screenshot_22.jpg",
|
| 143 |
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"clusters_01_screenshot_00.jpg",
|
| 144 |
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"clusters_01_screenshot_01.jpg",
|
| 145 |
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"clusters_01_screenshot_02.jpg",
|
| 146 |
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"clusters_01_screenshot_03.jpg",
|
| 147 |
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"clusters_01_screenshot_04.jpg",
|
| 148 |
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"clusters_01_screenshot_05.jpg",
|
| 149 |
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"clusters_01_screenshot_06.jpg",
|
| 150 |
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"clusters_01_screenshot_07.jpg",
|
| 151 |
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"clusters_01_screenshot_08.jpg",
|
| 152 |
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"clusters_01_screenshot_09.jpg",
|
| 153 |
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"clusters_01_screenshot_10.jpg",
|
| 154 |
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"clusters_01_screenshot_11.jpg",
|
| 155 |
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"clusters_01_screenshot_12.jpg",
|
| 156 |
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"clusters_01_screenshot_13.jpg",
|
| 157 |
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"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 |
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"clusters_01_screenshot_17.jpg",
|
| 161 |
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"clusters_01_screenshot_18.jpg",
|
| 162 |
+
"clusters_01_screenshot_19.jpg",
|
| 163 |
+
"pocket_01.pdb",
|
| 164 |
+
"pocket_02.pdb",
|
| 165 |
+
"pocket_03.pdb",
|
| 166 |
+
"pocket_04.pdb",
|
| 167 |
+
"pocket_05.pdb",
|
| 168 |
+
"pocket_06.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
+
"clusters",
|
| 172 |
+
"clusters-00",
|
| 173 |
+
"clusters-01",
|
| 174 |
+
"dist-perres",
|
| 175 |
+
"energies",
|
| 176 |
+
"fluctuation",
|
| 177 |
+
"hbonds",
|
| 178 |
+
"interactions",
|
| 179 |
+
"pca",
|
| 180 |
+
"pockets",
|
| 181 |
+
"rgyr",
|
| 182 |
+
"rmsd-pairwise",
|
| 183 |
+
"rmsd-perres",
|
| 184 |
+
"rmsds",
|
| 185 |
+
"sasa",
|
| 186 |
+
"tmscores"
|
| 187 |
+
],
|
| 188 |
+
"mdIndex": 0,
|
| 189 |
+
"mdNumber": 1,
|
| 190 |
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"refframe": 0,
|
| 191 |
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"internalId": "68410fe4f671eb2879021607",
|
| 192 |
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"creationDate": "2025-06-05T03:32:52.000Z",
|
| 193 |
+
"identifier": "A005F"
|
| 194 |
+
}
|
A005F/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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| 1 |
+
{
|
| 2 |
+
"accession": "A005S",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3OWT",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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"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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|
| 23 |
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|
| 24 |
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|
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| 29 |
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| 30 |
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| 33 |
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| 34 |
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|
| 35 |
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|
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|
| 37 |
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|
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"KMIDFATLSKLKKKYQIILD",
|
| 39 |
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|
| 40 |
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],
|
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|
| 42 |
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|
| 43 |
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|
| 44 |
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|
| 45 |
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|
| 46 |
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|
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| 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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"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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|
| 55 |
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| 56 |
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|
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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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"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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"name": "chain A-chain C interaction",
|
| 82 |
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|
| 83 |
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|
| 84 |
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"selection_1": "chain A",
|
| 85 |
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"selection_2": "chain C",
|
| 86 |
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"type": "protein-protein"
|
| 87 |
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},
|
| 88 |
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{
|
| 89 |
+
"name": "chain B-chain C interaction",
|
| 90 |
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"agent_1": "chain B",
|
| 91 |
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"agent_2": "chain C",
|
| 92 |
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"selection_1": "chain B",
|
| 93 |
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"selection_2": "chain C",
|
| 94 |
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"type": "protein-protein"
|
| 95 |
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}
|
| 96 |
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],
|
| 97 |
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|
| 98 |
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|
| 99 |
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|
| 100 |
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|
| 101 |
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|
| 102 |
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| 103 |
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| 104 |
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| 105 |
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|
| 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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],
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| 127 |
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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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| 137 |
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| 140 |
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| 141 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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| 149 |
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|
| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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|
| 156 |
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|
| 157 |
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| 158 |
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|
| 159 |
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|
| 160 |
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| 161 |
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| 162 |
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| 163 |
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| 164 |
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| 165 |
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| 166 |
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| 167 |
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| 168 |
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|
| 169 |
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|
| 170 |
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| 171 |
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|
| 172 |
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|
| 173 |
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|
| 174 |
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|
| 175 |
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| 176 |
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| 177 |
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| 178 |
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| 179 |
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| 181 |
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| 182 |
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| 183 |
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| 184 |
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| 185 |
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| 187 |
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| 188 |
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| 189 |
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| 190 |
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|
| 192 |
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|
| 193 |
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|
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|
| 196 |
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|
| 197 |
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|
| 198 |
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|
| 199 |
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|
| 200 |
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"clusters_03_screenshot_04.jpg",
|
| 201 |
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"clusters_03_screenshot_05.jpg",
|
| 202 |
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"clusters_03_screenshot_06.jpg",
|
| 203 |
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"clusters_03_screenshot_07.jpg",
|
| 204 |
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"clusters_03_screenshot_08.jpg",
|
| 205 |
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"clusters_03_screenshot_09.jpg",
|
| 206 |
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"clusters_03_screenshot_10.jpg",
|
| 207 |
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"clusters_03_screenshot_11.jpg",
|
| 208 |
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"clusters_03_screenshot_12.jpg",
|
| 209 |
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"clusters_03_screenshot_13.jpg",
|
| 210 |
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"clusters_03_screenshot_14.jpg",
|
| 211 |
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"clusters_03_screenshot_15.jpg",
|
| 212 |
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|
| 213 |
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"clusters_03_screenshot_17.jpg",
|
| 214 |
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"clusters_03_screenshot_18.jpg",
|
| 215 |
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"clusters_03_screenshot_19.jpg",
|
| 216 |
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"pocket_01.pdb"
|
| 217 |
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],
|
| 218 |
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"analyses": [
|
| 219 |
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"clusters",
|
| 220 |
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"clusters-00",
|
| 221 |
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"clusters-01",
|
| 222 |
+
"clusters-02",
|
| 223 |
+
"clusters-03",
|
| 224 |
+
"dist-perres",
|
| 225 |
+
"energies",
|
| 226 |
+
"fluctuation",
|
| 227 |
+
"hbonds",
|
| 228 |
+
"interactions",
|
| 229 |
+
"pca",
|
| 230 |
+
"pockets",
|
| 231 |
+
"rgyr",
|
| 232 |
+
"rmsd-pairwise",
|
| 233 |
+
"rmsd-perres",
|
| 234 |
+
"rmsds",
|
| 235 |
+
"sasa",
|
| 236 |
+
"tmscores"
|
| 237 |
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],
|
| 238 |
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"mdIndex": 0,
|
| 239 |
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|
| 240 |
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|
| 241 |
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"internalId": "68413679ced12d5ded327da3",
|
| 242 |
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"creationDate": "2025-06-05T06:17:29.000Z",
|
| 243 |
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"identifier": "A005S"
|
| 244 |
+
}
|
A005S/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005S", "accession": "A005S", "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 3OWT", "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": ["3OWT"], "FORCED_REFERENCES": null, "REFERENCES": 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A006Q/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A006Q",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4BRU",
|
| 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 |
+
"4BRU"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P39517",
|
| 31 |
+
"P39998"
|
| 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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"NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVDEFMDKHLHKPYEINLMEELTLKGITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLINWNDRFNLYKIEQELGTEIAAIPATIDKSLYVA",
|
| 38 |
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"HIDWQDDDVSKIKQQEDFDFQRNLGMFNK"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"ATP-dependent RNA helicase DHH1",
|
| 43 |
+
"Helicase ATP-binding",
|
| 44 |
+
"Helicase C-terminal",
