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data/files/A00A1/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A00A1",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5TL7",
|
| 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 |
+
"5TL7"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q64339",
|
| 31 |
+
"P0C6X7"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"PLSILVRNERGHSNIYEVFLTQTVDTLKKKVSQREQVHEDQFWLSFEGRPMEDKELLGEYGLKPQCTVIKHLRLRG",
|
| 38 |
+
"MEVKTIKVFTTVDNTNLHTQLVDMSMTYGQQFGPTYLDGADVTKIKPHVNHEGKTFFVLPSDDTLRSEAFEYYHTLDESFLGRYMSALNHTKKWKFPQVGGLTSIKWADNNCYLSSVLLALQQLEVKFNAPALQEAYYRARAGDAANFCALILAYSNKTVGELGDVRETMTHLLQHANLESAKRVLNVVXKHXGQKTTTLTGVEAVMYMGTLSYDNLKTGVSIPXVXGRDATQYLVQQESSFVMMSAPPAEYKLQQGTFLCANEYTGNYQCGHYTHITAKETLYRIDGAHLTKMSEYKGPVTDVFYKETSYTTTIK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ubiquitin-like protein ISG15",
|
| 43 |
+
"Ubiquitin-like 2",
|
| 44 |
+
"Involved in the ligation of specific target proteins",
|
| 45 |
+
"LRLRGG",
|
| 46 |
+
"Interacts with activating enzyme",
|
| 47 |
+
"Papain-like protease nsp3",
|
| 48 |
+
"Ubiquitin-like 2",
|
| 49 |
+
"Peptidase C16"
|
| 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": 6202,
|
| 61 |
+
"SYSTRES": 392,
|
| 62 |
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"PROTATS": 6202,
|
| 63 |
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"PROTRES": 392,
|
| 64 |
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"NUCLATS": 0,
|
| 65 |
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"NUCLRES": 0,
|
| 66 |
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"LIPIATS": 0,
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| 67 |
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"LIPIRES": 0,
|
| 68 |
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"CARBATS": 0,
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| 69 |
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"CARBRES": 0,
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| 70 |
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"SOLVATS": 0,
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| 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 |
+
"INTERACTIONS": [
|
| 76 |
+
{
|
| 77 |
+
"name": "chain A-chain B interaction",
|
| 78 |
+
"agent_1": "chain A",
|
| 79 |
+
"agent_2": "chain B",
|
| 80 |
+
"selection_1": "chain A",
|
| 81 |
+
"selection_2": "chain B",
|
| 82 |
+
"type": "protein-protein"
|
| 83 |
+
}
|
| 84 |
+
],
|
| 85 |
+
"PBC_SELECTION": null,
|
| 86 |
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"CHAINNAMES": null,
|
| 87 |
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"MEMBRANES": null,
|
| 88 |
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"CUSTOMS": null,
|
| 89 |
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"ORIENTATION": null,
|
| 90 |
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"PTM": [],
|
| 91 |
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"MULTIMERIC": null,
|
| 92 |
+
"COLLECTIONS": "dynarepo",
|
| 93 |
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"WARNINGS": [],
|
| 94 |
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"BOXSIZEX": 10.9484,
|
| 95 |
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"BOXSIZEY": 10.9484,
|
| 96 |
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"BOXSIZEZ": 7.75558,
|
| 97 |
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"mdName": "replica 1",
|
| 98 |
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"mdAtoms": 6202,
|
| 99 |
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"mdFrames": 5001
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| 100 |
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},
|
| 101 |
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"mds": [
|
| 102 |
+
"replica 1",
|
| 103 |
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"replica 2",
|
| 104 |
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"replica 3"
|
| 105 |
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],
|
| 106 |
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"mdref": 0,
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| 107 |
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"files": [
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| 108 |
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"topology.tpr",
|
| 109 |
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"screenshot.jpg",
|
| 110 |
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"trajectory.bin",
|
| 111 |
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"pca_trajectory_01.bin",
|
| 112 |
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"pca_trajectory_02.bin",
|
| 113 |
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"pca_trajectory_03.bin",
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| 114 |
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"pca_trajectory_04.bin",
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| 115 |
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"pca_trajectory_05.bin",
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| 116 |
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"pca_trajectory_06.bin",
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| 117 |
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"pca_trajectory_07.bin",
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| 118 |
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"pca_trajectory_08.bin",
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| 119 |
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"pca_trajectory_09.bin",
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| 120 |
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"pca_trajectory_10.bin",
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| 121 |
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"pca_trajectory_11.bin",
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| 122 |
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| 123 |
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| 124 |
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| 125 |
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"pca_trajectory_15.bin",
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| 126 |
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"pca_trajectory_16.bin",
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| 127 |
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"pca_trajectory_17.bin",
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| 128 |
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"structure.pdb",
|
| 129 |
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"trajectory.xtc",
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| 130 |
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"clusters_00_screenshot_00.jpg",
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| 131 |
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"clusters_00_screenshot_01.jpg",
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| 132 |
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"clusters_00_screenshot_02.jpg",
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| 133 |
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"clusters_00_screenshot_03.jpg",
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| 134 |
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"clusters_00_screenshot_04.jpg",
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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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"clusters_00_screenshot_10.jpg",
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| 141 |
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| 142 |
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| 143 |
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| 144 |
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"clusters_00_screenshot_14.jpg",
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| 145 |
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"clusters_00_screenshot_15.jpg",
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| 146 |
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"clusters_00_screenshot_16.jpg",
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| 147 |
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"clusters_00_screenshot_17.jpg",
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| 148 |
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"clusters_01_screenshot_00.jpg",
|
| 149 |
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"clusters_01_screenshot_01.jpg",
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| 150 |
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"clusters_01_screenshot_02.jpg",
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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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"clusters_01_screenshot_09.jpg",
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| 158 |
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"clusters_01_screenshot_10.jpg",
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| 159 |
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"clusters_01_screenshot_11.jpg",
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| 160 |
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"clusters_01_screenshot_12.jpg",
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| 161 |
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"clusters_01_screenshot_13.jpg",
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| 162 |
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"clusters_01_screenshot_14.jpg",
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| 163 |
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"clusters_01_screenshot_15.jpg",
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| 164 |
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"clusters_01_screenshot_16.jpg",
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| 165 |
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"clusters_01_screenshot_17.jpg",
|
| 166 |
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"clusters_01_screenshot_18.jpg",
|
| 167 |
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"pocket_01.pdb",
|
| 168 |
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"pocket_02.pdb",
|
| 169 |
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"pocket_03.pdb",
|
| 170 |
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"pocket_04.pdb",
|
| 171 |
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"pocket_05.pdb",
|
| 172 |
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"pocket_06.pdb",
|
| 173 |
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"pocket_07.pdb",
|
| 174 |
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"pocket_08.pdb",
|
| 175 |
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"pocket_09.pdb",
|
| 176 |
+
"pocket_10.pdb"
|
| 177 |
+
],
|
| 178 |
+
"analyses": [
|
| 179 |
+
"clusters",
|
| 180 |
+
"clusters-00",
|
| 181 |
+
"clusters-01",
|
| 182 |
+
"dist-perres",
|
| 183 |
+
"energies",
|
| 184 |
+
"fluctuation",
|
| 185 |
+
"hbonds",
|
| 186 |
+
"interactions",
|
| 187 |
+
"pca",
|
| 188 |
+
"pockets",
|
| 189 |
+
"rgyr",
|
| 190 |
+
"rmsd-pairwise",
|
| 191 |
+
"rmsd-perres",
|
| 192 |
+
"rmsds",
|
| 193 |
+
"sasa",
|
| 194 |
+
"tmscores"
|
| 195 |
+
],
|
| 196 |
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"mdIndex": 0,
|
| 197 |
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"mdNumber": 1,
|
| 198 |
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"refframe": 0,
|
| 199 |
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"internalId": "6842e96ed94c0dd189dafb79",
|
| 200 |
+
"creationDate": "2025-06-06T13:13:18.000Z",
|
| 201 |
+
"identifier": "A00A1"
|
| 202 |
+
}
|
data/files/A00A1/records.jsonl
ADDED
|
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| 1 |
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| 1 |
+
{
|
| 2 |
+
"accession": "A00A2",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5TVQ",
|
| 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 |
+
"5TVQ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9JJX7",
|
| 31 |
+
"P61957"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"LEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL",
|
| 38 |
+
"NNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQ"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tyrosyl-DNA phosphodiesterase 2",
|
| 43 |
+
"Interaction with 5' end of substrate DNA",
|
| 44 |
+
"Small ubiquitin-related modifier 2",
|
| 45 |
+
"Ubiquitin-like"
|
| 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": 5219,
|
| 57 |
+
"SYSTRES": 328,
|
| 58 |
+
"PROTATS": 5219,
|
| 59 |
+
"PROTRES": 328,
|
| 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": 9.82447,
|
| 91 |
+
"BOXSIZEY": 9.82447,
|
| 92 |
+
"BOXSIZEZ": 6.94483,
|
| 93 |
+
"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 5219,
|
| 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 |
+
"pca_trajectory_05.bin",
|
| 112 |
+
"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
+
"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"structure.pdb",
|
| 120 |
+
"trajectory.xtc",
|
| 121 |
+
"clusters_00_screenshot_00.jpg",
|
| 122 |
+
"clusters_00_screenshot_01.jpg",
|
| 123 |
+
"clusters_00_screenshot_02.jpg",
|
| 124 |
+
"clusters_00_screenshot_03.jpg",
|
| 125 |
+
"clusters_00_screenshot_04.jpg",
|
| 126 |
+
"clusters_00_screenshot_05.jpg",
|
| 127 |
+
"clusters_00_screenshot_06.jpg",
|
| 128 |
+
"clusters_00_screenshot_07.jpg",
|
| 129 |
+
"clusters_00_screenshot_08.jpg",
|
| 130 |
+
"clusters_00_screenshot_09.jpg",
|
| 131 |
+
"clusters_00_screenshot_10.jpg",
|
| 132 |
+
"clusters_00_screenshot_11.jpg",
|
| 133 |
+
"clusters_00_screenshot_12.jpg",
|
| 134 |
+
"clusters_00_screenshot_13.jpg",
|
| 135 |
+
"clusters_00_screenshot_14.jpg",
|
| 136 |
+
"clusters_00_screenshot_15.jpg",
|
| 137 |
+
"clusters_00_screenshot_16.jpg",
|
| 138 |
+
"clusters_00_screenshot_17.jpg",
|
| 139 |
+
"clusters_00_screenshot_18.jpg",
|
| 140 |
+
"clusters_00_screenshot_19.jpg",
|
| 141 |
+
"clusters_01_screenshot_00.jpg",
|
| 142 |
+
"clusters_01_screenshot_01.jpg",
|
| 143 |
+
"clusters_01_screenshot_02.jpg",
|
| 144 |
+
"clusters_01_screenshot_03.jpg",
|
| 145 |
+
"clusters_01_screenshot_04.jpg",
|
| 146 |
+
"clusters_01_screenshot_05.jpg",
|
| 147 |
+
"clusters_01_screenshot_06.jpg",
|
| 148 |
+
"clusters_01_screenshot_07.jpg",
|
| 149 |
+
"clusters_01_screenshot_08.jpg",
|
| 150 |
+
"clusters_01_screenshot_09.jpg",
|
| 151 |
+
"clusters_01_screenshot_10.jpg",
|
| 152 |
+
"clusters_01_screenshot_11.jpg",
|
| 153 |
+
"clusters_01_screenshot_12.jpg",
|
| 154 |
+
"clusters_01_screenshot_13.jpg",