|
| 45 |
+
"Q motif",
|
| 46 |
+
"DEAD box",
|
| 47 |
+
"Enhancer of mRNA-decapping protein 3",
|
| 48 |
+
"DFDF",
|
| 49 |
+
"Disordered"
|
| 50 |
+
],
|
| 51 |
+
"FRAMESTEP": 0.1,
|
| 52 |
+
"TIMESTEP": 2,
|
| 53 |
+
"TEMP": 310,
|
| 54 |
+
"ENSEMBLE": "NPT",
|
| 55 |
+
"FF": [
|
| 56 |
+
"CHARMM36m"
|
| 57 |
+
],
|
| 58 |
+
"WAT": "TIP3P",
|
| 59 |
+
"BOXTYPE": "Dodecahedron",
|
| 60 |
+
"SYSTATS": 6549,
|
| 61 |
+
"SYSTRES": 404,
|
| 62 |
+
"PROTATS": 6549,
|
| 63 |
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"PROTRES": 404,
|
| 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,
|
| 68 |
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"CARBATS": 0,
|
| 69 |
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"CARBRES": 0,
|
| 70 |
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"SOLVATS": 0,
|
| 71 |
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"SOLVRES": 0,
|
| 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 |
+
"CHAINNAMES": null,
|
| 87 |
+
"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 |
+
"WARNINGS": [],
|
| 94 |
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"BOXSIZEX": 10.9822,
|
| 95 |
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"BOXSIZEY": 10.9822,
|
| 96 |
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"BOXSIZEZ": 7.77325,
|
| 97 |
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"mdName": "replica 1",
|
| 98 |
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"mdAtoms": 6549,
|
| 99 |
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"mdFrames": 5001
|
| 100 |
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},
|
| 101 |
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"mds": [
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"replica 1",
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"replica 2",
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"files": [
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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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|
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|
| 162 |
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|
| 163 |
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|
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| 165 |
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|
| 166 |
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| 167 |
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"fluctuation",
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| 168 |
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"hbonds",
|
| 169 |
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"interactions",
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| 170 |
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"pca",
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"pockets",
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| 172 |
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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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|
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"identifier": "A006Q"
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}
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A006Q/records.jsonl
ADDED
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|
A007R/project.json
ADDED
|
@@ -0,0 +1,252 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A007R",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4LRX",
|
| 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 |
+
"4LRX"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P76015",
|
| 31 |
+
"P76016"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK",
|
| 38 |
+
"ISPLIATSWERCNKLMKRETWNVPHQAQGVTFASIYRRKKAMLTLGQAALEDAWEYMAPRECALFILDETACILSRNGDPQTLQQLSALGFNDGTYCAEGIIGTCALSLAAISGQAVKTMADQHFKQVLWNWAFCATPLFDSKGRLTGTIALACPVEQTTAADLPLTLAIAREVGNLLLTDSLLAETNRHLNQLNALLESMDDGVISWDEQGNLQFINAQAARVLRLDATASQGRAITELLTLPAVLQQAIKQAHPLKHVEATFESQHQFIDAVITLKPIIETQGTSFILLLHPV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK",
|
| 43 |
+
"DhaK",
|
| 44 |
+
"PTS-dependent dihydroxyacetone kinase operon regulatory protein",
|
| 45 |
+
"GAF",
|
| 46 |
+
"PAS",
|
| 47 |
+
"Sensor domain"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 19784,
|
| 59 |
+
"SYSTRES": 1302,
|
| 60 |
+
"PROTATS": 19784,
|
| 61 |
+
"PROTRES": 1302,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
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|
| 72 |
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| 73 |
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|
| 74 |
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{
|
| 75 |
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"name": "chain A-chain B interaction",
|
| 76 |
+
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|
| 77 |
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|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
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},
|
| 82 |
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{
|
| 83 |
+
"name": "chain A-chain C interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
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|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "chain C-chain D interaction",
|
| 92 |
+
"agent_1": "chain C",
|
| 93 |
+
"agent_2": "chain D",
|
| 94 |
+
"selection_1": "chain A",
|
| 95 |
+
"selection_2": "chain D",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
}
|
| 98 |
+
],
|
| 99 |
+
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|
| 100 |
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"CHAINNAMES": null,
|
| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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|
| 106 |
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|
| 107 |
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|
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|
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|
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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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|
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|
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|
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|
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|
| 132 |
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|
| 134 |
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|
| 137 |
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| 138 |
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| 139 |
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| 140 |
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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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|
| 156 |
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|
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|
| 158 |
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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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| 182 |
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| 189 |
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| 191 |
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| 192 |
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| 195 |
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|
| 198 |
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|
| 199 |
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|
| 200 |
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|
| 201 |
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|
| 202 |
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|
| 203 |
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|
| 204 |
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|
| 205 |
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|
| 206 |
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|
| 207 |
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"clusters_03_screenshot_13.jpg",
|
| 208 |
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"clusters_03_screenshot_14.jpg",
|
| 209 |
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"clusters_03_screenshot_15.jpg",
|
| 210 |
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"clusters_03_screenshot_16.jpg",
|
| 211 |
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"clusters_03_screenshot_17.jpg",
|
| 212 |
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"clusters_03_screenshot_18.jpg",
|
| 213 |
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"clusters_03_screenshot_19.jpg",
|
| 214 |
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"clusters_03_screenshot_20.jpg",
|
| 215 |
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"pocket_01.pdb",
|
| 216 |
+
"pocket_02.pdb",
|
| 217 |
+
"pocket_03.pdb",
|
| 218 |
+
"pocket_04.pdb",
|
| 219 |
+
"pocket_05.pdb",
|
| 220 |
+
"pocket_06.pdb",
|
| 221 |
+
"pocket_07.pdb",
|
| 222 |
+
"pocket_08.pdb",
|
| 223 |
+
"pocket_09.pdb",
|
| 224 |
+
"pocket_10.pdb"
|
| 225 |
+
],
|
| 226 |
+
"analyses": [
|
| 227 |
+
"clusters",
|
| 228 |
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"clusters-00",
|
| 229 |
+
"clusters-01",
|
| 230 |
+
"clusters-02",
|
| 231 |
+
"clusters-03",
|
| 232 |
+
"dist-perres",
|
| 233 |
+
"energies",
|
| 234 |
+
"fluctuation",
|
| 235 |
+
"hbonds",
|
| 236 |
+
"interactions",
|
| 237 |
+
"pca",
|
| 238 |
+
"pockets",
|
| 239 |
+
"rgyr",
|
| 240 |
+
"rmsd-pairwise",
|
| 241 |
+
"rmsd-perres",
|
| 242 |
+
"rmsds",
|
| 243 |
+
"sasa",
|
| 244 |
+
"tmscores"
|
| 245 |
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],
|
| 246 |
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"mdIndex": 0,
|
| 247 |
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"mdNumber": 1,
|
| 248 |
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"refframe": 1,
|
| 249 |
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"internalId": "684223b5a78b2532bb43a39b",
|
| 250 |
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"creationDate": "2025-06-05T23:09:41.000Z",
|
| 251 |
+
"identifier": "A007R"
|
| 252 |
+
}
|
A007R/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A007R", "accession": "A007R", "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 4LRX", "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": ["4LRX"], "FORCED_REFERENCES": null, "REFERENCES": 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| 1 |
+
{
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| 2 |
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"accession": "A007S",
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| 3 |
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"published": true,
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| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4LRZ",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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| 13 |
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|
| 14 |
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],
|
| 15 |
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|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
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| 18 |
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| 19 |
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| 20 |
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| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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| 26 |
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|
| 27 |
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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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| 39 |
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| 40 |
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| 41 |
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|
| 42 |
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| 43 |
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| 44 |
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| 45 |
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| 46 |
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| 47 |
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| 48 |
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| 50 |
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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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|
| 77 |
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| 81 |
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| 83 |
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| 84 |
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| 96 |
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| 99 |
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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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| 112 |
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"creationDate": "2025-06-05T23:26:09.000Z",
|
| 314 |
+
"identifier": "A007S"
|
| 315 |
+
}
|
A007S/records.jsonl
ADDED
|
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A007V/project.json
ADDED
|
@@ -0,0 +1,197 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A007V",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4M0W",
|
| 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 |
+
"4M0W"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0C6U8",
|
| 31 |
+
"P62992"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"VKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNSYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVXKHXGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPXVXGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVS",