|
| 155 |
+
"clusters_01_screenshot_14.jpg",
|
| 156 |
+
"clusters_01_screenshot_15.jpg",
|
| 157 |
+
"clusters_01_screenshot_16.jpg",
|
| 158 |
+
"clusters_01_screenshot_17.jpg",
|
| 159 |
+
"clusters_01_screenshot_18.jpg",
|
| 160 |
+
"pocket_01.pdb",
|
| 161 |
+
"pocket_02.pdb",
|
| 162 |
+
"pocket_03.pdb",
|
| 163 |
+
"pocket_04.pdb",
|
| 164 |
+
"pocket_05.pdb",
|
| 165 |
+
"pocket_06.pdb",
|
| 166 |
+
"pocket_07.pdb"
|
| 167 |
+
],
|
| 168 |
+
"analyses": [
|
| 169 |
+
"clusters",
|
| 170 |
+
"clusters-00",
|
| 171 |
+
"clusters-01",
|
| 172 |
+
"dist-perres",
|
| 173 |
+
"energies",
|
| 174 |
+
"fluctuation",
|
| 175 |
+
"hbonds",
|
| 176 |
+
"interactions",
|
| 177 |
+
"pca",
|
| 178 |
+
"pockets",
|
| 179 |
+
"rgyr",
|
| 180 |
+
"rmsd-pairwise",
|
| 181 |
+
"rmsd-perres",
|
| 182 |
+
"rmsds",
|
| 183 |
+
"sasa",
|
| 184 |
+
"tmscores"
|
| 185 |
+
],
|
| 186 |
+
"mdIndex": 0,
|
| 187 |
+
"mdNumber": 1,
|
| 188 |
+
"refframe": 1,
|
| 189 |
+
"internalId": "6842ebd05d732e6d8f2e7a9d",
|
| 190 |
+
"creationDate": "2025-06-06T13:23:28.000Z",
|
| 191 |
+
"identifier": "A00A2"
|
| 192 |
+
}
|
data/files/A00A2/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
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|
|
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|
| 1 |
+
{"project_identifier": "A00A2", "accession": "A00A2", "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 5TVQ", "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": ["5TVQ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9JJX7", "P61957"], 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data/files/A00A3/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00A3",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5UK5",
|
| 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 |
+
"5UK5"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q07008",
|
| 31 |
+
"Q63722"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ECQLMPNACQNGGTCHNSHGGYNCVCVNGWTGEDCSENIDDCASAACFQGATCHDRVASFYCECPHGRTGLLCHLNDACISNPCNEGSNCDTNPVNGKAICTCPSGYTGPACSQDVDECALGANPCEHAGKCLNTLGSFECQCLQGYTGPRCEIDVNECISNPCQNDATCLDQIGEFQCICMPGYEGVYCESGR",
|
| 38 |
+
"ADPRLGQFELEILSMQNVNGELQNGNCCGGARNPGDRKCTGDECNTYFKVCLKEYQSRVRAGGPCSFGSGSTPVIGGNTFNLKASRGNDRNRIVLPFSFAWPRSYTLLVEAWDSSNDTIQPDSIIEKASHSGMINPSRQWQTLKQNTGIAHFEYRIRVTCDDHYYGFGCNKFCRPRDDFFGHYACDQNGNKTCMEGWMGPECNKAICRQGCSPKHGSCKLPGDCRCQYGWQGLYCDKCIPHPGCVHGTCNEPWQCLCETNWGGQLCDKDLNYCGTHQPCLNRGTCSNTGPDKYQCSCPEGYSGPNCEA"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Neurogenic locus notch homolog protein 1",
|
| 43 |
+
"EGF-like 8; calcium-binding",
|
| 44 |
+
"EGF-like 9; calcium-binding",
|
| 45 |
+
"EGF-like 10",
|
| 46 |
+
"EGF-like 11; calcium-binding",
|
| 47 |
+
"EGF-like 12; calcium-binding",
|
| 48 |
+
"EGF-like 13; calcium-binding",
|
| 49 |
+
"Interaction with DLL4",
|
| 50 |
+
"Protein jagged-1",
|
| 51 |
+
"DSL",
|
| 52 |
+
"EGF-like 1",
|
| 53 |
+
"EGF-like 2; atypical",
|
| 54 |
+
"EGF-like 3",
|
| 55 |
+
"Important for interaction with NOTCH1"
|
| 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": 7187,
|
| 67 |
+
"SYSTRES": 502,
|
| 68 |
+
"PROTATS": 7187,
|
| 69 |
+
"PROTRES": 502,
|
| 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": "chain A-chain B interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain B",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain B",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
}
|
| 90 |
+
],
|
| 91 |
+
"PBC_SELECTION": null,
|
| 92 |
+
"CHAINNAMES": null,
|
| 93 |
+
"MEMBRANES": null,
|
| 94 |
+
"CUSTOMS": null,
|
| 95 |
+
"ORIENTATION": null,
|
| 96 |
+
"PTM": [],
|
| 97 |
+
"MULTIMERIC": null,
|
| 98 |
+
"COLLECTIONS": "dynarepo",
|
| 99 |
+
"WARNINGS": [],
|
| 100 |
+
"BOXSIZEX": 18.3155,
|
| 101 |
+
"BOXSIZEY": 18.3155,
|
| 102 |
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|
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|
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|
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|
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|
| 168 |
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|
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"clusters_01_screenshot_19.jpg",
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| 170 |
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"pocket_01.pdb"
|
| 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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"dist-perres",
|
| 177 |
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|
| 178 |
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"fluctuation",
|
| 179 |
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"hbonds",
|
| 180 |
+
"interactions",
|
| 181 |
+
"pca",
|
| 182 |
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"pockets",
|
| 183 |
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"rgyr",
|
| 184 |
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"rmsd-pairwise",
|
| 185 |
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"rmsd-perres",
|
| 186 |
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"rmsds",
|
| 187 |
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"sasa",
|
| 188 |
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|
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|
| 195 |
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|
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data/files/A00A3/records.jsonl
ADDED
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data/files/A00A4/project.json
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{
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"accession": "A00A4",
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"published": true,
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"metadata": {
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"NAME": "Dynarepo 5UN7",
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
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"AUTHORS": [
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"Omid Mokhtari",
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"Hamed Khakzad",
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+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
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|
| 13 |
+
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|
| 14 |
+
],
|
| 15 |
+
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|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
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|
| 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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|
| 23 |
+
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|
| 24 |
+
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|
| 25 |
+
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|
| 26 |
+
"5UN7"
|
| 27 |
+
],
|
| 28 |
+
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|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9NUX5",
|
| 31 |
+
"Q96AP0"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EHQGALVCLAESCLTLEGPCTAPPVTHWAASRCKATGEAVYTVPSSMLCISENDQLILSSL",
|
| 38 |
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"LSATILTDHQYLERTPLCAILKQKAPQQYRIRAKLRSYKPRRLFQSVKLHXPKXHLLQEVPHEGDLDIIFQDGATKTPDVKLQNTSLYDSKIWTTKNQKGRKVAVHFVKNNGILPLSNECLLLIEGGTLSEICKLSNKFNSVIPVRSGHEDLELLDLSAPFLIQGTIHHYGXKQXSSLRSIQNLNSLVDKTSWIPSSVAEALGIVPLQYVFVMTFTLDDGTGVLEAYLMDSDKFFQIPASEVLMDDDLQKSVDMIMDMFCPPGIKIDAYPWLECFIKSYNVTNGTDNQICYQIFDTTVAEDV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Protection of telomeres protein 1",
|
| 43 |
+
"Adrenocortical dysplasia protein homolog",
|
| 44 |
+
"Interaction with POT1"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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"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 |
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|
| 82 |
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|
| 83 |
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|
| 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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|
| 90 |
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|
| 91 |
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|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 5684,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"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 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"structure.pdb",
|
| 118 |
+
"trajectory.xtc",
|
| 119 |
+
"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
+
"clusters_00_screenshot_02.jpg",
|
| 122 |
+
"clusters_00_screenshot_03.jpg",
|
| 123 |
+
"clusters_00_screenshot_04.jpg",
|
| 124 |
+
"clusters_00_screenshot_05.jpg",
|
| 125 |
+
"clusters_00_screenshot_06.jpg",
|
| 126 |
+
"clusters_00_screenshot_07.jpg",
|
| 127 |
+
"clusters_00_screenshot_08.jpg",
|
| 128 |
+
"clusters_00_screenshot_09.jpg",
|
| 129 |
+
"clusters_00_screenshot_10.jpg",
|
| 130 |
+
"clusters_00_screenshot_11.jpg",
|
| 131 |
+
"clusters_00_screenshot_12.jpg",
|
| 132 |
+
"clusters_00_screenshot_13.jpg",
|
| 133 |
+
"clusters_00_screenshot_14.jpg",
|
| 134 |
+
"clusters_00_screenshot_15.jpg",
|
| 135 |
+
"clusters_00_screenshot_16.jpg",
|
| 136 |
+
"clusters_00_screenshot_17.jpg",
|
| 137 |
+
"clusters_00_screenshot_18.jpg",
|
| 138 |
+
"clusters_00_screenshot_19.jpg",
|
| 139 |
+
"clusters_01_screenshot_00.jpg",
|
| 140 |
+
"clusters_01_screenshot_01.jpg",
|
| 141 |
+
"clusters_01_screenshot_02.jpg",
|
| 142 |
+
"clusters_01_screenshot_03.jpg",
|
| 143 |
+
"clusters_01_screenshot_04.jpg",
|
| 144 |
+
"clusters_01_screenshot_05.jpg",
|
| 145 |
+
"clusters_01_screenshot_06.jpg",
|
| 146 |
+
"clusters_01_screenshot_07.jpg",
|
| 147 |
+
"clusters_01_screenshot_08.jpg",
|
| 148 |
+
"clusters_01_screenshot_09.jpg",
|
| 149 |
+
"clusters_01_screenshot_10.jpg",
|
| 150 |
+
"clusters_01_screenshot_11.jpg",
|
| 151 |
+
"clusters_01_screenshot_12.jpg",
|
| 152 |
+
"clusters_01_screenshot_13.jpg",
|
| 153 |
+
"clusters_01_screenshot_14.jpg",
|
| 154 |
+
"clusters_01_screenshot_15.jpg",
|
| 155 |
+
"clusters_01_screenshot_16.jpg",
|
| 156 |
+
"clusters_01_screenshot_17.jpg",
|
| 157 |
+
"clusters_01_screenshot_18.jpg",
|
| 158 |
+
"clusters_01_screenshot_19.jpg",
|
| 159 |
+
"pocket_01.pdb",
|
| 160 |
+
"pocket_02.pdb",
|
| 161 |
+
"pocket_03.pdb",
|
| 162 |
+
"pocket_04.pdb",
|
| 163 |
+
"pocket_05.pdb",
|
| 164 |
+
"pocket_06.pdb",
|
| 165 |
+
"pocket_07.pdb",
|
| 166 |
+
"pocket_08.pdb",
|
| 167 |
+
"pocket_09.pdb",
|
| 168 |
+
"pocket_10.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 |
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"mdIndex": 0,
|
| 189 |
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"mdNumber": 1,
|
| 190 |
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"refframe": 1,
|
| 191 |
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"internalId": "6842f13a58ce3c30d15e8ff9",
|
| 192 |
+
"creationDate": "2025-06-06T13:46:34.000Z",
|
| 193 |
+
"identifier": "A00A4"
|
| 194 |
+
}
|
data/files/A00A4/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00A4", "accession": "A00A4", "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 5UN7", "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": ["5UN7"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NUX5", "Q96AP0"], 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data/files/A00A5/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00A5",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5UPK",
|
| 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 |
+
"5UPK"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O96013",
|
| 31 |
+
"P60953"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQN",
|
| 38 |
+
"KRKKRVEISAPSNFEHRVHTGFDQHEQKFTGLPRQWQSLI",
|
| 39 |
+
"QTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGLEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQRGLKNVFDEAILAALLE"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Serine/threonine-protein kinase PAK 4",
|
| 44 |
+
"CRIB",
|
| 45 |
+
"Protein kinase",
|
| 46 |
+
"Linker",
|
| 47 |
+
"Disordered",
|
| 48 |
+
"GEF-interaction domain (GID)",
|
| 49 |
+
"Cell division control protein 42 homolog",
|
| 50 |
+
"Effector region"
|
| 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": 8105,
|
| 62 |
+
"SYSTRES": 507,
|
| 63 |
+
"PROTATS": 8105,
|
| 64 |
+
"PROTRES": 507,
|
| 65 |
+
"NUCLATS": 0,
|
| 66 |
+
"NUCLRES": 0,
|
| 67 |
+
"LIPIATS": 0,
|
| 68 |
+
"LIPIRES": 0,
|
| 69 |
+
"CARBATS": 0,
|
| 70 |
+
"CARBRES": 0,
|
| 71 |
+
"SOLVATS": 0,
|
| 72 |
+
"SOLVRES": 0,
|
| 73 |
+
"COUNCAT": 0,
|
| 74 |
+
"COUNANI": 0,
|
| 75 |
+
"COUNION": 0,
|
| 76 |
+
"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
},
|
| 85 |
+
{
|
| 86 |
+
"name": "chain A-chain C interaction",
|
| 87 |
+
"agent_1": "chain A",
|
| 88 |
+
"agent_2": "chain C",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain C",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "chain B-chain C interaction",
|
| 95 |
+
"agent_1": "chain B",
|
| 96 |
+
"agent_2": "chain C",
|
| 97 |
+
"selection_1": "chain B",
|
| 98 |
+
"selection_2": "chain C",
|
| 99 |
+
"type": "protein-protein"
|
| 100 |
+
}
|
| 101 |
+
],
|
| 102 |
+
"PBC_SELECTION": null,
|
| 103 |
+
"CHAINNAMES": null,
|
| 104 |
+
"MEMBRANES": null,
|
| 105 |
+
"CUSTOMS": null,
|
| 106 |
+
"ORIENTATION": null,
|
| 107 |
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"PTM": [],
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| 219 |
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|
| 221 |
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|
| 222 |
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"pocket_01.pdb",
|
| 223 |
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"pocket_02.pdb",
|
| 224 |
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"pocket_03.pdb",
|
| 225 |
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"pocket_04.pdb",
|
| 226 |
+
"pocket_05.pdb",
|
| 227 |
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"pocket_06.pdb",
|
| 228 |
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"pocket_07.pdb",
|
| 229 |
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"pocket_08.pdb"
|
| 230 |
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|
| 231 |
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|
| 232 |
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|
| 233 |
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|
| 234 |
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|
| 235 |
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"clusters-02",
|
| 236 |
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"clusters-03",
|
| 237 |
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|
| 238 |
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|