|
| 38 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Replicase polyprotein 1a",
|
| 43 |
+
"Papain-like protease nsp3",
|
| 44 |
+
"Ubiquitin-like 2",
|
| 45 |
+
"Peptidase C16",
|
| 46 |
+
"Ubiquitin",
|
| 47 |
+
"Ubiquitin-like",
|
| 48 |
+
"Disordered",
|
| 49 |
+
"Interacts with activating enzyme",
|
| 50 |
+
"Essential for function"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 6169,
|
| 62 |
+
"SYSTRES": 393,
|
| 63 |
+
"PROTATS": 6169,
|
| 64 |
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"PROTRES": 393,
|
| 65 |
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"NUCLATS": 0,
|
| 66 |
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"NUCLRES": 0,
|
| 67 |
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"LIPIATS": 0,
|
| 68 |
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"LIPIRES": 0,
|
| 69 |
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"CARBATS": 0,
|
| 70 |
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"CARBRES": 0,
|
| 71 |
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"SOLVATS": 0,
|
| 72 |
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"SOLVRES": 0,
|
| 73 |
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"COUNCAT": 0,
|
| 74 |
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"COUNANI": 0,
|
| 75 |
+
"COUNION": 0,
|
| 76 |
+
"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
}
|
| 85 |
+
],
|
| 86 |
+
"PBC_SELECTION": null,
|
| 87 |
+
"CHAINNAMES": null,
|
| 88 |
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"MEMBRANES": null,
|
| 89 |
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"CUSTOMS": null,
|
| 90 |
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"ORIENTATION": null,
|
| 91 |
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"PTM": [],
|
| 92 |
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"MULTIMERIC": null,
|
| 93 |
+
"COLLECTIONS": "dynarepo",
|
| 94 |
+
"WARNINGS": [],
|
| 95 |
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"BOXSIZEX": 11.6703,
|
| 96 |
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"BOXSIZEY": 11.6703,
|
| 97 |
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"BOXSIZEZ": 8.21633,
|
| 98 |
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"mdName": "replica 1",
|
| 99 |
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"mdAtoms": 6169,
|
| 100 |
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"mdFrames": 5001
|
| 101 |
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},
|
| 102 |
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"mds": [
|
| 103 |
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"replica 1",
|
| 104 |
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"replica 2",
|
| 105 |
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"replica 3"
|
| 106 |
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],
|
| 107 |
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"mdref": 0,
|
| 108 |
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"files": [
|
| 109 |
+
"topology.tpr",
|
| 110 |
+
"screenshot.jpg",
|
| 111 |
+
"trajectory.bin",
|
| 112 |
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"pca_trajectory_01.bin",
|
| 113 |
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"pca_trajectory_02.bin",
|
| 114 |
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"pca_trajectory_03.bin",
|
| 115 |
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"pca_trajectory_04.bin",
|
| 116 |
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"pca_trajectory_05.bin",
|
| 117 |
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"pca_trajectory_06.bin",
|
| 118 |
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"pca_trajectory_07.bin",
|
| 119 |
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"pca_trajectory_08.bin",
|
| 120 |
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"structure.pdb",
|
| 121 |
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"trajectory.xtc",
|
| 122 |
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"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
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"clusters_00_screenshot_02.jpg",
|
| 125 |
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"clusters_00_screenshot_03.jpg",
|
| 126 |
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"clusters_00_screenshot_04.jpg",
|
| 127 |
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"clusters_00_screenshot_05.jpg",
|
| 128 |
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"clusters_00_screenshot_06.jpg",
|
| 129 |
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"clusters_00_screenshot_07.jpg",
|
| 130 |
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"clusters_00_screenshot_08.jpg",
|
| 131 |
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"clusters_00_screenshot_09.jpg",
|
| 132 |
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"clusters_00_screenshot_10.jpg",
|
| 133 |
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"clusters_00_screenshot_11.jpg",
|
| 134 |
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"clusters_00_screenshot_12.jpg",
|
| 135 |
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"clusters_00_screenshot_13.jpg",
|
| 136 |
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"clusters_00_screenshot_14.jpg",
|
| 137 |
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"clusters_00_screenshot_15.jpg",
|
| 138 |
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"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
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"clusters_00_screenshot_18.jpg",
|
| 141 |
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"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_00_screenshot_20.jpg",
|
| 143 |
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"clusters_01_screenshot_00.jpg",
|
| 144 |
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"clusters_01_screenshot_01.jpg",
|
| 145 |
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"clusters_01_screenshot_02.jpg",
|
| 146 |
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"clusters_01_screenshot_03.jpg",
|
| 147 |
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"clusters_01_screenshot_04.jpg",
|
| 148 |
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"clusters_01_screenshot_05.jpg",
|
| 149 |
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"clusters_01_screenshot_06.jpg",
|
| 150 |
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"clusters_01_screenshot_07.jpg",
|
| 151 |
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"clusters_01_screenshot_08.jpg",
|
| 152 |
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"clusters_01_screenshot_09.jpg",
|
| 153 |
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"clusters_01_screenshot_10.jpg",
|
| 154 |
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"clusters_01_screenshot_11.jpg",
|
| 155 |
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"clusters_01_screenshot_12.jpg",
|
| 156 |
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"clusters_01_screenshot_13.jpg",
|
| 157 |
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"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 |
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"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 |
+
"pocket_09.pdb"
|
| 172 |
+
],
|
| 173 |
+
"analyses": [
|
| 174 |
+
"clusters",
|
| 175 |
+
"clusters-00",
|
| 176 |
+
"clusters-01",
|
| 177 |
+
"dist-perres",
|
| 178 |
+
"energies",
|
| 179 |
+
"fluctuation",
|
| 180 |
+
"hbonds",
|
| 181 |
+
"interactions",
|
| 182 |
+
"pca",
|
| 183 |
+
"pockets",
|
| 184 |
+
"rgyr",
|
| 185 |
+
"rmsd-pairwise",
|
| 186 |
+
"rmsd-perres",
|
| 187 |
+
"rmsds",
|
| 188 |
+
"sasa",
|
| 189 |
+
"tmscores"
|
| 190 |
+
],
|
| 191 |
+
"mdIndex": 0,
|
| 192 |
+
"mdNumber": 1,
|
| 193 |
+
"refframe": 0,
|
| 194 |
+
"internalId": "68422c772cd8cf4bd3b87d90",
|
| 195 |
+
"creationDate": "2025-06-05T23:47:03.000Z",
|
| 196 |
+
"identifier": "A007V"
|
| 197 |
+
}
|
A007V/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A007V", "accession": "A007V", "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 4M0W", "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": ["4M0W"], "FORCED_REFERENCES": null, "REFERENCES": ["P0C6U8", "P62992"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNSYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVXKHXGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPXVXGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIKPVS", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"], "NUCLSEQ": [], "DOMAINS": ["Replicase polyprotein 1a", "Papain-like protease nsp3", "Ubiquitin-like 2", "Peptidase C16", "Ubiquitin", "Ubiquitin-like", "Disordered", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6169, "SYSTRES": 393, "PROTATS": 6169, "PROTRES": 393, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, 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+
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A007Z/project.json
ADDED
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@@ -0,0 +1,200 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A007Z",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4MRT",
|
| 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 |
+
"4MRT"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O30409",
|
| 31 |
+
"P39135"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MKIYGIYMDRPLSQEENERFMTFISPEKREKCRRFYHKEDAHRTLLGDVLVRSVISRQYQLDKSDIRFSTQEYGKPCIPDLPDAHFNISHSGRWVIGAFDSQPIGIDIEKTKPISLEIAKRFFSKTEYSDLLAKDKDEQTDYFYHLWSMKESFIKQEGKGLSLPLDSFSVRLHQDGQVSIELPDSHSPCYIKTYEVDPGYKMAVCAAHPDFPEDITMVSYEELLR",
|
| 38 |
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"YVAPTNAVESKLAEIWERVLGVSGIGILDNFFQIGGHALKAMAVAAQVHREYQVELPLKVLFAQPTIKALAQYVATR"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tyrocidine synthase 3",
|
| 43 |
+
"Carrier 3",
|
| 44 |
+
"Domain 3 (tyrosine-activating)",
|
| 45 |
+
"4'-phosphopantetheinyl transferase Sfp",
|
| 46 |
+
"Peptidyl carrier protein binding"
|
| 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": 4868,
|
| 58 |
+
"SYSTRES": 302,
|
| 59 |
+
"PROTATS": 4868,
|
| 60 |
+
"PROTRES": 302,
|
| 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 |
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"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": 8.52286,
|
| 92 |
+
"BOXSIZEY": 8.52286,
|
| 93 |
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"BOXSIZEZ": 6.06781,
|
| 94 |
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"mdName": "replica 1",
|
| 95 |
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"mdAtoms": 4868,
|
| 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",
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| 100 |
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"replica 2",
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"replica 3"
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],
|
| 103 |
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"mdref": 0,
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"files": [
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"topology.tpr",
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"screenshot.jpg",
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"trajectory.bin",
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"pca_trajectory_01.bin",
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"pca_trajectory_02.bin",
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"pca_trajectory_03.bin",
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"pca_trajectory_04.bin",
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"pca_trajectory_05.bin",
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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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"pca_trajectory_09.bin",
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"structure.pdb",
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"trajectory.xtc",
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"clusters_00_screenshot_00.jpg",
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"clusters_00_screenshot_01.jpg",
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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",
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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_15.jpg",
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"clusters_00_screenshot_18.jpg",
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"clusters_00_screenshot_19.jpg",
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"clusters_00_screenshot_20.jpg",
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"clusters_00_screenshot_21.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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"clusters_01_screenshot_04.jpg",
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"clusters_01_screenshot_06.jpg",
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"clusters_01_screenshot_07.jpg",
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"clusters_01_screenshot_08.jpg",
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"clusters_01_screenshot_09.jpg",
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"clusters_01_screenshot_10.jpg",
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"clusters_01_screenshot_11.jpg",
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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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"clusters_01_screenshot_19.jpg",
|
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"clusters_01_screenshot_20.jpg",
|
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+
"clusters_01_screenshot_21.jpg",
|
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+
"clusters_01_screenshot_22.jpg",
|
| 164 |