| 239 |
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"fluctuation",
|
| 240 |
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"hbonds",
|
| 241 |
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"interactions",
|
| 242 |
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"pca",
|
| 243 |
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"pockets",
|
| 244 |
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"rgyr",
|
| 245 |
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"rmsd-pairwise",
|
| 246 |
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"rmsd-perres",
|
| 247 |
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"rmsds",
|
| 248 |
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"sasa",
|
| 249 |
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"tmscores"
|
| 250 |
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|
| 251 |
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|
| 256 |
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"identifier": "A00A5"
|
| 257 |
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}
|
data/files/A00A5/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
|
|
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|
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|
|
| 1 |
+
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data/files/A00A6/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A00A6",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5UZU",
|
| 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 |
+
"5UZU"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q2G0X2",
|
| 31 |
+
"P05164"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"KVYSQNGLVLHDDANFLEHELSYIDVLLDKNADQATKDNLRSYFADKGLHSIKDIINKAKQDGFDVSK",
|
| 38 |
+
"CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAARASFVTGVNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREA"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"89 kDa myeloperoxidase",
|
| 43 |
+
"84 kDa myeloperoxidase",
|
| 44 |
+
"Myeloperoxidase",
|
| 45 |
+
"Myeloperoxidase light chain",
|
| 46 |
+
"Myeloperoxidase heavy chain",
|
| 47 |
+
"Transition state stabilizer"
|
| 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": 10291,
|
| 59 |
+
"SYSTRES": 646,
|
| 60 |
+
"PROTATS": 10291,
|
| 61 |
+
"PROTRES": 646,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
}
|
| 82 |
+
],
|
| 83 |
+
"PBC_SELECTION": null,
|
| 84 |
+
"CHAINNAMES": null,
|
| 85 |
+
"MEMBRANES": null,
|
| 86 |
+
"CUSTOMS": null,
|
| 87 |
+
"ORIENTATION": null,
|
| 88 |
+
"PTM": [],
|
| 89 |
+
"MULTIMERIC": null,
|
| 90 |
+
"COLLECTIONS": "dynarepo",
|
| 91 |
+
"WARNINGS": [],
|
| 92 |
+
"BOXSIZEX": 11.0623,
|
| 93 |
+
"BOXSIZEY": 11.0623,
|
| 94 |
+
"BOXSIZEZ": 7.85544,
|
| 95 |
+
"mdName": "replica 1",
|
| 96 |
+
"mdAtoms": 10291,
|
| 97 |
+
"mdFrames": 5001
|
| 98 |
+
},
|
| 99 |
+
"mds": [
|
| 100 |
+
"replica 1",
|
| 101 |
+
"replica 2",
|
| 102 |
+
"replica 3"
|
| 103 |
+
],
|
| 104 |
+
"mdref": 0,
|
| 105 |
+
"files": [
|
| 106 |
+
"topology.tpr",
|
| 107 |
+
"screenshot.jpg",
|
| 108 |
+
"trajectory.bin",
|
| 109 |
+
"pca_trajectory_01.bin",
|
| 110 |
+
"pca_trajectory_02.bin",
|
| 111 |
+
"pca_trajectory_03.bin",
|
| 112 |
+
"pca_trajectory_04.bin",
|
| 113 |
+
"pca_trajectory_05.bin",
|
| 114 |
+
"pca_trajectory_06.bin",
|
| 115 |
+
"pca_trajectory_07.bin",
|
| 116 |
+
"pca_trajectory_08.bin",
|
| 117 |
+
"pca_trajectory_09.bin",
|
| 118 |
+
"pca_trajectory_10.bin",
|
| 119 |
+
"pca_trajectory_11.bin",
|
| 120 |
+
"pca_trajectory_12.bin",
|
| 121 |
+
"pca_trajectory_13.bin",
|
| 122 |
+
"pca_trajectory_14.bin",
|
| 123 |
+
"pca_trajectory_15.bin",
|
| 124 |
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"pca_trajectory_16.bin",
|
| 125 |
+
"pca_trajectory_17.bin",
|
| 126 |
+
"pca_trajectory_18.bin",
|
| 127 |
+
"structure.pdb",
|
| 128 |
+
"trajectory.xtc",
|
| 129 |
+
"clusters_00_screenshot_00.jpg",
|
| 130 |
+
"clusters_00_screenshot_01.jpg",
|
| 131 |
+
"clusters_00_screenshot_02.jpg",
|
| 132 |
+
"clusters_00_screenshot_03.jpg",
|
| 133 |
+
"clusters_00_screenshot_04.jpg",
|
| 134 |
+
"clusters_00_screenshot_05.jpg",
|
| 135 |
+
"clusters_00_screenshot_06.jpg",
|
| 136 |
+
"clusters_00_screenshot_07.jpg",
|
| 137 |
+
"clusters_00_screenshot_08.jpg",
|
| 138 |
+
"clusters_00_screenshot_09.jpg",
|
| 139 |
+
"clusters_00_screenshot_10.jpg",
|
| 140 |
+
"clusters_00_screenshot_11.jpg",
|
| 141 |
+
"clusters_00_screenshot_12.jpg",
|
| 142 |
+
"clusters_00_screenshot_13.jpg",
|
| 143 |
+
"clusters_00_screenshot_14.jpg",
|
| 144 |
+
"clusters_00_screenshot_15.jpg",
|
| 145 |
+
"clusters_00_screenshot_16.jpg",
|
| 146 |
+
"clusters_00_screenshot_17.jpg",
|
| 147 |
+
"clusters_01_screenshot_00.jpg",
|
| 148 |
+
"clusters_01_screenshot_01.jpg",
|
| 149 |
+
"clusters_01_screenshot_02.jpg",
|
| 150 |
+
"clusters_01_screenshot_03.jpg",
|
| 151 |
+
"clusters_01_screenshot_04.jpg",
|
| 152 |
+
"clusters_01_screenshot_05.jpg",
|
| 153 |
+
"clusters_01_screenshot_06.jpg",
|
| 154 |
+
"clusters_01_screenshot_07.jpg",
|
| 155 |
+
"clusters_01_screenshot_08.jpg",
|
| 156 |
+
"clusters_01_screenshot_09.jpg",
|
| 157 |
+
"clusters_01_screenshot_10.jpg",
|
| 158 |
+
"clusters_01_screenshot_11.jpg",
|
| 159 |
+
"clusters_01_screenshot_12.jpg",
|
| 160 |
+
"clusters_01_screenshot_13.jpg",
|
| 161 |
+
"clusters_01_screenshot_14.jpg",
|
| 162 |
+
"clusters_01_screenshot_15.jpg",
|
| 163 |
+
"clusters_01_screenshot_16.jpg",
|
| 164 |
+
"clusters_01_screenshot_17.jpg",
|
| 165 |
+
"clusters_01_screenshot_18.jpg",
|
| 166 |
+
"pocket_01.pdb",
|
| 167 |
+
"pocket_02.pdb",
|
| 168 |
+
"pocket_03.pdb",
|
| 169 |
+
"pocket_04.pdb",
|
| 170 |
+
"pocket_05.pdb",
|
| 171 |
+
"pocket_06.pdb",
|
| 172 |
+
"pocket_07.pdb",
|
| 173 |
+
"pocket_08.pdb",
|
| 174 |
+
"pocket_09.pdb",
|
| 175 |
+
"pocket_10.pdb"
|
| 176 |
+
],
|
| 177 |
+
"analyses": [
|
| 178 |
+
"clusters",
|
| 179 |
+
"clusters-00",
|
| 180 |
+
"clusters-01",
|
| 181 |
+
"dist-perres",
|
| 182 |
+
"energies",
|
| 183 |
+
"fluctuation",
|
| 184 |
+
"hbonds",
|
| 185 |
+
"interactions",
|
| 186 |
+
"pca",
|
| 187 |
+
"pockets",
|
| 188 |
+
"rgyr",
|
| 189 |
+
"rmsd-pairwise",
|
| 190 |
+
"rmsd-perres",
|
| 191 |
+
"rmsds",
|
| 192 |
+
"sasa",
|
| 193 |
+
"tmscores"
|
| 194 |
+
],
|
| 195 |
+
"mdIndex": 0,
|
| 196 |
+
"mdNumber": 1,
|
| 197 |
+
"refframe": 0,
|
| 198 |
+
"internalId": "6842f79dbc8aefbb1814e8d8",
|
| 199 |
+
"creationDate": "2025-06-06T14:13:49.000Z",
|
| 200 |
+
"identifier": "A00A6"
|
| 201 |
+
}
|
data/files/A00A6/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
| 1 |
+
{"project_identifier": "A00A6", "accession": "A00A6", "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 5UZU", "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": ["5UZU"], "FORCED_REFERENCES": null, "REFERENCES": ["Q2G0X2", "P05164"], 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data/files/A00A7/project.json
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| 1 |
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 9 |
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| 11 |
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| 12 |
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| 14 |
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| 16 |
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| 17 |
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|
| 286 |
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|
| 287 |
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|
| 288 |
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"clusters_05_screenshot_18.jpg",
|
| 289 |
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"clusters_05_screenshot_19.jpg",
|
| 290 |
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"clusters_05_screenshot_20.jpg",
|
| 291 |
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|
| 292 |
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|
| 293 |
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|
| 294 |
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"clusters_06_screenshot_03.jpg",
|
| 295 |
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|
| 296 |
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|
| 297 |
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|
| 298 |
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|
| 299 |
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"clusters_06_screenshot_08.jpg",
|
| 300 |
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"clusters_06_screenshot_09.jpg",
|
| 301 |
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"clusters_06_screenshot_10.jpg",
|
| 302 |
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"clusters_06_screenshot_11.jpg",
|
| 303 |
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"clusters_06_screenshot_12.jpg",
|
| 304 |
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"clusters_06_screenshot_13.jpg",
|
| 305 |
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"clusters_06_screenshot_14.jpg",
|
| 306 |
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"clusters_06_screenshot_15.jpg",
|
| 307 |
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"clusters_06_screenshot_16.jpg",
|
| 308 |
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"clusters_06_screenshot_17.jpg",
|
| 309 |
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"clusters_06_screenshot_18.jpg",
|
| 310 |
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"clusters_06_screenshot_19.jpg",
|
| 311 |
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"clusters_06_screenshot_20.jpg",
|
| 312 |
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"pocket_01.pdb",
|
| 313 |
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"pocket_02.pdb",
|
| 314 |
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"pocket_03.pdb",
|
| 315 |
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"pocket_04.pdb",
|
| 316 |
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"pocket_05.pdb"
|
| 317 |
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],
|
| 318 |
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"analyses": [
|
| 319 |
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"clusters",
|
| 320 |
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"clusters-00",
|
| 321 |
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"clusters-01",
|
| 322 |
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"clusters-02",
|
| 323 |
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"clusters-03",
|
| 324 |
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"clusters-04",
|
| 325 |
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"clusters-05",
|
| 326 |
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"clusters-06",
|
| 327 |
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"dist-perres",
|
| 328 |
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"energies",
|
| 329 |
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"fluctuation",
|
| 330 |
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"hbonds",
|
| 331 |
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"interactions",
|
| 332 |
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"pca",
|
| 333 |
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"pockets",
|
| 334 |
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"rgyr",
|
| 335 |
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"rmsd-pairwise",
|
| 336 |
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"rmsd-perres",
|
| 337 |
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"rmsds",
|
| 338 |
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"sasa",
|
| 339 |
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"tmscores"
|
| 340 |
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|
| 341 |
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|
| 342 |
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| 344 |
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|
| 346 |
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"identifier": "A00A7"
|
| 347 |
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}
|
data/files/A00A7/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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|
data/files/A00A8/project.json
ADDED
|
@@ -0,0 +1,259 @@
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|
| 1 |
+
{
|
| 2 |
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"accession": "A00A8",
|
| 3 |
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"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
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"NAME": "Dynarepo 5WB7",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 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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"5WB7"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P00533",
|
| 31 |
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"O14944"
|
| 32 |
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],
|
| 33 |
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|
| 34 |
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|
| 35 |
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|
| 36 |
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"PROTSEQ": [
|
| 37 |
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| 38 |
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|
| 39 |
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|
| 40 |
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|
| 41 |
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],
|
| 42 |
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"NUCLSEQ": [],
|
| 43 |
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"DOMAINS": [
|
| 44 |
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"Epidermal growth factor receptor",
|
| 45 |
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"Proepiregulin",
|
| 46 |
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"Epiregulin",
|
| 47 |
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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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|
| 53 |
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|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
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|
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|
| 64 |
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|
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|
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|
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|
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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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"name": "chain A-chain B interaction",
|
| 76 |
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"agent_1": "chain A",
|
| 77 |
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"agent_2": "chain B",
|
| 78 |
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"selection_1": "chain A",
|
| 79 |
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"selection_2": "chain B",
|
| 80 |
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"type": "protein-protein"
|
| 81 |
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},
|
| 82 |
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{
|
| 83 |
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"name": "chain A-chain C interaction",
|
| 84 |
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"agent_1": "chain A",
|
| 85 |
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|
| 86 |
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"selection_1": "chain A",
|
| 87 |
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|
| 88 |
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"type": "protein-protein"
|
| 89 |
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},
|
| 90 |
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{
|
| 91 |
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"name": "chain B-chain D interaction",
|
| 92 |
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"agent_1": "chain B",
|
| 93 |
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"agent_2": "chain D",
|
| 94 |
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"selection_1": "chain A",
|
| 95 |
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"selection_2": "chain D",
|
| 96 |
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"type": "protein-protein"
|
| 97 |
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}
|
| 98 |
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],
|
| 99 |
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|
| 100 |
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|
| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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|
| 106 |
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"COLLECTIONS": "dynarepo",
|
| 107 |
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|
| 108 |
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|
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|
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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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|
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|
| 117 |
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|
| 118 |
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|
| 119 |
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],
|
| 120 |
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"mdref": 0,
|
| 121 |
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|
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|
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"clusters_03_screenshot_19.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb",
|
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"pocket_08.pdb",
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"pocket_09.pdb",
|
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"pocket_10.pdb"
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+
],
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+
"analyses": [
|
| 234 |
+
"clusters",
|
| 235 |
+
"clusters-00",
|
| 236 |
+
"clusters-01",
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| 237 |
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"clusters-02",
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| 238 |
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"clusters-03",
|
| 239 |
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"dist-perres",
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| 240 |
+
"energies",
|
| 241 |
+
"fluctuation",
|
| 242 |
+
"hbonds",
|
| 243 |
+
"interactions",
|
| 244 |
+
"pca",
|
| 245 |
+
"pockets",
|
| 246 |
+
"rgyr",
|
| 247 |
+
"rmsd-pairwise",
|
| 248 |
+
"rmsd-perres",
|
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+
"rmsds",
|
| 250 |
+
"sasa",
|
| 251 |
+
"tmscores"
|
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],
|
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+
"mdIndex": 0,
|
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+
"mdNumber": 1,
|
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+
"refframe": 4,
|
| 256 |
+
"internalId": "68430095a810011a433d848a",
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| 257 |
+
"creationDate": "2025-06-06T14:52:05.000Z",
|
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+
"identifier": "A00A8"
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+
}
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data/files/A00A8/records.jsonl
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00A9",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5WQL",
|
| 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 |
+
"5WQL"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0AFB1",
|
| 31 |
+
"P23865"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"AAAAAA",
|
| 38 |
+
"AAAA",
|
| 39 |
+
"DITRADQIPVLKEETQHATVSERVTSRFTRSHYRQFDLDQAFSAKIFDRYLNLLDYSHNVLLASDVEQFAKKKTELGDELRSGKLDVFYDLYNLAQKRRFERYQYALSVLEKPMDFTGNDTYNLDRSKAPWPKNEAELNALWDSKVKFDELSLKLTGKTDKEIRETLTRRYKFAIRRLAQTNSEDVFSLAMTAFAREIDPHTNYLSPRNTEQFNTEMSLSLEGIGAVLQMDDDYTVINSMVAGGPAAKSKAISVGDKIVGVGQTGKPMVDVIGWRLDDVVALIKGPKGSKVRLEILPAGKGTKTRTVTLTRERIRLEDRAVKMSVKTVGKEKVGVLDIPGFYVGLTDDVKVQLQKLEKQNVSSVIIDLRSNGGGALTEAVSLSGLFIPAGPIVQVRDNNGKVREDSDTDGQVFYKGPLVVLVDRFSASASEIFAAAMQDYGRALVVGEPTFGAGTVQQYRSLNRIYDQMLRPEWPALGSVQYTIQKFYRVNGGSTQRKGVTPDIIMPTGNEETETGEKFEDNALPWDSIDAATYVKSGDLTAFEPELLKEHNARIAKDPEFQNIMKDIARFNAMKDKRNIVSLNYAVREKENNEDDATRLARLNERFKREGKPELKKLDDLPKDYQEPDPYLDETVNIALDLAKLEKAR",
|
| 40 |
+
"NTSWRKSEVLAVPLQPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQWGWNIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEHRYALLELSLLGQDQDDL"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Lipoprotein NlpI",
|
| 45 |
+
"Tail-specific protease",
|
| 46 |
+
"PDZ",
|
| 47 |
+
"Disordered"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 14705,
|
| 59 |
+
"SYSTRES": 927,
|
| 60 |
+
"PROTATS": 14705,
|
| 61 |
+
"PROTRES": 927,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"name": "chain B-chain C interaction",
|
| 84 |
+
"agent_1": "chain B",
|
| 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 D interaction",
|
| 92 |
+
"agent_1": "chain B",
|
| 93 |
+
"agent_2": "chain D",
|
| 94 |
+
"selection_1": "chain A",
|
| 95 |
+
"selection_2": "chain D",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
}
|
| 98 |
+
],
|
| 99 |
+
"PBC_SELECTION": null,
|
| 100 |
+
"CHAINNAMES": null,
|
| 101 |
+
"MEMBRANES": null,
|
| 102 |
+
"CUSTOMS": null,
|
| 103 |
+
"ORIENTATION": null,
|
| 104 |
+
"PTM": [],
|
| 105 |
+
"MULTIMERIC": null,
|
| 106 |
+
"COLLECTIONS": "dynarepo",
|
| 107 |
+
"WARNINGS": [],
|
| 108 |
+
"BOXSIZEX": 13.9567,
|
| 109 |
+
"BOXSIZEY": 13.9567,
|
| 110 |
+
"BOXSIZEZ": 9.82868,
|
| 111 |
+
"mdName": "replica 1",
|
| 112 |
+
"mdAtoms": 14705,
|
| 113 |
+
"mdFrames": 5001
|
| 114 |
+
},
|
| 115 |
+
"mds": [
|
| 116 |
+
"replica 1",
|
| 117 |
+
"replica 2",
|
| 118 |
+
"replica 3"
|
| 119 |
+
],
|
| 120 |
+
"mdref": 0,
|
| 121 |
+
"files": [
|
| 122 |
+
"topology.tpr",
|
| 123 |
+
"screenshot.jpg",
|
| 124 |
+
"trajectory.bin",
|
| 125 |
+
"pca_trajectory_01.bin",
|
| 126 |
+
"pca_trajectory_02.bin",
|
| 127 |
+
"pca_trajectory_03.bin",
|
| 128 |
+
"pca_trajectory_04.bin",
|
| 129 |
+
"pca_trajectory_05.bin",
|
| 130 |
+
"pca_trajectory_06.bin",
|
| 131 |
+
"pca_trajectory_07.bin",
|
| 132 |
+
"pca_trajectory_08.bin",
|
| 133 |
+
"pca_trajectory_09.bin",
|
| 134 |
+
"pca_trajectory_10.bin",
|
| 135 |
+
"pca_trajectory_11.bin",
|
| 136 |
+
"pca_trajectory_12.bin",
|
| 137 |
+
"structure.pdb",
|
| 138 |
+
"trajectory.xtc",
|
| 139 |
+
"clusters_00_screenshot_00.jpg",
|
| 140 |
+
"clusters_00_screenshot_01.jpg",
|
| 141 |
+
"clusters_00_screenshot_02.jpg",
|
| 142 |
+
"clusters_00_screenshot_03.jpg",
|
| 143 |
+
"clusters_00_screenshot_04.jpg",
|
| 144 |
+
"clusters_00_screenshot_05.jpg",
|
| 145 |
+
"clusters_00_screenshot_06.jpg",
|
| 146 |
+
"clusters_00_screenshot_07.jpg",
|
| 147 |
+
"clusters_00_screenshot_08.jpg",
|
| 148 |
+
"clusters_00_screenshot_09.jpg",
|
| 149 |
+
"clusters_00_screenshot_10.jpg",
|
| 150 |
+
"clusters_00_screenshot_11.jpg",
|
| 151 |
+
"clusters_00_screenshot_12.jpg",
|
| 152 |
+
"clusters_00_screenshot_13.jpg",
|
| 153 |
+
"clusters_00_screenshot_14.jpg",
|
| 154 |
+
"clusters_00_screenshot_15.jpg",
|
| 155 |
+
"clusters_00_screenshot_16.jpg",
|
| 156 |
+
"clusters_00_screenshot_17.jpg",
|
| 157 |
+
"clusters_00_screenshot_18.jpg",
|
| 158 |
+
"clusters_00_screenshot_19.jpg",
|
| 159 |
+
"clusters_01_screenshot_00.jpg",
|
| 160 |
+
"clusters_01_screenshot_01.jpg",
|
| 161 |
+
"clusters_01_screenshot_02.jpg",
|
| 162 |
+
"clusters_01_screenshot_03.jpg",
|
| 163 |
+
"clusters_01_screenshot_04.jpg",
|
| 164 |
+
"clusters_01_screenshot_05.jpg",
|
| 165 |
+
"clusters_01_screenshot_06.jpg",
|
| 166 |
+
"clusters_01_screenshot_07.jpg",
|
| 167 |
+
"clusters_01_screenshot_08.jpg",
|
| 168 |
+
"clusters_01_screenshot_09.jpg",
|
| 169 |
+
"clusters_01_screenshot_10.jpg",
|
| 170 |
+
"clusters_01_screenshot_11.jpg",
|
| 171 |
+
"clusters_01_screenshot_12.jpg",
|
| 172 |
+
"clusters_01_screenshot_13.jpg",
|
| 173 |
+
"clusters_01_screenshot_14.jpg",
|
| 174 |
+
"clusters_01_screenshot_15.jpg",
|
| 175 |
+
"clusters_01_screenshot_16.jpg",
|
| 176 |
+
"clusters_01_screenshot_17.jpg",
|
| 177 |
+
"clusters_01_screenshot_18.jpg",
|
| 178 |
+
"clusters_01_screenshot_19.jpg",
|
| 179 |
+
"clusters_01_screenshot_20.jpg",
|
| 180 |
+
"clusters_01_screenshot_21.jpg",
|
| 181 |
+
"clusters_01_screenshot_22.jpg",
|
| 182 |
+
"clusters_02_screenshot_00.jpg",
|
| 183 |
+
"clusters_02_screenshot_01.jpg",
|
| 184 |
+
"clusters_02_screenshot_02.jpg",
|
| 185 |
+
"clusters_02_screenshot_03.jpg",
|
| 186 |
+
"clusters_02_screenshot_04.jpg",
|
| 187 |
+
"clusters_02_screenshot_05.jpg",
|
| 188 |
+
"clusters_02_screenshot_06.jpg",
|
| 189 |
+
"clusters_02_screenshot_07.jpg",
|
| 190 |
+
"clusters_02_screenshot_08.jpg",
|
| 191 |
+
"clusters_02_screenshot_09.jpg",
|
| 192 |
+
"clusters_02_screenshot_10.jpg",
|
| 193 |
+
"clusters_02_screenshot_11.jpg",
|
| 194 |
+
"clusters_02_screenshot_12.jpg",
|
| 195 |
+
"clusters_02_screenshot_13.jpg",
|
| 196 |
+
"clusters_02_screenshot_14.jpg",
|
| 197 |
+
"clusters_02_screenshot_15.jpg",
|
| 198 |
+
"clusters_02_screenshot_16.jpg",
|
| 199 |
+
"clusters_02_screenshot_17.jpg",
|
| 200 |
+
"clusters_02_screenshot_18.jpg",
|
| 201 |
+
"clusters_02_screenshot_19.jpg",
|
| 202 |
+
"clusters_03_screenshot_00.jpg",
|
| 203 |
+
"clusters_03_screenshot_01.jpg",
|
| 204 |
+
"clusters_03_screenshot_02.jpg",
|
| 205 |
+
"clusters_03_screenshot_03.jpg",
|
| 206 |
+
"clusters_03_screenshot_04.jpg",
|
| 207 |
+
"clusters_03_screenshot_05.jpg",
|
| 208 |
+
"clusters_03_screenshot_06.jpg",
|
| 209 |
+
"clusters_03_screenshot_07.jpg",
|
| 210 |
+
"clusters_03_screenshot_08.jpg",
|
| 211 |
+
"clusters_03_screenshot_09.jpg",
|
| 212 |
+
"clusters_03_screenshot_10.jpg",
|
| 213 |
+
"clusters_03_screenshot_11.jpg",
|
| 214 |
+
"clusters_03_screenshot_12.jpg",
|
| 215 |
+
"clusters_03_screenshot_13.jpg",
|
| 216 |
+
"clusters_03_screenshot_14.jpg",
|
| 217 |
+
"clusters_03_screenshot_15.jpg",
|
| 218 |
+
"clusters_03_screenshot_16.jpg",
|
| 219 |
+
"clusters_03_screenshot_17.jpg",
|
| 220 |
+
"clusters_03_screenshot_18.jpg",
|
| 221 |
+
"clusters_03_screenshot_19.jpg",
|
| 222 |
+
"pocket_01.pdb",
|
| 223 |
+
"pocket_02.pdb",
|
| 224 |
+
"pocket_03.pdb",
|
| 225 |
+
"pocket_04.pdb",
|
| 226 |
+
"pocket_05.pdb",
|
| 227 |
+
"pocket_06.pdb",
|
| 228 |
+
"pocket_07.pdb",
|
| 229 |
+
"pocket_08.pdb",
|
| 230 |
+
"pocket_09.pdb",
|
| 231 |
+
"pocket_10.pdb"
|
| 232 |
+
],
|
| 233 |
+
"analyses": [
|
| 234 |
+
"clusters",
|
| 235 |
+
"clusters-00",
|
| 236 |
+
"clusters-01",
|
| 237 |
+
"clusters-02",
|
| 238 |
+
"clusters-03",
|
| 239 |
+
"dist-perres",
|
| 240 |
+
"energies",
|
| 241 |
+
"fluctuation",
|
| 242 |
+
"hbonds",
|
| 243 |
+
"interactions",
|
| 244 |
+
"pca",
|
| 245 |
+
"pockets",
|
| 246 |
+
"rgyr",
|
| 247 |
+
"rmsd-pairwise",
|
| 248 |
+
"rmsd-perres",
|
| 249 |
+
"rmsds",
|
| 250 |
+
"sasa",
|
| 251 |
+
"tmscores"
|
| 252 |
+
],
|
| 253 |
+
"mdIndex": 0,
|
| 254 |
+
"mdNumber": 1,
|
| 255 |
+
"refframe": 0,
|
| 256 |
+
"internalId": "6843061faa71f968f4e12c1a",
|
| 257 |
+
"creationDate": "2025-06-06T15:15:43.000Z",
|
| 258 |
+
"identifier": "A00A9"
|
| 259 |
+
}
|
data/files/A00A9/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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data/files/A00AA/project.json
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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 |
+
"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 |
+
"PDBIDS": [
|
| 26 |
+
"5WUJ"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"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": [],
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| 35 |
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"LIGANDNAMES": null,
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| 36 |
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"PROTSEQ": [
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| 37 |
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"FSEEEVRYEIILEKIRGTLKERPDEIAMLFKLLIKDE",
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| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
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| 41 |
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"DOMAINS": [
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| 42 |
+
"Flagellar motor switch protein FliG"
|
| 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 |
+
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|
| 54 |
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|
| 55 |
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|
| 56 |
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"PROTRES": 142,
|
| 57 |
+
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|
| 58 |
+
"NUCLRES": 0,
|
| 59 |
+
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|
| 60 |
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|
| 61 |
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|
| 62 |
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"CARBRES": 0,
|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 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 |
+
"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 |
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|