+
"clusters_01_screenshot_23.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb",
|
| 173 |
+
"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",
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+
"rmsds",
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| 191 |
+
"sasa",
|
| 192 |
+
"tmscores"
|
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+
],
|
| 194 |
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"mdIndex": 0,
|
| 195 |
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"mdNumber": 1,
|
| 196 |
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"refframe": 0,
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| 197 |
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"internalId": "684231cece6d4b51c040151e",
|
| 198 |
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"creationDate": "2025-06-06T00:09:50.000Z",
|
| 199 |
+
"identifier": "A007Z"
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| 200 |
+
}
|
A007Z/records.jsonl
ADDED
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|
A0083/project.json
ADDED
|
@@ -0,0 +1,190 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0083",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4NL9",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"4NL9"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q6ZW76",
|
| 31 |
+
"Q68DC2"
|
| 32 |
+
],
|
| 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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"APYSGPQDLAALLEQIGCLKYLQVFEEQDVDLREFLTLTESDLKEIGITLFGPKRKMTSAIARW",
|
| 38 |
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"ELTGILKKLSLEKYQPIFEEQEVDMEAFLTLTDGDLKELGIKTDGSRQQILAAISELNAG"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
+
"Ankyrin repeat and SAM domain-containing protein 3",
|
| 43 |
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"SAM",
|
| 44 |
+
"Interaction with NEK7",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Ankyrin repeat and SAM domain-containing protein 6",
|
| 47 |
+
"SAM",
|
| 48 |
+
"Essential for ANKS3 interaction"
|
| 49 |
+
],
|
| 50 |
+
"FRAMESTEP": 0.1,
|
| 51 |
+
"TIMESTEP": 2,
|
| 52 |
+
"TEMP": 310,
|
| 53 |
+
"ENSEMBLE": "NPT",
|
| 54 |
+
"FF": [
|
| 55 |
+
"CHARMM36m"
|
| 56 |
+
],
|
| 57 |
+
"WAT": "TIP3P",
|
| 58 |
+
"BOXTYPE": "Dodecahedron",
|
| 59 |
+
"SYSTATS": 1974,
|
| 60 |
+
"SYSTRES": 124,
|
| 61 |
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"PROTATS": 1974,
|
| 62 |
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"PROTRES": 124,
|
| 63 |
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"NUCLATS": 0,
|
| 64 |
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"NUCLRES": 0,
|
| 65 |
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"LIPIATS": 0,
|
| 66 |
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"LIPIRES": 0,
|
| 67 |
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"CARBATS": 0,
|
| 68 |
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"CARBRES": 0,
|
| 69 |
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"SOLVATS": 0,
|
| 70 |
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"SOLVRES": 0,
|
| 71 |
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"COUNCAT": 0,
|
| 72 |
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"COUNANI": 0,
|
| 73 |
+
"COUNION": 0,
|
| 74 |
+
"INTERACTIONS": [
|
| 75 |
+
{
|
| 76 |
+
"name": "chain A-chain B interaction",
|
| 77 |
+
"agent_1": "chain A",
|
| 78 |
+
"agent_2": "chain B",
|
| 79 |
+
"selection_1": "chain A",
|
| 80 |
+
"selection_2": "chain B",
|
| 81 |
+
"type": "protein-protein"
|
| 82 |
+
}
|
| 83 |
+
],
|
| 84 |
+
"PBC_SELECTION": null,
|
| 85 |
+
"CHAINNAMES": null,
|
| 86 |
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"MEMBRANES": null,
|
| 87 |
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"CUSTOMS": null,
|
| 88 |
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"ORIENTATION": null,
|
| 89 |
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"PTM": [],
|
| 90 |
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"MULTIMERIC": null,
|
| 91 |
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"COLLECTIONS": "dynarepo",
|
| 92 |
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"WARNINGS": [],
|
| 93 |
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"BOXSIZEX": 7.47311,
|
| 94 |
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"BOXSIZEY": 7.47311,
|
| 95 |
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"BOXSIZEZ": 5.27624,
|
| 96 |
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"mdName": "replica 1",
|
| 97 |
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"mdAtoms": 1974,
|
| 98 |
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"mdFrames": 5001
|
| 99 |
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},
|
| 100 |
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"mds": [
|
| 101 |
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"replica 1",
|
| 102 |
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"replica 2",
|
| 103 |
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"replica 3"
|
| 104 |
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],
|
| 105 |
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"mdref": 0,
|
| 106 |
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"files": [
|
| 107 |
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"topology.tpr",
|
| 108 |
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"screenshot.jpg",
|
| 109 |
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"trajectory.bin",
|
| 110 |
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"pca_trajectory_01.bin",
|
| 111 |
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"pca_trajectory_02.bin",
|
| 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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"pca_trajectory_09.bin",
|
| 119 |
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"pca_trajectory_10.bin",
|
| 120 |
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"structure.pdb",
|
| 121 |
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"trajectory.xtc",
|
| 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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"clusters_00_screenshot_07.jpg",
|
| 130 |
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"clusters_00_screenshot_08.jpg",
|
| 131 |
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"clusters_00_screenshot_09.jpg",
|
| 132 |
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"clusters_00_screenshot_10.jpg",
|
| 133 |
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"clusters_00_screenshot_11.jpg",
|
| 134 |
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"clusters_00_screenshot_12.jpg",
|
| 135 |
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"clusters_00_screenshot_13.jpg",
|
| 136 |
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"clusters_00_screenshot_14.jpg",
|
| 137 |
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"clusters_00_screenshot_15.jpg",
|
| 138 |
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"clusters_00_screenshot_16.jpg",
|
| 139 |
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"clusters_00_screenshot_17.jpg",
|
| 140 |
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"clusters_00_screenshot_18.jpg",
|
| 141 |
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"clusters_00_screenshot_19.jpg",
|
| 142 |
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"clusters_00_screenshot_20.jpg",
|
| 143 |
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"clusters_00_screenshot_21.jpg",
|
| 144 |
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"clusters_01_screenshot_00.jpg",
|
| 145 |
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"clusters_01_screenshot_01.jpg",
|
| 146 |
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"clusters_01_screenshot_02.jpg",
|
| 147 |
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"clusters_01_screenshot_03.jpg",
|
| 148 |
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"clusters_01_screenshot_04.jpg",
|
| 149 |
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"clusters_01_screenshot_05.jpg",
|
| 150 |
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"clusters_01_screenshot_06.jpg",
|
| 151 |
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"clusters_01_screenshot_07.jpg",
|
| 152 |
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"clusters_01_screenshot_08.jpg",
|
| 153 |
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"clusters_01_screenshot_09.jpg",
|
| 154 |
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"clusters_01_screenshot_10.jpg",
|
| 155 |
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"clusters_01_screenshot_11.jpg",
|
| 156 |
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"clusters_01_screenshot_12.jpg",
|
| 157 |
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"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
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"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"clusters_01_screenshot_17.jpg",
|
| 162 |
+
"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"clusters_01_screenshot_19.jpg",
|
| 164 |
+
"pocket_01.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 |
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"mdIndex": 0,
|
| 185 |
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"mdNumber": 1,
|
| 186 |
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"refframe": 1,
|
| 187 |
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"internalId": "684236caea1775be7ff1a7a2",
|
| 188 |
+
"creationDate": "2025-06-06T00:31:06.000Z",
|
| 189 |
+
"identifier": "A0083"
|
| 190 |
+
}
|
A0083/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
A008P/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A008P",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4ZRK",
|
| 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 |
+
"4ZRK"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P46662",
|
| 31 |
+
"O95835"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"PKFGTHHKALQEIRNSLLPFA",
|
| 38 |
+
"KTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKVYCPPEASVLLASYAVQAKYGDYDPSVHKRGFLAQEELLPKRVINLYQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFTIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRR"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Merlin",
|
| 43 |
+
"FERM",
|
| 44 |
+
"Serine/threonine-protein kinase LATS1",
|
| 45 |
+
"Disordered"
|
| 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": 5236,
|
| 57 |
+
"SYSTRES": 313,
|
| 58 |
+
"PROTATS": 5236,
|
| 59 |
+
"PROTRES": 313,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
+
"CARBATS": 0,
|
| 65 |
+
"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
+
"COUNCAT": 0,
|
| 69 |
+
"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 |
+
"CUSTOMS": null,
|
| 85 |
+
"ORIENTATION": null,
|
| 86 |
+
"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
+
"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
+
"BOXSIZEX": 9.94764,
|
| 91 |
+
"BOXSIZEY": 9.94764,
|
| 92 |
+
"BOXSIZEZ": 6.99963,
|
| 93 |
+
"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 5236,
|
| 95 |
+
"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
+
"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
+
"files": [
|
| 104 |
+
"topology.tpr",
|
| 105 |
+
"screenshot.jpg",
|
| 106 |
+
"trajectory.bin",
|
| 107 |
+
"pca_trajectory_01.bin",
|
| 108 |
+
"pca_trajectory_02.bin",
|
| 109 |
+
"pca_trajectory_03.bin",
|
| 110 |
+
"pca_trajectory_04.bin",
|
| 111 |
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"pca_trajectory_05.bin",
|
| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
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"pca_trajectory_07.bin",
|
| 114 |
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"pca_trajectory_08.bin",
|
| 115 |
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"pca_trajectory_09.bin",
|
| 116 |
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"pca_trajectory_10.bin",
|
| 117 |
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"pca_trajectory_11.bin",
|
| 118 |
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"structure.pdb",
|
| 119 |
+
"trajectory.xtc",
|
| 120 |
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"clusters_00_screenshot_00.jpg",
|
| 121 |
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"clusters_00_screenshot_01.jpg",
|
| 122 |
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"clusters_00_screenshot_02.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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],
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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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| 168 |
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "68425886d17842061c1757b1",
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"creationDate": "2025-06-06T02:55:02.000Z",
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"identifier": "A008P"
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}
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A008P/records.jsonl
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| 3 |
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|
A008W/project.json
ADDED
|
@@ -0,0 +1,190 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A008W",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5CZF",
|
| 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 |
+
"5CZF"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q8XAD5",
|
| 31 |
+
"A0A0H3JHG3"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"HLPVLWLESADTDLDDITSYIARFDIDAAERLWQRLRGCVLPLSEHPYLYPPSDRVPGLREIVAHPNYIILYRVTTSSVEVVNVIHARRQFP",
|
| 38 |
+
"EQENSYNEWLRAKVATSLADPRPAIPHDEVERRMAERFAKMRKER"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Stability determinant"
|