| 82 |
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|
| 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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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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},
|
| 94 |
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"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 |
+
"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 |
+
"structure.pdb",
|
| 115 |
+
"trajectory.xtc",
|
| 116 |
+
"clusters_00_screenshot_00.jpg",
|
| 117 |
+
"clusters_00_screenshot_01.jpg",
|
| 118 |
+
"clusters_00_screenshot_02.jpg",
|
| 119 |
+
"clusters_00_screenshot_03.jpg",
|
| 120 |
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"clusters_00_screenshot_04.jpg",
|
| 121 |
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"clusters_00_screenshot_05.jpg",
|
| 122 |
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"clusters_00_screenshot_06.jpg",
|
| 123 |
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"clusters_00_screenshot_07.jpg",
|
| 124 |
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"clusters_00_screenshot_08.jpg",
|
| 125 |
+
"clusters_00_screenshot_09.jpg",
|
| 126 |
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"clusters_00_screenshot_10.jpg",
|
| 127 |
+
"clusters_00_screenshot_11.jpg",
|
| 128 |
+
"clusters_00_screenshot_12.jpg",
|
| 129 |
+
"clusters_00_screenshot_13.jpg",
|
| 130 |
+
"clusters_00_screenshot_14.jpg",
|
| 131 |
+
"clusters_00_screenshot_15.jpg",
|
| 132 |
+
"clusters_00_screenshot_16.jpg",
|
| 133 |
+
"clusters_00_screenshot_17.jpg",
|
| 134 |
+
"clusters_00_screenshot_18.jpg",
|
| 135 |
+
"clusters_00_screenshot_19.jpg",
|
| 136 |
+
"clusters_01_screenshot_00.jpg",
|
| 137 |
+
"clusters_01_screenshot_01.jpg",
|
| 138 |
+
"clusters_01_screenshot_02.jpg",
|
| 139 |
+
"clusters_01_screenshot_03.jpg",
|
| 140 |
+
"clusters_01_screenshot_04.jpg",
|
| 141 |
+
"clusters_01_screenshot_05.jpg",
|
| 142 |
+
"clusters_01_screenshot_06.jpg",
|
| 143 |
+
"clusters_01_screenshot_07.jpg",
|
| 144 |
+
"clusters_01_screenshot_08.jpg",
|
| 145 |
+
"clusters_01_screenshot_09.jpg",
|
| 146 |
+
"clusters_01_screenshot_10.jpg",
|
| 147 |
+
"clusters_01_screenshot_11.jpg",
|
| 148 |
+
"clusters_01_screenshot_12.jpg",
|
| 149 |
+
"clusters_01_screenshot_13.jpg",
|
| 150 |
+
"clusters_01_screenshot_14.jpg",
|
| 151 |
+
"clusters_01_screenshot_15.jpg",
|
| 152 |
+
"clusters_01_screenshot_16.jpg",
|
| 153 |
+
"clusters_01_screenshot_17.jpg",
|
| 154 |
+
"clusters_01_screenshot_18.jpg",
|
| 155 |
+
"clusters_01_screenshot_19.jpg",
|
| 156 |
+
"clusters_01_screenshot_20.jpg",
|
| 157 |
+
"clusters_01_screenshot_21.jpg",
|
| 158 |
+
"pocket_01.pdb",
|
| 159 |
+
"pocket_02.pdb",
|
| 160 |
+
"pocket_03.pdb"
|
| 161 |
+
],
|
| 162 |
+
"analyses": [
|
| 163 |
+
"clusters",
|
| 164 |
+
"clusters-00",
|
| 165 |
+
"clusters-01",
|
| 166 |
+
"dist-perres",
|
| 167 |
+
"energies",
|
| 168 |
+
"fluctuation",
|
| 169 |
+
"hbonds",
|
| 170 |
+
"interactions",
|
| 171 |
+
"pca",
|
| 172 |
+
"pockets",
|
| 173 |
+
"rgyr",
|
| 174 |
+
"rmsd-pairwise",
|
| 175 |
+
"rmsd-perres",
|
| 176 |
+
"rmsds",
|
| 177 |
+
"sasa",
|
| 178 |
+
"tmscores"
|
| 179 |
+
],
|
| 180 |
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"mdIndex": 0,
|
| 181 |
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"mdNumber": 1,
|
| 182 |
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"refframe": 0,
|
| 183 |
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"internalId": "6843098b92d1955a681df748",
|
| 184 |
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"creationDate": "2025-06-06T15:30:19.000Z",
|
| 185 |
+
"identifier": "A00AA"
|
| 186 |
+
}
|
data/files/A00AA/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00AA", "accession": "A00AA", "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 5WUJ", "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": ["5WUJ"], "FORCED_REFERENCES": null, "REFERENCES": ["O25118", "O25119"], 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data/files/A00AB/project.json
ADDED
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| 1 |
+
{
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| 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 |
+
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|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"5XQZ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9H8S9",
|
| 31 |
+
"Q9Y2H1"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"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 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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"PROTRES": 245,
|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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|
| 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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|
| 90 |
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"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 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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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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"pca_trajectory_02.bin",
|
| 108 |
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"pca_trajectory_03.bin",
|
| 109 |
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"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
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"pca_trajectory_06.bin",
|
| 112 |
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"pca_trajectory_07.bin",
|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
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"pca_trajectory_09.bin",
|
| 115 |
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"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 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 |
+
"clusters_00_screenshot_01.jpg",
|
| 122 |
+
"clusters_00_screenshot_02.jpg",
|
| 123 |
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"clusters_00_screenshot_03.jpg",
|
| 124 |
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"clusters_00_screenshot_04.jpg",
|
| 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 |
+
"clusters_00_screenshot_14.jpg",
|
| 135 |
+
"clusters_00_screenshot_15.jpg",
|
| 136 |
+
"clusters_00_screenshot_16.jpg",
|
| 137 |
+
"clusters_00_screenshot_17.jpg",
|
| 138 |
+
"clusters_00_screenshot_18.jpg",
|
| 139 |
+
"clusters_00_screenshot_19.jpg",
|
| 140 |
+
"clusters_01_screenshot_00.jpg",
|
| 141 |
+
"clusters_01_screenshot_01.jpg",
|
| 142 |
+
"clusters_01_screenshot_02.jpg",
|
| 143 |
+
"clusters_01_screenshot_03.jpg",
|
| 144 |
+
"clusters_01_screenshot_04.jpg",
|
| 145 |
+
"clusters_01_screenshot_05.jpg",
|
| 146 |
+
"clusters_01_screenshot_06.jpg",
|
| 147 |
+
"clusters_01_screenshot_07.jpg",
|
| 148 |
+
"clusters_01_screenshot_08.jpg",
|
| 149 |
+
"clusters_01_screenshot_09.jpg",
|
| 150 |
+
"clusters_01_screenshot_10.jpg",
|
| 151 |
+
"clusters_01_screenshot_11.jpg",
|
| 152 |
+
"clusters_01_screenshot_12.jpg",
|
| 153 |
+
"clusters_01_screenshot_13.jpg",
|
| 154 |
+
"clusters_01_screenshot_14.jpg",
|
| 155 |
+
"clusters_01_screenshot_15.jpg",
|
| 156 |
+
"clusters_01_screenshot_16.jpg",
|
| 157 |
+
"clusters_01_screenshot_17.jpg",
|
| 158 |
+
"clusters_01_screenshot_18.jpg",
|
| 159 |
+
"clusters_01_screenshot_19.jpg",
|
| 160 |
+
"clusters_01_screenshot_20.jpg",
|
| 161 |
+
"clusters_01_screenshot_21.jpg",
|
| 162 |
+
"pocket_01.pdb",
|
| 163 |
+
"pocket_02.pdb",
|
| 164 |
+
"pocket_03.pdb",
|
| 165 |
+
"pocket_04.pdb",
|
| 166 |
+
"pocket_05.pdb",
|
| 167 |
+
"pocket_06.pdb"
|
| 168 |
+
],
|
| 169 |
+
"analyses": [
|
| 170 |
+
"clusters",
|
| 171 |
+
"clusters-00",
|
| 172 |
+
"clusters-01",
|
| 173 |
+
"dist-perres",
|
| 174 |
+
"energies",
|
| 175 |
+
"fluctuation",
|
| 176 |
+
"hbonds",
|
| 177 |
+
"interactions",
|
| 178 |
+
"pca",
|
| 179 |
+
"pockets",
|
| 180 |
+
"rgyr",
|
| 181 |
+
"rmsd-pairwise",
|
| 182 |
+
"rmsd-perres",
|
| 183 |
+
"rmsds",
|
| 184 |
+
"sasa",
|
| 185 |
+
"tmscores"
|
| 186 |
+
],
|
| 187 |
+
"mdIndex": 0,
|
| 188 |
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"mdNumber": 1,
|
| 189 |
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"refframe": 0,
|
| 190 |
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"internalId": "68430b3144794522ce78e639",
|
| 191 |
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"creationDate": "2025-06-06T15:37:21.000Z",
|
| 192 |
+
"identifier": "A00AB"
|
| 193 |
+
}
|
data/files/A00AB/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00AB", "accession": "A00AB", "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 5XQZ", "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": ["5XQZ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9H8S9", "Q9Y2H1"], 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| 3 |
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data/files/A00AC/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AC",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5Y1Z",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"5Y1Z"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q16643",
|
| 31 |
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"Q9ULU4"
|
| 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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"MAGVSFSGHRLELLAAYEEVIREESAADWALYTYEDGSDDLKLAASGEGGLQELSGHFENQKVMYGFCSVKDSQAALPKYVLINWVGEDVPDARKCACASHVAKVAEFFQGVDVIVNASSVEDIDAGAIGQRL",
|
| 38 |
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"NDFYXWVCHREGQVLCXELXPRVYHAKXLRLTSEPEGDWFXPEXEKITVAECIETQSKAMTMLTIEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEMNEIEVXPEXYLAACQKRDNWFCEPXSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVENIRRKFGVFNYSPFRTPYTPNSQYQMLLDPTNPSAGTAK"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Drebrin",
|
| 43 |
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"ADF-H",
|
| 44 |
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"MYND-type zinc finger-containing chromatin reader ZMYND8",
|
| 45 |
+
"Bromo",
|
| 46 |
+
"PWWP",
|
| 47 |
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"Required for interaction with CCNT1",
|
| 48 |
+
"Interaction with histone H3K14ac",
|
| 49 |
+
"Interaction with histone H3K4me0",
|
| 50 |
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"Required for interaction with histone H3 and histone H4"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
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"TIMESTEP": 2,
|
| 54 |
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"TEMP": 310,
|
| 55 |
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"ENSEMBLE": "NPT",
|
| 56 |
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"FF": [
|
| 57 |
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"CHARMM36m"
|
| 58 |
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],
|
| 59 |
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"WAT": "TIP3P",
|
| 60 |
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"BOXTYPE": "Dodecahedron",
|
| 61 |
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"SYSTATS": 6845,
|
| 62 |
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"SYSTRES": 437,
|
| 63 |
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"PROTATS": 6845,
|
| 64 |
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"PROTRES": 437,
|
| 65 |
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| 66 |
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"NUCLRES": 0,
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| 67 |
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| 68 |
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| 69 |
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| 70 |
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| 71 |
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| 72 |
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| 73 |
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|
| 74 |
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"COUNANI": 0,
|
| 75 |
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"COUNION": 0,
|
| 76 |
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"INTERACTIONS": [
|
| 77 |
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{
|
| 78 |
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"name": "chain A-chain B interaction",
|
| 79 |
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"agent_1": "chain A",
|
| 80 |
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"agent_2": "chain B",
|
| 81 |
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"selection_1": "chain A",
|
| 82 |
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"selection_2": "chain B",
|
| 83 |
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"type": "protein-protein"
|
| 84 |
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}
|
| 85 |
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],
|
| 86 |
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"PBC_SELECTION": null,
|
| 87 |
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"CHAINNAMES": null,
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| 88 |
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| 89 |
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| 90 |
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| 91 |
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"PTM": [],
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| 92 |
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| 93 |
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"COLLECTIONS": "dynarepo",
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| 94 |
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"WARNINGS": [],
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| 95 |
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| 96 |
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| 97 |
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| 99 |
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},
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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],
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| 107 |
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"mdref": 0,
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| 108 |
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"files": [
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| 109 |
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| 110 |
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| 111 |
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| 112 |
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| 116 |
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| 119 |
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| 122 |
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|
| 123 |
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| 124 |
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|
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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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|
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|
| 173 |
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|
| 174 |
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|
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|
| 176 |
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|
| 177 |
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],
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"analyses": [
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| 182 |
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|
| 183 |
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|
| 185 |
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"hbonds",
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| 186 |
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"interactions",
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| 187 |
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"pca",
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"pockets",
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| 189 |
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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": "68430d815c38e92bbe450085",
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"creationDate": "2025-06-06T15:47:13.000Z",
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"identifier": "A00AC"
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}
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data/files/A00AC/records.jsonl
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| 1 |
+
{
|
| 2 |
+
"accession": "A00AD",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5YIR",
|
| 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 |
+
"5YIR"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9DCD6",
|
| 31 |
+
"Q01484"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EEWVIVSDEEIEEARQKA",
|
| 38 |
+
"MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Gamma-aminobutyric acid receptor-associated protein",
|
| 43 |
+
"Interaction with beta-tubulin",
|
| 44 |
+
"Interaction with GPHN",
|
| 45 |
+
"Interaction with GABRG2",
|
| 46 |
+
"Interaction with LIR (LC3 nteracting Region) motif of ATG3",
|
| 47 |
+
"Cleavage; by ATG4B",
|
| 48 |
+
"Ankyrin-2"
|
| 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": 2268,
|
| 60 |
+
"SYSTRES": 135,
|
| 61 |
+
"PROTATS": 2268,
|
| 62 |
+
"PROTRES": 135,
|
| 63 |
+
"NUCLATS": 0,
|
| 64 |
+
"NUCLRES": 0,
|
| 65 |
+
"LIPIATS": 0,
|
| 66 |
+
"LIPIRES": 0,
|
| 67 |
+
"CARBATS": 0,
|
| 68 |
+
"CARBRES": 0,
|
| 69 |
+
"SOLVATS": 0,
|
| 70 |
+
"SOLVRES": 0,
|
| 71 |
+
"COUNCAT": 0,
|
| 72 |
+
"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 |
+
"MEMBRANES": null,
|
| 87 |
+
"CUSTOMS": null,
|
| 88 |
+
"ORIENTATION": null,
|
| 89 |
+
"PTM": [],
|
| 90 |
+
"MULTIMERIC": null,
|
| 91 |
+
"COLLECTIONS": "dynarepo",
|
| 92 |
+
"WARNINGS": [],
|
| 93 |
+
"BOXSIZEX": 7.41097,
|
| 94 |
+
"BOXSIZEY": 7.41097,
|
| 95 |
+
"BOXSIZEZ": 5.23605,
|
| 96 |
+
"mdName": "replica 1",
|
| 97 |
+
"mdAtoms": 2268,
|
| 98 |
+
"mdFrames": 5001
|
| 99 |
+
},
|
| 100 |
+
"mds": [
|
| 101 |
+
"replica 1",
|
| 102 |
+
"replica 2",
|
| 103 |
+
"replica 3"
|
| 104 |
+
],
|
| 105 |
+
"mdref": 0,
|
| 106 |
+
"files": [
|
| 107 |
+
"topology.tpr",
|
| 108 |
+
"screenshot.jpg",
|
| 109 |
+
"trajectory.bin",
|
| 110 |
+
"pca_trajectory_01.bin",
|
| 111 |
+
"pca_trajectory_02.bin",
|
| 112 |
+
"pca_trajectory_03.bin",
|
| 113 |
+
"pca_trajectory_04.bin",
|
| 114 |
+
"pca_trajectory_05.bin",
|
| 115 |
+
"pca_trajectory_06.bin",
|
| 116 |
+
"pca_trajectory_07.bin",
|
| 117 |
+
"pca_trajectory_08.bin",
|
| 118 |
+
"pca_trajectory_09.bin",
|
| 119 |
+
"pca_trajectory_10.bin",
|
| 120 |
+
"pca_trajectory_11.bin",
|
| 121 |
+
"pca_trajectory_12.bin",
|
| 122 |
+
"pca_trajectory_13.bin",
|
| 123 |
+
"pca_trajectory_14.bin",
|
| 124 |
+
"pca_trajectory_15.bin",
|
| 125 |
+
"pca_trajectory_16.bin",
|
| 126 |
+
"structure.pdb",
|
| 127 |
+
"trajectory.xtc",
|
| 128 |
+
"clusters_00_screenshot_00.jpg",
|
| 129 |
+
"clusters_00_screenshot_01.jpg",
|
| 130 |
+
"clusters_00_screenshot_02.jpg",
|
| 131 |
+
"clusters_00_screenshot_03.jpg",
|
| 132 |
+
"clusters_00_screenshot_04.jpg",
|
| 133 |
+
"clusters_00_screenshot_05.jpg",
|
| 134 |
+
"clusters_00_screenshot_06.jpg",
|
| 135 |
+
"clusters_00_screenshot_07.jpg",
|
| 136 |
+
"clusters_00_screenshot_08.jpg",
|
| 137 |
+
"clusters_00_screenshot_09.jpg",
|
| 138 |
+
"clusters_00_screenshot_10.jpg",
|
| 139 |
+
"clusters_00_screenshot_11.jpg",
|
| 140 |
+
"clusters_00_screenshot_12.jpg",
|
| 141 |
+
"clusters_00_screenshot_13.jpg",
|
| 142 |
+
"clusters_00_screenshot_14.jpg",
|
| 143 |
+
"clusters_00_screenshot_15.jpg",
|
| 144 |
+
"clusters_00_screenshot_16.jpg",
|
| 145 |
+
"clusters_00_screenshot_17.jpg",
|
| 146 |
+
"clusters_00_screenshot_18.jpg",
|
| 147 |
+
"clusters_00_screenshot_19.jpg",
|
| 148 |
+
"clusters_01_screenshot_00.jpg",
|
| 149 |
+
"clusters_01_screenshot_01.jpg",
|
| 150 |
+
"clusters_01_screenshot_02.jpg",
|
| 151 |
+
"clusters_01_screenshot_03.jpg",
|
| 152 |
+
"clusters_01_screenshot_04.jpg",
|
| 153 |
+
"clusters_01_screenshot_05.jpg",
|
| 154 |
+
"clusters_01_screenshot_06.jpg",
|
| 155 |
+
"clusters_01_screenshot_07.jpg",
|
| 156 |
+
"clusters_01_screenshot_08.jpg",
|
| 157 |
+
"clusters_01_screenshot_09.jpg",
|
| 158 |
+
"clusters_01_screenshot_10.jpg",
|
| 159 |
+
"clusters_01_screenshot_11.jpg",
|
| 160 |
+
"clusters_01_screenshot_12.jpg",
|
| 161 |
+
"clusters_01_screenshot_13.jpg",
|
| 162 |
+
"clusters_01_screenshot_14.jpg",
|
| 163 |
+
"clusters_01_screenshot_15.jpg",
|
| 164 |
+
"clusters_01_screenshot_16.jpg",
|
| 165 |
+
"clusters_01_screenshot_17.jpg",
|
| 166 |
+
"clusters_01_screenshot_18.jpg",
|
| 167 |
+
"pocket_01.pdb",
|
| 168 |
+
"pocket_02.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": 1,
|
| 191 |
+
"internalId": "68430f7f62757f32cdee17e7",
|
| 192 |
+
"creationDate": "2025-06-06T15:55:43.000Z",
|
| 193 |
+
"identifier": "A00AD"
|
| 194 |
+
}
|
data/files/A00AD/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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| 1 |
+
{"project_identifier": "A00AD", "accession": "A00AD", "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 5YIR", "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": ["5YIR"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9DCD6", "Q01484"], 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|
data/files/A00AE/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A00AE",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5YOY",
|
| 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"
|
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|
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|
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|
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|
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|
| 367 |
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|
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|
| 369 |
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|
| 370 |
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|
| 371 |
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|
| 372 |
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|
| 373 |
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|
| 374 |
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|
| 375 |
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|
| 376 |
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|
| 377 |
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|
| 378 |
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|
| 379 |
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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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|
| 386 |
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|
| 387 |
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|
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|
| 389 |
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|
| 390 |
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|
| 391 |
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|
| 392 |
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|
| 393 |
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|
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|
| 395 |
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|
| 396 |
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|
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|
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|
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|
| 400 |
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|
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|
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|
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|
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|
| 405 |
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|
| 406 |
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|
| 407 |
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|
| 408 |
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|
| 409 |
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|
| 410 |
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|
| 411 |
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|
| 412 |
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|
| 413 |
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|
| 414 |
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|
| 415 |
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|
| 416 |
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|
| 417 |
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|
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|
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| 433 |
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|
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|
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| 437 |
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|
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|
| 445 |
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|
| 446 |
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|
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|
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|
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|
| 453 |
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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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|
| 466 |
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|
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|
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|
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|
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| 473 |
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|
| 474 |
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|
| 475 |
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|
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|
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|
| 478 |
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|
| 479 |
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|
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|
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|
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|
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|
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|
| 486 |
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|
| 487 |
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|
| 488 |
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|
| 489 |
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|
| 490 |
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|
| 491 |
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|
| 492 |
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|
| 493 |
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"clusters_12_screenshot_18.jpg",
|
| 494 |
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"clusters_12_screenshot_19.jpg",
|
| 495 |
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"clusters_13_screenshot_00.jpg",
|
| 496 |
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"clusters_13_screenshot_01.jpg",
|
| 497 |
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|
| 498 |
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|
| 499 |
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|
| 500 |
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|
| 501 |
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|
| 502 |
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|
| 503 |
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|
| 504 |
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|
| 505 |
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|
| 506 |
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"clusters_13_screenshot_11.jpg",
|
| 507 |
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|
| 508 |
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|
| 509 |
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|
| 510 |
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|
| 511 |
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|
| 512 |
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"clusters_13_screenshot_17.jpg",
|
| 513 |
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|
| 514 |
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|
| 515 |
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|
| 516 |
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|
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|
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|
| 519 |
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|
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|
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|
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|
| 523 |
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|
| 524 |
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|
| 525 |
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|
| 526 |
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|
| 527 |
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|