| 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": 2260,
|
| 54 |
+
"SYSTRES": 137,
|
| 55 |
+
"PROTATS": 2260,
|
| 56 |
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"PROTRES": 137,
|
| 57 |
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"NUCLATS": 0,
|
| 58 |
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"NUCLRES": 0,
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| 59 |
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"LIPIATS": 0,
|
| 60 |
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"LIPIRES": 0,
|
| 61 |
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"CARBATS": 0,
|
| 62 |
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"CARBRES": 0,
|
| 63 |
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"SOLVATS": 0,
|
| 64 |
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"SOLVRES": 0,
|
| 65 |
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"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 |
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"BOXSIZEX": 7.38609,
|
| 88 |
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"BOXSIZEY": 7.38609,
|
| 89 |
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"BOXSIZEZ": 5.21591,
|
| 90 |
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"mdName": "replica 1",
|
| 91 |
+
"mdAtoms": 2260,
|
| 92 |
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"mdFrames": 5001
|
| 93 |
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},
|
| 94 |
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"mds": [
|
| 95 |
+
"replica 1",
|
| 96 |
+
"replica 2",
|
| 97 |
+
"replica 3"
|
| 98 |
+
],
|
| 99 |
+
"mdref": 0,
|
| 100 |
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"files": [
|
| 101 |
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"topology.tpr",
|
| 102 |
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"screenshot.jpg",
|
| 103 |
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"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 |
+
"pca_trajectory_09.bin",
|
| 113 |
+
"pca_trajectory_10.bin",
|
| 114 |
+
"pca_trajectory_11.bin",
|
| 115 |
+
"pca_trajectory_12.bin",
|
| 116 |
+
"pca_trajectory_13.bin",
|
| 117 |
+
"pca_trajectory_14.bin",
|
| 118 |
+
"pca_trajectory_15.bin",
|
| 119 |
+
"pca_trajectory_16.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
+
"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.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 |
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"refframe": 0,
|
| 187 |
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"internalId": "684265067ab9692c85fd3a85",
|
| 188 |
+
"creationDate": "2025-06-06T03:48:22.000Z",
|
| 189 |
+
"identifier": "A008W"
|
| 190 |
+
}
|
A008W/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
|
|
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| 1 |
+
{"project_identifier": "A008W", "accession": "A008W", "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 5CZF", "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": ["5CZF"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8XAD5", "A0A0H3JHG3"], 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| 3 |
+
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| 1 |
+
{
|
| 2 |
+
"accession": "A009O",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5M2M",
|
| 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 |
+
"5M2M"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01375",
|
| 31 |
+
"P01764"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"QLQESGGGLVQPGGSLRLSCAASGRTFSDHSGYTYTIGWFRQAPGKEREFVARIYWSSGNTYYADSVKGRFAISRDIAKNTVDLTMNNLEPEDTAVYYCAARDGIPTSRSVESYNYWGQGTQVTVSS",
|
| 38 |
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"TPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tumor necrosis factor, membrane form",
|
| 43 |
+
"Tumor necrosis factor, soluble form",
|
| 44 |
+
"THD",
|
| 45 |
+
"Immunoglobulin heavy variable 3-23",
|
| 46 |
+
"Ig-like",
|
| 47 |
+
"Framework-1",
|
| 48 |
+
"Complementarity-determining-1",
|
| 49 |
+
"Framework-2",
|
| 50 |
+
"Complementarity-determining-2",
|
| 51 |
+
"Framework-3",
|
| 52 |
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"Complementarity-determining-3"
|
| 53 |
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],
|
| 54 |
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"FRAMESTEP": 0.1,
|
| 55 |
+
"TIMESTEP": 2,
|
| 56 |
+
"TEMP": 310,
|
| 57 |
+
"ENSEMBLE": "NPT",
|
| 58 |
+
"FF": [
|
| 59 |
+
"CHARMM36m"
|
| 60 |
+
],
|
| 61 |
+
"WAT": "TIP3P",
|
| 62 |
+
"BOXTYPE": "Dodecahedron",
|
| 63 |
+
"SYSTATS": 12792,
|
| 64 |
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"SYSTRES": 834,
|
| 65 |
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"PROTATS": 12792,
|
| 66 |
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"PROTRES": 834,
|
| 67 |
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"NUCLATS": 0,
|
| 68 |
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"NUCLRES": 0,
|
| 69 |
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"LIPIATS": 0,
|
| 70 |
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"LIPIRES": 0,
|
| 71 |
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"CARBATS": 0,
|
| 72 |
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"CARBRES": 0,
|
| 73 |
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"SOLVATS": 0,
|
| 74 |
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"SOLVRES": 0,
|
| 75 |
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"COUNCAT": 0,
|
| 76 |
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"COUNANI": 0,
|
| 77 |
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"COUNION": 0,
|
| 78 |
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"INTERACTIONS": [
|
| 79 |
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{
|
| 80 |
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"name": "chain A-chain B interaction",
|
| 81 |
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"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain B",
|
| 83 |
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"selection_1": "chain A",
|
| 84 |
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"selection_2": "chain B",
|
| 85 |
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"type": "protein-protein"
|
| 86 |
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},
|
| 87 |
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{
|
| 88 |
+
"name": "chain A-chain C interaction",
|
| 89 |
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"agent_1": "chain A",
|
| 90 |
+
"agent_2": "chain C",
|
| 91 |
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"selection_1": "chain A",
|
| 92 |
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"selection_2": "chain C",
|
| 93 |
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"type": "protein-protein"
|
| 94 |
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},
|
| 95 |
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{
|
| 96 |
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"name": "chain A-chain F interaction",
|
| 97 |
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"agent_1": "chain A",
|
| 98 |
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"agent_2": "chain F",
|
| 99 |
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"selection_1": "chain A",
|
| 100 |
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"selection_2": "chain D",
|
| 101 |
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"type": "protein-protein"
|
| 102 |
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},
|
| 103 |
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{
|
| 104 |
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"name": "chain B-chain C interaction",
|
| 105 |
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"agent_1": "chain B",
|
| 106 |
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"agent_2": "chain C",
|
| 107 |
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"selection_1": "chain A",
|
| 108 |
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"selection_2": "chain E",
|
| 109 |
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"type": "protein-protein"
|
| 110 |
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},
|
| 111 |
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{
|
| 112 |
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"name": "chain B-chain D interaction",
|
| 113 |
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"agent_1": "chain B",
|
| 114 |
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"agent_2": "chain D",
|
| 115 |
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"selection_1": "chain A",
|
| 116 |
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"selection_2": "chain F",
|
| 117 |
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"type": "protein-protein"
|
| 118 |
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},
|
| 119 |
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{
|
| 120 |
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"name": "chain C-chain E interaction",
|
| 121 |
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"agent_1": "chain C",
|
| 122 |
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"agent_2": "chain E",
|
| 123 |
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"selection_1": "chain B",
|
| 124 |
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"selection_2": "chain C",
|
| 125 |
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"type": "protein-protein"
|
| 126 |
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}
|
| 127 |
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],
|
| 128 |
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"PBC_SELECTION": null,
|
| 129 |
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"CHAINNAMES": null,
|
| 130 |
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"MEMBRANES": null,
|
| 131 |
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"CUSTOMS": null,
|
| 132 |
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"ORIENTATION": null,
|
| 133 |
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"PTM": [],
|
| 134 |
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"MULTIMERIC": null,
|
| 135 |
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"COLLECTIONS": "dynarepo",
|
| 136 |
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"WARNINGS": [],
|
| 137 |
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"BOXSIZEX": 11.953,
|
| 138 |
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"BOXSIZEY": 11.953,
|
| 139 |
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"BOXSIZEZ": 8.44665,
|
| 140 |
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"mdName": "replica 1",
|
| 141 |
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"mdAtoms": 12792,
|
| 142 |
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"mdFrames": 5001
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| 143 |
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},
|
| 144 |
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"mds": [
|
| 145 |
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"replica 1",
|
| 146 |
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"replica 2",
|
| 147 |
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"replica 3"
|
| 148 |
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],
|
| 149 |
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"mdref": 0,
|
| 150 |
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"files": [
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| 151 |
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| 152 |
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"screenshot.jpg",
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| 241 |
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"clusters_03_screenshot_16.jpg",
|
| 242 |
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|
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"clusters_04_screenshot_00.jpg",
|
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"clusters_04_screenshot_01.jpg",
|
| 245 |
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"clusters_04_screenshot_02.jpg",
|
| 246 |
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"clusters_04_screenshot_03.jpg",
|
| 247 |
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"clusters_04_screenshot_04.jpg",
|
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"clusters_04_screenshot_05.jpg",
|
| 249 |
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"clusters_04_screenshot_06.jpg",
|
| 250 |
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"clusters_04_screenshot_07.jpg",
|
| 251 |
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"clusters_04_screenshot_08.jpg",
|
| 252 |
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"clusters_04_screenshot_09.jpg",
|
| 253 |
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"clusters_04_screenshot_10.jpg",
|
| 254 |
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"clusters_04_screenshot_11.jpg",
|
| 255 |
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"clusters_04_screenshot_12.jpg",
|
| 256 |
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"clusters_04_screenshot_13.jpg",
|
| 257 |
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"clusters_04_screenshot_14.jpg",
|
| 258 |
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"clusters_04_screenshot_15.jpg",
|
| 259 |
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"clusters_04_screenshot_16.jpg",
|
| 260 |
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"clusters_04_screenshot_17.jpg",
|
| 261 |
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"clusters_04_screenshot_18.jpg",
|
| 262 |
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"clusters_04_screenshot_19.jpg",
|
| 263 |
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"clusters_05_screenshot_00.jpg",
|
| 264 |