| 528 |
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|
| 529 |
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|
| 530 |
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|
| 531 |
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|
| 532 |
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|
| 533 |
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"clusters_14_screenshot_18.jpg",
|
| 534 |
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"pocket_01.pdb",
|
| 535 |
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"pocket_02.pdb",
|
| 536 |
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"pocket_03.pdb",
|
| 537 |
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"pocket_04.pdb",
|
| 538 |
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"pocket_05.pdb",
|
| 539 |
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"pocket_06.pdb",
|
| 540 |
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"pocket_07.pdb",
|
| 541 |
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"pocket_08.pdb",
|
| 542 |
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"pocket_09.pdb",
|
| 543 |
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"pocket_10.pdb"
|
| 544 |
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],
|
| 545 |
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"analyses": [
|
| 546 |
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"clusters",
|
| 547 |
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"clusters-00",
|
| 548 |
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"clusters-01",
|
| 549 |
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"clusters-02",
|
| 550 |
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"clusters-03",
|
| 551 |
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|
| 552 |
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|
| 553 |
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"clusters-06",
|
| 554 |
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|
| 555 |
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"clusters-08",
|
| 556 |
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|
| 557 |
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"clusters-10",
|
| 558 |
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"clusters-11",
|
| 559 |
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"clusters-12",
|
| 560 |
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"clusters-13",
|
| 561 |
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"clusters-14",
|
| 562 |
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"dist-perres",
|
| 563 |
+
"energies",
|
| 564 |
+
"fluctuation",
|
| 565 |
+
"hbonds",
|
| 566 |
+
"interactions",
|
| 567 |
+
"pca",
|
| 568 |
+
"pockets",
|
| 569 |
+
"rgyr",
|
| 570 |
+
"rmsd-pairwise",
|
| 571 |
+
"rmsd-perres",
|
| 572 |
+
"rmsds",
|
| 573 |
+
"sasa",
|
| 574 |
+
"tmscores"
|
| 575 |
+
],
|
| 576 |
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"mdIndex": 0,
|
| 577 |
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"mdNumber": 1,
|
| 578 |
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"refframe": 3,
|
| 579 |
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"internalId": "6843148e6d4af78e835ee5de",
|
| 580 |
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"creationDate": "2025-06-06T16:17:18.000Z",
|
| 581 |
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"identifier": "A00AE"
|
| 582 |
+
}
|
data/files/A00AE/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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data/files/A00AF/project.json
ADDED
|
@@ -0,0 +1,333 @@
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 9 |
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"Hamed Khakzad",
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| 10 |
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| 11 |
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],
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| 12 |
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 325 |
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"tmscores"
|
| 326 |
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|
| 327 |
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|
| 328 |
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| 329 |
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| 331 |
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|
| 332 |
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|
| 333 |
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|
data/files/A00AF/records.jsonl
ADDED
|
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data/files/A00AG/project.json
ADDED
|
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| 1 |
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{
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| 2 |
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"accession": "A00AG",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 6A6I",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
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"Delta team, Inria center at the University of Lorraine"
|
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|
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"PROGRAM": "GROMACS",
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
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"LICENSE": "Apache License 2.0",
|
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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"6A6I"
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| 29 |
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| 31 |
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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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"Ubiquitin",
|
| 43 |
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"Ubiquitin-like 1",
|
| 44 |
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"Interacts with activating enzyme",
|
| 45 |
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"Essential for function"
|
| 46 |
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],
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| 47 |
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| 48 |
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| 49 |
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| 50 |
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| 51 |
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"CHARMM36m"
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"WAT": "TIP3P",
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"INTERACTIONS": [
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| 72 |
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{
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| 73 |
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"name": "chain A-chain B interaction",
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| 74 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
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| 79 |
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}
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| 80 |
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],
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"COLLECTIONS": "dynarepo",
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| 137 |
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| 138 |
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| 140 |
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| 141 |
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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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"clusters",
|
| 171 |
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|
| 172 |
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| 173 |
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| 174 |
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| 175 |
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|
| 176 |
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|
| 177 |
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|
| 178 |
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|
| 179 |
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| 180 |
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|
| 181 |
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| 182 |
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| 183 |
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| 184 |
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| 185 |
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"internalId": "68431a5a6902422a132f0630",
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| 191 |
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"creationDate": "2025-06-06T16:42:02.000Z",
|
| 192 |
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"identifier": "A00AG"
|
| 193 |
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}
|
data/files/A00AG/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00AG", "accession": "A00AG", "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 6A6I", "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": ["6A6I"], "FORCED_REFERENCES": null, "REFERENCES": ["Q59FF6", "P0CG47"], 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data/files/A00AH/project.json
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|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AH",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6A7V",
|
| 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 |
+
"6A7V"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P9WFA5",
|
| 31 |
+
"P9WLU3"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"HHHASILIDTSAWVEYFRATGSIAAVEVRRLLSEEAARIAMCEPIAMEILSGALDDNTHTTLERLVNGLPSLNVDDAIDFRAAAGIYRAARRAGETVRSINDCLIAALAIRHGARIVHRDADFDVIARITNLQAASFR",
|
| 38 |
+
"ASILIDTSAWVEYFRATGSIAAVEVRRLLSEEAARIAMCEPIAMEILSGALDDNTHTTLERLVNGLPSLNVDDAIDFRAAAGIYRAARRAGETVRSINDCLIAALAIRHGARIVHRDADFDVIARITNLQAASFR",
|
| 39 |
+
"HHHHASILIDTSAWVEYFRATGSIAAVEVRRLLSEEAARIAMCEPIAMEILSGALDDNTHTTLERLVNGLPSLNVDDAIDFRAAAGIYRAARRAGETVRSINDCLIAALAIRHGARIVHRDADFDVIARITNLQAASFR",
|
| 40 |
+
"SRTNIDIDDELAAEVMRRFGLTTKRAAVDLALRRLVGSPLSREFLLGLEGVGWEGDLDDLRS"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Ribonuclease VapC11",
|
| 45 |
+
"PINc",
|
| 46 |
+
"Antitoxin VapB11"
|
| 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": 12299,
|
| 58 |
+
"SYSTRES": 795,
|
| 59 |
+
"PROTATS": 12299,
|
| 60 |
+
"PROTRES": 795,
|
| 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 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain A-chain D interaction",
|
| 91 |
+
"agent_1": "chain A",
|
| 92 |
+
"agent_2": "chain D",
|
| 93 |
+
"selection_1": "chain A",
|
| 94 |
+
"selection_2": "chain D",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
},
|
| 97 |
+
{
|
| 98 |
+
"name": "chain A-chain E interaction",
|
| 99 |
+
"agent_1": "chain A",
|
| 100 |
+
"agent_2": "chain E",
|
| 101 |
+
"selection_1": "chain A",
|
| 102 |
+
"selection_2": "chain E",
|
| 103 |
+
"type": "protein-protein"
|
| 104 |
+
},
|
| 105 |
+
{
|
| 106 |
+
"name": "chain A-chain G interaction",
|
| 107 |
+
"agent_1": "chain A",
|
| 108 |
+
"agent_2": "chain G",
|
| 109 |
+
"selection_1": "chain A",
|
| 110 |
+
"selection_2": "chain F",
|
| 111 |
+
"type": "protein-protein"
|
| 112 |
+
},
|
| 113 |
+
{
|
| 114 |
+
"name": "chain A-chain H interaction",
|
| 115 |
+
"agent_1": "chain A",
|
| 116 |
+
"agent_2": "chain H",
|
| 117 |
+
"selection_1": "chain A",
|
| 118 |
+
"selection_2": "chain G",
|
| 119 |
+
"type": "protein-protein"
|
| 120 |
+
},
|
| 121 |
+
{
|
| 122 |
+
"name": "chain B-chain C interaction",
|
| 123 |
+
"agent_1": "chain B",
|
| 124 |
+
"agent_2": "chain C",
|
| 125 |
+
"selection_1": "chain A",
|
| 126 |
+
"selection_2": "chain H",
|
| 127 |
+
"type": "protein-protein"
|
| 128 |
+
},
|
| 129 |
+
{
|
| 130 |
+
"name": "chain B-chain D interaction",
|
| 131 |
+
"agent_1": "chain B",
|
| 132 |
+
"agent_2": "chain D",
|
| 133 |
+
"selection_1": "chain B",
|
| 134 |
+
"selection_2": "chain C",
|
| 135 |
+
"type": "protein-protein"
|
| 136 |
+
},
|
| 137 |
+
{
|
| 138 |
+
"name": "chain B-chain G interaction",
|
| 139 |
+
"agent_1": "chain B",
|
| 140 |
+
"agent_2": "chain G",
|
| 141 |
+
"selection_1": "chain B",
|
| 142 |
+
"selection_2": "chain D",
|
| 143 |
+
"type": "protein-protein"
|
| 144 |
+
},
|
| 145 |
+
{
|
| 146 |
+
"name": "chain B-chain H interaction",
|
| 147 |
+
"agent_1": "chain B",
|
| 148 |
+
"agent_2": "chain H",
|
| 149 |
+
"selection_1": "chain B",
|
| 150 |
+
"selection_2": "chain E",
|
| 151 |
+
"type": "protein-protein"
|
| 152 |
+
},
|
| 153 |
+
{
|
| 154 |
+
"name": "chain C-chain D interaction",
|
| 155 |
+
"agent_1": "chain C",
|
| 156 |
+
"agent_2": "chain D",
|
| 157 |
+
"selection_1": "chain B",
|
| 158 |
+
"selection_2": "chain F",
|
| 159 |
+
"type": "protein-protein"
|
| 160 |
+
},
|
| 161 |
+
{
|
| 162 |
+
"name": "chain C-chain E interaction",
|
| 163 |
+
"agent_1": "chain C",
|
| 164 |
+
"agent_2": "chain E",
|
| 165 |
+
"selection_1": "chain B",
|
| 166 |
+
"selection_2": "chain G",
|
| 167 |
+
"type": "protein-protein"
|
| 168 |
+
},
|
| 169 |
+
{
|
| 170 |
+
"name": "chain C-chain F interaction",
|
| 171 |
+
"agent_1": "chain C",
|
| 172 |
+
"agent_2": "chain F",
|
| 173 |
+
"selection_1": "chain B",
|
| 174 |
+
"selection_2": "chain H",
|
| 175 |
+
"type": "protein-protein"
|
| 176 |
+
},
|
| 177 |
+
{
|
| 178 |
+
"name": "chain C-chain G interaction",
|
| 179 |
+
"agent_1": "chain C",
|
| 180 |
+
"agent_2": "chain G",
|
| 181 |
+
"selection_1": "chain C",
|
| 182 |
+
"selection_2": "chain D",
|
| 183 |
+
"type": "protein-protein"
|
| 184 |
+
},
|
| 185 |
+
{
|
| 186 |
+
"name": "chain D-chain E interaction",
|
| 187 |
+
"agent_1": "chain D",
|
| 188 |
+
"agent_2": "chain E",
|
| 189 |
+
"selection_1": "chain C",
|
| 190 |
+
"selection_2": "chain E",
|
| 191 |
+
"type": "protein-protein"
|
| 192 |
+
},
|
| 193 |
+
{
|
| 194 |
+
"name": "chain D-chain F interaction",
|
| 195 |
+
"agent_1": "chain D",
|
| 196 |
+
"agent_2": "chain F",
|
| 197 |
+
"selection_1": "chain C",
|
| 198 |
+
"selection_2": "chain F",
|
| 199 |
+
"type": "protein-protein"
|
| 200 |
+
},
|
| 201 |
+
{
|
| 202 |
+
"name": "chain E-chain F interaction",
|
| 203 |
+
"agent_1": "chain E",
|
| 204 |
+
"agent_2": "chain F",
|
| 205 |
+
"selection_1": "chain C",
|
| 206 |
+
"selection_2": "chain G",
|
| 207 |
+
"type": "protein-protein"
|
| 208 |
+
},
|
| 209 |
+
{
|
| 210 |
+
"name": "chain E-chain G interaction",
|
| 211 |
+
"agent_1": "chain E",
|
| 212 |
+
"agent_2": "chain G",
|
| 213 |
+
"selection_1": "chain C",
|
| 214 |
+