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"clusters_05_screenshot_01.jpg",
|
| 265 |
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"clusters_05_screenshot_02.jpg",
|
| 266 |
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"clusters_05_screenshot_03.jpg",
|
| 267 |
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"clusters_05_screenshot_04.jpg",
|
| 268 |
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"clusters_05_screenshot_05.jpg",
|
| 269 |
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"clusters_05_screenshot_06.jpg",
|
| 270 |
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"clusters_05_screenshot_07.jpg",
|
| 271 |
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"clusters_05_screenshot_08.jpg",
|
| 272 |
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"clusters_05_screenshot_09.jpg",
|
| 273 |
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"clusters_05_screenshot_10.jpg",
|
| 274 |
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"clusters_05_screenshot_11.jpg",
|
| 275 |
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"clusters_05_screenshot_12.jpg",
|
| 276 |
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"clusters_05_screenshot_13.jpg",
|
| 277 |
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"clusters_05_screenshot_14.jpg",
|
| 278 |
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"clusters_05_screenshot_15.jpg",
|
| 279 |
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"clusters_05_screenshot_16.jpg",
|
| 280 |
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"clusters_05_screenshot_17.jpg",
|
| 281 |
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"clusters_05_screenshot_18.jpg",
|
| 282 |
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"clusters_05_screenshot_19.jpg",
|
| 283 |
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"clusters_06_screenshot_00.jpg",
|
| 284 |
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"clusters_06_screenshot_01.jpg",
|
| 285 |
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"clusters_06_screenshot_02.jpg",
|
| 286 |
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"clusters_06_screenshot_03.jpg",
|
| 287 |
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"clusters_06_screenshot_04.jpg",
|
| 288 |
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"clusters_06_screenshot_05.jpg",
|
| 289 |
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"clusters_06_screenshot_06.jpg",
|
| 290 |
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"clusters_06_screenshot_07.jpg",
|
| 291 |
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"clusters_06_screenshot_08.jpg",
|
| 292 |
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"clusters_06_screenshot_09.jpg",
|
| 293 |
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"clusters_06_screenshot_10.jpg",
|
| 294 |
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"clusters_06_screenshot_11.jpg",
|
| 295 |
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"clusters_06_screenshot_12.jpg",
|
| 296 |
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"clusters_06_screenshot_13.jpg",
|
| 297 |
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"clusters_06_screenshot_14.jpg",
|
| 298 |
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"clusters_06_screenshot_15.jpg",
|
| 299 |
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"clusters_06_screenshot_16.jpg",
|
| 300 |
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"clusters_06_screenshot_17.jpg",
|
| 301 |
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"clusters_06_screenshot_18.jpg",
|
| 302 |
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"pocket_01.pdb",
|
| 303 |
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"pocket_02.pdb",
|
| 304 |
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"pocket_03.pdb",
|
| 305 |
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"pocket_04.pdb",
|
| 306 |
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"pocket_05.pdb",
|
| 307 |
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"pocket_06.pdb",
|
| 308 |
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"pocket_07.pdb",
|
| 309 |
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"pocket_08.pdb",
|
| 310 |
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"pocket_09.pdb",
|
| 311 |
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"pocket_10.pdb"
|
| 312 |
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],
|
| 313 |
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"analyses": [
|
| 314 |
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"clusters",
|
| 315 |
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"clusters-00",
|
| 316 |
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"clusters-01",
|
| 317 |
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"clusters-02",
|
| 318 |
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"clusters-03",
|
| 319 |
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"clusters-04",
|
| 320 |
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"clusters-05",
|
| 321 |
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"clusters-06",
|
| 322 |
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"dist-perres",
|
| 323 |
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"energies",
|
| 324 |
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"fluctuation",
|
| 325 |
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"hbonds",
|
| 326 |
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"interactions",
|
| 327 |
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"pca",
|
| 328 |
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"pockets",
|
| 329 |
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"rgyr",
|
| 330 |
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"rmsd-pairwise",
|
| 331 |
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"rmsd-perres",
|
| 332 |
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"rmsds",
|
| 333 |
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"sasa",
|
| 334 |
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"tmscores"
|
| 335 |
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],
|
| 336 |
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"mdIndex": 0,
|
| 337 |
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|
| 338 |
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|
| 339 |
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"internalId": "6842bf3ee544b716662922a4",
|
| 340 |
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"creationDate": "2025-06-06T10:13:18.000Z",
|
| 341 |
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"identifier": "A009O"
|
| 342 |
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}
|
A009O/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A00AA/project.json
ADDED
|
@@ -0,0 +1,186 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AA",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5WUJ",
|
| 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 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"5WUJ"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"O25118",
|
| 31 |
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"O25119"
|
| 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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"FSEEEVRYEIILEKIRGTLKERPDEIAMLFKLLIKDE",
|
| 38 |
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"PKQKAQLDELSMSEKIAILLIQVGEDTTGEILRHLDIDSITEISKQIVQLNGTDKQIGAAVLEEFFAIFQSNQYINTGGLEYARELLTRTLGSEEAKKVMDKLTK"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Flagellar motor switch protein FliG"
|
| 43 |
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],
|
| 44 |
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"FRAMESTEP": 0.1,
|
| 45 |
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"TIMESTEP": 2,
|
| 46 |
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"TEMP": 310,
|
| 47 |
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"ENSEMBLE": "NPT",
|
| 48 |
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"FF": [
|
| 49 |
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"CHARMM36m"
|
| 50 |
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],
|
| 51 |
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"WAT": "TIP3P",
|
| 52 |
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"BOXTYPE": "Dodecahedron",
|
| 53 |
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"SYSTATS": 2319,
|
| 54 |
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"SYSTRES": 142,
|
| 55 |
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"PROTATS": 2319,
|
| 56 |
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"PROTRES": 142,
|
| 57 |
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"NUCLATS": 0,
|
| 58 |
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"NUCLRES": 0,
|
| 59 |
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"LIPIATS": 0,
|
| 60 |
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"LIPIRES": 0,
|
| 61 |
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"CARBATS": 0,
|
| 62 |
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"CARBRES": 0,
|
| 63 |
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"SOLVATS": 0,
|
| 64 |
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"SOLVRES": 0,
|
| 65 |
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"COUNCAT": 0,
|
| 66 |
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"COUNANI": 0,
|
| 67 |
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"COUNION": 0,
|
| 68 |
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"INTERACTIONS": [
|
| 69 |
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{
|
| 70 |
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"name": "chain A-chain B interaction",
|
| 71 |
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"agent_1": "chain A",
|
| 72 |
+
"agent_2": "chain B",
|
| 73 |
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"selection_1": "chain A",
|
| 74 |
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"selection_2": "chain B",
|
| 75 |
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"type": "protein-protein"
|
| 76 |
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}
|
| 77 |
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],
|
| 78 |
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"PBC_SELECTION": null,
|
| 79 |
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|
| 80 |
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"MEMBRANES": null,
|
| 81 |
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|
| 82 |
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|
| 83 |
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|
| 84 |
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"MULTIMERIC": null,
|
| 85 |
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"COLLECTIONS": "dynarepo",
|
| 86 |
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|
| 87 |
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|
| 88 |
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"BOXSIZEY": 8.27824,
|
| 89 |
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"BOXSIZEZ": 5.83848,
|
| 90 |
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|
| 91 |
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|
| 92 |
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"mdFrames": 5001
|
| 93 |
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},
|
| 94 |
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"mds": [
|
| 95 |
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"replica 1",
|
| 96 |
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"replica 2",
|
| 97 |
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"replica 3"
|
| 98 |
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],
|
| 99 |
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"mdref": 0,
|
| 100 |
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"files": [
|
| 101 |
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"topology.tpr",
|
| 102 |
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"screenshot.jpg",
|
| 103 |
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"trajectory.bin",
|
| 104 |
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"pca_trajectory_01.bin",
|
| 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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"structure.pdb",
|
| 115 |
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|
| 116 |
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|
| 117 |
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|
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|
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|
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|
| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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"clusters_01_screenshot_20.jpg",
|
| 157 |
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"clusters_01_screenshot_21.jpg",
|
| 158 |
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"pocket_01.pdb",
|
| 159 |
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"pocket_02.pdb",
|
| 160 |
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"pocket_03.pdb"
|
| 161 |
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],
|
| 162 |
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"analyses": [
|
| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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| 167 |
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|
| 168 |
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|
| 169 |
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|
| 170 |
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|
| 171 |
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|
| 172 |
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|
| 173 |
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|
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| 175 |
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|
| 176 |
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| 177 |
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|
| 178 |
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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": "6843098b92d1955a681df748",
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"creationDate": "2025-06-06T15:30:19.000Z",
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"identifier": "A00AA"
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}
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| 3 |
+
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A00AB/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AB",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5XQZ",
|
| 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 |
+
"5XQZ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9H8S9",
|
| 31 |
+
"Q9Y2H1"
|
| 32 |
+
],
|
| 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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"SGHMKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQHARKETEFLRLKRTRL",
|
| 38 |
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"EATLGSGNLRQAVMLPEGEDLNEWIAVNTVDFFNQINMLYGTITEFXTEASXPVMSAGPRYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDETLFPSKIGVPFPKNFMSVAKTILKRLFRVYAHIYHQHFDSVMQLQEEAHLNTSFKHFIFFVQEFNLIDRRELAPLQELIEKLG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"MOB kinase activator 1A",
|
| 43 |
+
"Serine/threonine-protein kinase 38-like",
|
| 44 |
+
"S100B binding"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 4033,
|
| 56 |
+
"SYSTRES": 245,
|
| 57 |
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"PROTATS": 4033,
|
| 58 |
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"PROTRES": 245,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
+
"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 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 9.54514,
|
| 90 |
+
"BOXSIZEY": 9.54514,
|
| 91 |
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"BOXSIZEZ": 6.73619,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 4033,
|
| 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": [
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| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
|
| 105 |
+
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|
| 106 |
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|
| 107 |
+
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"clusters_01_screenshot_21.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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],
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"analyses": [
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| 170 |
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"clusters",
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| 171 |
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"clusters-00",
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"clusters-01",
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| 173 |
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"dist-perres",
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"energies",
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| 175 |
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"fluctuation",
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| 176 |
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"hbonds",
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| 177 |
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"interactions",
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| 178 |
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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": "68430b3144794522ce78e639",
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"creationDate": "2025-06-06T15:37:21.000Z",
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"identifier": "A00AB"
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}
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A00AB/records.jsonl
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| 1 |
+
{
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| 2 |
+
"accession": "A00AI",
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| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6B12",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
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| 10 |
+
"Yasaman Karami"
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| 11 |
+
],
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| 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",
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| 19 |
+
"METHOD": "Classical MD",
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| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"6B12"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q4K3B6",
|
| 31 |
+
"Q4K3B5"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"MISDFERIREDGKVIDENMTVDQMIALGWSPCRVVEARWRWQEQLLSVVNSRGLLAIVVPDRQHLAILWNDDDTGVAATLYVVSGDRQQQIRIADQLLINGQLEAGIYSWFEQFPQVSPSIFTCMFSRQRDQAMFRVDIDASTGDIVSIQHSR",
|
| 38 |
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"AWLEGTQVKTEIVPPGRQYQMVVAKGQAEAIMQGKPAFGGFAAPEPIPSQAYARDKLVILDRFKTDVSHVITVETTAPQKIHSGITGPLENYKGGVQQVEFVGDRNLKIVGTPGVLPVE"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [],
|
| 42 |
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"FRAMESTEP": 0.1,
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| 43 |
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"TIMESTEP": 2,
|
| 44 |
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"TEMP": 310,
|
| 45 |
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"ENSEMBLE": "NPT",
|
| 46 |
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"FF": [
|
| 47 |
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"CHARMM36m"
|
| 48 |
+
],
|
| 49 |
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"WAT": "TIP3P",
|
| 50 |
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"BOXTYPE": "Dodecahedron",
|
| 51 |
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"SYSTATS": 4265,
|
| 52 |
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"SYSTRES": 272,
|
| 53 |
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| 54 |
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"PROTRES": 272,
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| 55 |
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"NUCLATS": 0,
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| 56 |
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"NUCLRES": 0,
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| 58 |
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| 59 |
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| 60 |
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"CARBRES": 0,
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| 61 |
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|
| 62 |
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|
| 63 |
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"COUNCAT": 0,
|
| 64 |
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"COUNANI": 0,
|
| 65 |
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"COUNION": 0,
|
| 66 |
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"INTERACTIONS": [
|
| 67 |
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{
|
| 68 |
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"name": "chain A-chain B interaction",
|
| 69 |
+
"agent_1": "chain A",
|
| 70 |
+
"agent_2": "chain B",
|
| 71 |
+
"selection_1": "chain A",
|
| 72 |
+
"selection_2": "chain B",
|
| 73 |
+
"type": "protein-protein"
|
| 74 |
+
}
|
| 75 |
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],
|
| 76 |
+
"PBC_SELECTION": null,
|
| 77 |
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"CHAINNAMES": null,
|
| 78 |
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"MEMBRANES": null,
|
| 79 |
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|
| 80 |
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"ORIENTATION": null,
|
| 81 |
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"PTM": [],
|
| 82 |
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"MULTIMERIC": null,
|
| 83 |
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"COLLECTIONS": "dynarepo",
|
| 84 |
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"WARNINGS": [],
|
| 85 |
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"BOXSIZEX": 9.10967,
|
| 86 |
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"BOXSIZEY": 9.10967,
|
| 87 |
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"BOXSIZEZ": 6.4598,
|
| 88 |
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"mdName": "replica 1",
|
| 89 |
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"mdAtoms": 4265,
|
| 90 |
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"mdFrames": 5001
|
| 91 |
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},
|
| 92 |
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"mds": [
|
| 93 |
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"replica 1",
|
| 94 |
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"replica 2",
|
| 95 |
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"replica 3"
|
| 96 |
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],
|
| 97 |
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"mdref": 0,
|
| 98 |
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"files": [
|
| 99 |
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"topology.tpr",
|
| 100 |
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"screenshot.jpg",
|
| 101 |
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"trajectory.bin",
|
| 102 |
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"pca_trajectory_01.bin",
|
| 103 |
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"pca_trajectory_02.bin",
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| 104 |
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"pca_trajectory_03.bin",
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| 105 |
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"pca_trajectory_04.bin",
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| 106 |
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"pca_trajectory_05.bin",
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| 107 |
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"pca_trajectory_06.bin",
|
| 108 |
+
"pca_trajectory_07.bin",
|
| 109 |
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"pca_trajectory_08.bin",
|
| 110 |
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"pca_trajectory_09.bin",
|
| 111 |
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"pca_trajectory_10.bin",
|
| 112 |
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"pca_trajectory_11.bin",
|
| 113 |
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"pca_trajectory_12.bin",
|
| 114 |
+
"pca_trajectory_13.bin",
|
| 115 |
+
"pca_trajectory_14.bin",
|
| 116 |
+
"structure.pdb",
|
| 117 |
+
"trajectory.xtc",
|
| 118 |
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"clusters_00_screenshot_00.jpg",
|
| 119 |
+
"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",
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| 122 |
+
"clusters_00_screenshot_04.jpg",
|
| 123 |
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"clusters_00_screenshot_05.jpg",
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| 124 |
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"clusters_00_screenshot_06.jpg",
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"clusters_00_screenshot_07.jpg",
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"clusters_00_screenshot_08.jpg",
|
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"clusters_00_screenshot_09.jpg",
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| 128 |
+
"clusters_00_screenshot_10.jpg",
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"clusters_00_screenshot_11.jpg",
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| 130 |
+
"clusters_00_screenshot_12.jpg",
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| 131 |
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"clusters_00_screenshot_13.jpg",
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| 132 |
+
"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",
|
| 137 |
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"clusters_00_screenshot_19.jpg",
|
| 138 |
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"clusters_01_screenshot_00.jpg",
|
| 139 |
+
"clusters_01_screenshot_01.jpg",
|
| 140 |
+
"clusters_01_screenshot_02.jpg",
|
| 141 |
+
"clusters_01_screenshot_03.jpg",
|
| 142 |
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"clusters_01_screenshot_04.jpg",
|
| 143 |
+
"clusters_01_screenshot_05.jpg",
|
| 144 |
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"clusters_01_screenshot_06.jpg",
|
| 145 |
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"clusters_01_screenshot_07.jpg",
|
| 146 |
+
"clusters_01_screenshot_08.jpg",
|
| 147 |
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"clusters_01_screenshot_09.jpg",
|
| 148 |
+
"clusters_01_screenshot_10.jpg",
|
| 149 |
+
"clusters_01_screenshot_11.jpg",
|
| 150 |
+
"clusters_01_screenshot_12.jpg",
|
| 151 |
+
"clusters_01_screenshot_13.jpg",
|
| 152 |
+
"clusters_01_screenshot_14.jpg",
|
| 153 |
+
"clusters_01_screenshot_15.jpg",
|
| 154 |
+
"clusters_01_screenshot_16.jpg",
|
| 155 |
+
"pocket_01.pdb",
|
| 156 |
+
"pocket_02.pdb",
|
| 157 |
+
"pocket_03.pdb",
|
| 158 |
+
"pocket_04.pdb",
|
| 159 |
+
"pocket_05.pdb",
|
| 160 |
+
"pocket_06.pdb",
|
| 161 |
+
"pocket_07.pdb",
|
| 162 |
+
"pocket_08.pdb"
|
| 163 |
+
],
|
| 164 |
+
"analyses": [
|
| 165 |
+
"clusters",
|
| 166 |
+
"clusters-00",
|
| 167 |
+
"clusters-01",
|
| 168 |
+
"dist-perres",
|
| 169 |
+
"energies",
|
| 170 |
+
"fluctuation",
|
| 171 |
+
"hbonds",
|
| 172 |
+
"interactions",
|
| 173 |
+
"pca",
|
| 174 |
+
"pockets",
|
| 175 |
+
"rgyr",
|
| 176 |
+
"rmsd-pairwise",
|
| 177 |
+
"rmsd-perres",
|
| 178 |
+
"rmsds",
|
| 179 |
+
"sasa",
|
| 180 |
+
"tmscores"
|
| 181 |
+
],
|
| 182 |
+
"mdIndex": 0,
|
| 183 |
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"mdNumber": 1,
|
| 184 |
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"refframe": 0,
|
| 185 |
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"internalId": "68432097b29020b346ec8086",
|
| 186 |
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"creationDate": "2025-06-06T17:08:39.000Z",
|
| 187 |
+
"identifier": "A00AI"
|
| 188 |
+
}
|
A00AI/records.jsonl
ADDED
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{"project_identifier": "A00AI", "accession": "A00AI", "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 6B12", "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": ["6B12"], "FORCED_REFERENCES": null, "REFERENCES": ["Q4K3B6", "Q4K3B5"], 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|
A00AN/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AN",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6CO2",
|
| 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 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"6CO2"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"Q96DE0",
|
| 31 |
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"Q12888"
|
| 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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"GAKRLELGEALALGSGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHLTEGPHRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGLL",
|
| 38 |
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"SFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"U8 snoRNA-decapping enzyme",
|
| 43 |
+
"Nudix hydrolase",
|
| 44 |
+
"Nudix box",
|
| 45 |
+
"TP53-binding protein 1",
|
| 46 |
+
"Tudor-like",
|
| 47 |
+
"Interaction with dimethylated histone H4"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 7509,
|
| 59 |
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"SYSTRES": 478,
|
| 60 |
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"PROTATS": 7509,
|
| 61 |
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"PROTRES": 478,
|
| 62 |
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"NUCLATS": 0,
|
| 63 |
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"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
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"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
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"SOLVRES": 0,
|
| 70 |
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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"name": "chain A-chain C interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain C",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "chain B-chain C interaction",
|
| 92 |
+
"agent_1": "chain B",
|
| 93 |
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"agent_2": "chain C",
|
| 94 |
+
"selection_1": "chain B",
|
| 95 |
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"selection_2": "chain C",
|
| 96 |
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"type": "protein-protein"
|
| 97 |
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}
|
| 98 |
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],
|
| 99 |
+
"PBC_SELECTION": null,
|
| 100 |
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"CHAINNAMES": null,
|
| 101 |
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"MEMBRANES": null,
|
| 102 |
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"CUSTOMS": null,
|
| 103 |
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"ORIENTATION": null,
|
| 104 |
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"PTM": [],
|
| 105 |
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"MULTIMERIC": null,
|
| 106 |
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"COLLECTIONS": "dynarepo",
|
| 107 |
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"WARNINGS": [],
|
| 108 |
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"BOXSIZEX": 11.6008,
|
| 109 |
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"BOXSIZEY": 11.6008,
|
| 110 |
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"BOXSIZEZ": 8.23039,
|
| 111 |
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"mdName": "replica 1",
|
| 112 |
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"mdAtoms": 7509,
|
| 113 |
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"mdFrames": 5001
|
| 114 |
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},
|
| 115 |
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"mds": [
|
| 116 |
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"replica 1",
|
| 117 |
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"replica 2",
|
| 118 |
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"replica 3"
|
| 119 |
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],
|
| 120 |
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"mdref": 0,
|
| 121 |
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"files": [
|
| 122 |
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"topology.tpr",
|
| 123 |
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"screenshot.jpg",
|
| 124 |
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"trajectory.bin",
|
| 125 |
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"pca_trajectory_01.bin",
|
| 126 |
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"pca_trajectory_02.bin",
|
| 127 |
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"pca_trajectory_03.bin",
|
| 128 |
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"pca_trajectory_04.bin",
|
| 129 |
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"pca_trajectory_05.bin",
|
| 130 |
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"pca_trajectory_06.bin",
|
| 131 |
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"pca_trajectory_07.bin",
|
| 132 |
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"pca_trajectory_08.bin",
|
| 133 |
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"pca_trajectory_09.bin",
|
| 134 |
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"pca_trajectory_10.bin",
|
| 135 |
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"pca_trajectory_11.bin",
|
| 136 |
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"structure.pdb",
|
| 137 |
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"trajectory.xtc",
|
| 138 |
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"clusters_00_screenshot_00.jpg",
|
| 139 |
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|
| 140 |
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|
| 141 |
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| 142 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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| 157 |
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| 158 |
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| 159 |
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| 160 |
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|
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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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],
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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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| 231 |
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"clusters-02",
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"clusters-03",
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "68433049b96ba5f83fd5f931",
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"creationDate": "2025-06-06T18:15:37.000Z",
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"identifier": "A00AN"
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+
}
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A00AN/records.jsonl
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A00CN/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00CN",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4V0O",
|
| 6 |
+
"DESCRIPTION": "PPIs from test53, 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 |
+
"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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"4V0O"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"A8JF99",
|
| 31 |
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"Q3V3N7"
|
| 32 |
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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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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
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| 37 |
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"VRSVWLDAFNDPVAGISAYTPCVHTCNLFGDGENRLVIADEDRKLKIWKGTQKASEHPLLDTPVAICSYPALAVAAGSHIYIYRNLRPYYKFVLPPETVITCMDVVKQAIDEPDAVSCLVVGTESGRILILNPAGTAIVKNIWVGITPAMIAVQGELDVGYRITVAGRDGKLYHIRNGELSQTIIQLEAQPVGLVRLAKHVAVGCMNDVVHAYTPTGHKSWSLYLPCHILAMQRMEVTGQRNTKALIVALSNGEVRVYNEKLLVSVHVSPNPVTALWFGRYGREDNTLLAITKSGALDIKMLPRTANLE",
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| 38 |
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"SKKVNVLVVGLDNSGKTTIIERLKPRPRQAAEVAPTVGFTVDEVEKGPLTFTVFDMSGAGRYRTLWEQYYREADAVVFVVDSADKLRMVVARDEMEHMLKHSNMRKVPILYFANKKDLPVAMPPVEIAQALGLDDIKDRPWQIVPSNGLTGEGVDKGIDWLAERLS"
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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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"BBSome complex member BBS1"
|
| 43 |
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],
|
| 44 |
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"FRAMESTEP": 0.1,
|
| 45 |
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"TIMESTEP": 2,
|
| 46 |
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"TEMP": 310,
|
| 47 |
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"ENSEMBLE": "NPT",
|
| 48 |
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"FF": [
|
| 49 |
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"CHARMM36m"
|
| 50 |
+
],
|
| 51 |
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"WAT": "TIP3P",
|
| 52 |
+
"BOXTYPE": "Dodecahedron",
|
| 53 |
+
"SYSTATS": 7453,
|
| 54 |
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"SYSTRES": 475,
|
| 55 |
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"PROTATS": 7453,
|
| 56 |
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"PROTRES": 475,
|
| 57 |
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"NUCLATS": 0,
|
| 58 |
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"NUCLRES": 0,
|
| 59 |
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"LIPIATS": 0,
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| 60 |
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"LIPIRES": 0,
|
| 61 |
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"CARBATS": 0,
|
| 62 |
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"CARBRES": 0,
|
| 63 |
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"SOLVATS": 0,
|
| 64 |
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"SOLVRES": 0,
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| 65 |
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"COUNCAT": 0,
|
| 66 |
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"COUNANI": 0,
|
| 67 |
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"COUNION": 0,
|
| 68 |
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"INTERACTIONS": [
|
| 69 |
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{
|
| 70 |
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"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 |
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"type": "protein-protein"
|
| 76 |
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}
|
| 77 |
+
],
|
| 78 |
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"PBC_SELECTION": null,
|
| 79 |
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"CHAINNAMES": null,
|
| 80 |
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"MEMBRANES": null,
|
| 81 |
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"CUSTOMS": null,
|
| 82 |
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"ORIENTATION": null,
|
| 83 |
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"PTM": [],
|
| 84 |
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"MULTIMERIC": null,
|
| 85 |
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"COLLECTIONS": "dynarepo",
|
| 86 |
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"WARNINGS": [],
|
| 87 |
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"BOXSIZEX": 11.0373,
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| 88 |
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"BOXSIZEY": 11.0373,
|
| 89 |
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"BOXSIZEZ": 7.80488,
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| 90 |
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"mdName": "replica 1",
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| 91 |
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"mdAtoms": 7453,
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| 92 |
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"mdFrames": 5001
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| 93 |
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},
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| 94 |
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"mds": [
|
| 95 |
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"replica 1",
|
| 96 |
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