"selection_2": "chain H",
|
| 215 |
+
"type": "protein-protein"
|
| 216 |
+
},
|
| 217 |
+
{
|
| 218 |
+
"name": "chain E-chain H interaction",
|
| 219 |
+
"agent_1": "chain E",
|
| 220 |
+
"agent_2": "chain H",
|
| 221 |
+
"selection_1": "chain D",
|
| 222 |
+
"selection_2": "chain E",
|
| 223 |
+
"type": "protein-protein"
|
| 224 |
+
},
|
| 225 |
+
{
|
| 226 |
+
"name": "chain F-chain G interaction",
|
| 227 |
+
"agent_1": "chain F",
|
| 228 |
+
"agent_2": "chain G",
|
| 229 |
+
"selection_1": "chain D",
|
| 230 |
+
"selection_2": "chain F",
|
| 231 |
+
"type": "protein-protein"
|
| 232 |
+
},
|
| 233 |
+
{
|
| 234 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 779 |
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|
| 780 |
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|
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|
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|
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|
| 786 |
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|
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"identifier": "A00AH"
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| 794 |
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data/files/A00AH/records.jsonl
ADDED
|
The diff for this file is too large to render.
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data/files/A00AI/project.json
ADDED
|
@@ -0,0 +1,188 @@
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| 1 |
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{
|
| 2 |
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"accession": "A00AI",
|
| 3 |
+
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|
| 4 |
+
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|
| 5 |
+
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|
| 6 |
+
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|
| 7 |
+
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|
| 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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|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
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|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
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|
| 20 |
+
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|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
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|
| 23 |
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|
| 24 |
+
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|
| 25 |
+
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|
| 26 |
+
"6B12"
|
| 27 |
+
],
|
| 28 |
+
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|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q4K3B6",
|
| 31 |
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"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 |
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|
| 38 |
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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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"FF": [
|
| 47 |
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"CHARMM36m"
|
| 48 |
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],
|
| 49 |
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"WAT": "TIP3P",
|
| 50 |
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|
| 51 |
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|
| 52 |
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|
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| 61 |
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| 62 |
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| 63 |
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|
| 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 |
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"PBC_SELECTION": null,
|
| 77 |
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"CHAINNAMES": null,
|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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|
| 82 |
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|
| 83 |
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"COLLECTIONS": "dynarepo",
|
| 84 |
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| 85 |
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| 86 |
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| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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"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",
|
| 104 |
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"pca_trajectory_03.bin",
|
| 105 |
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"pca_trajectory_04.bin",
|
| 106 |
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"pca_trajectory_05.bin",
|
| 107 |
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"pca_trajectory_06.bin",
|
| 108 |
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"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 |
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"pca_trajectory_13.bin",
|
| 115 |
+
"pca_trajectory_14.bin",
|
| 116 |
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"structure.pdb",
|
| 117 |
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"trajectory.xtc",
|
| 118 |
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"clusters_00_screenshot_00.jpg",
|
| 119 |
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"clusters_00_screenshot_01.jpg",
|
| 120 |
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"clusters_00_screenshot_02.jpg",
|
| 121 |
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"clusters_00_screenshot_03.jpg",
|
| 122 |
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"clusters_00_screenshot_04.jpg",
|
| 123 |
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"clusters_00_screenshot_05.jpg",
|
| 124 |
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"clusters_00_screenshot_06.jpg",
|
| 125 |
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"clusters_00_screenshot_07.jpg",
|
| 126 |
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"clusters_00_screenshot_08.jpg",
|
| 127 |
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"clusters_00_screenshot_09.jpg",
|
| 128 |
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"clusters_00_screenshot_10.jpg",
|
| 129 |
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"clusters_00_screenshot_11.jpg",
|
| 130 |
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"clusters_00_screenshot_12.jpg",
|
| 131 |
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"clusters_00_screenshot_13.jpg",
|
| 132 |
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"clusters_00_screenshot_14.jpg",
|
| 133 |
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"clusters_00_screenshot_15.jpg",
|
| 134 |
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"clusters_00_screenshot_16.jpg",
|
| 135 |
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"clusters_00_screenshot_17.jpg",
|
| 136 |
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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 |
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"clusters_01_screenshot_01.jpg",
|
| 140 |
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"clusters_01_screenshot_02.jpg",
|
| 141 |
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"clusters_01_screenshot_03.jpg",
|
| 142 |
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"clusters_01_screenshot_04.jpg",
|
| 143 |
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"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 |
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"clusters_01_screenshot_08.jpg",
|
| 147 |
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"clusters_01_screenshot_09.jpg",
|
| 148 |
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"clusters_01_screenshot_10.jpg",
|
| 149 |
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"clusters_01_screenshot_11.jpg",
|
| 150 |
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"clusters_01_screenshot_12.jpg",
|
| 151 |
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"clusters_01_screenshot_13.jpg",
|
| 152 |
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"clusters_01_screenshot_14.jpg",
|
| 153 |
+
"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 |
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"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 |
+
}
|
data/files/A00AI/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"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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data/files/A00AJ/project.json
ADDED
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@@ -0,0 +1,196 @@
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| 1 |
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{
|
| 2 |
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"accession": "A00AJ",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 6B6U",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 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",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
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| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"6B6U"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P14618"
|
| 31 |
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],
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| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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| 35 |
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| 36 |
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|
| 37 |
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"IQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMNVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLAPITSDPTEATAVGAVEASFKCCSGAIIVLTKSGRYAHQVARYRPRAPIIAVTRNPQTARQAHLYRGIFPVLCKDPVQEAWAEDVDLRVNFAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP"
|
| 38 |
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],
|
| 39 |
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"NUCLSEQ": [],
|
| 40 |
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"DOMAINS": [
|
| 41 |
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"Pyruvate kinase PKM",
|
| 42 |
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"Interaction with POU5F1",
|
| 43 |
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"Intersubunit contact",
|
| 44 |
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"Transition state stabilizer",
|
| 45 |
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"Crucial for phosphotyrosine binding"
|
| 46 |
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],
|
| 47 |
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"FRAMESTEP": 0.1,
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| 48 |
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| 49 |
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"TEMP": 310,
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| 50 |
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| 51 |
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"FF": [
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| 52 |
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"CHARMM36m"
|
| 53 |
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],
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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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| 70 |
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| 71 |
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"INTERACTIONS": [
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| 72 |
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{
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| 73 |
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"name": "chain A-chain B interaction",
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| 74 |
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"agent_1": "chain A",
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| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
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| 77 |
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|
| 78 |
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"type": "protein-protein"
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| 79 |
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}
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| 80 |
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| 81 |
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| 82 |
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| 89 |
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| 90 |
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| 94 |
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},
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| 99 |
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| 100 |
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| 101 |
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],
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| 102 |
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| 103 |
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| 104 |
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| 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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| 119 |
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|
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|
| 170 |
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|
| 171 |
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],
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|
| 178 |
+
"fluctuation",
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| 179 |
+
"hbonds",
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| 180 |
+
"interactions",
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| 181 |
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"pca",
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| 182 |
+
"pockets",
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| 183 |
+
"rgyr",
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| 184 |
+
"rmsd-pairwise",
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| 185 |
+
"rmsd-perres",
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| 186 |
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"rmsds",
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| 187 |
+
"sasa",
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| 188 |
+
"tmscores"
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| 189 |
+
],
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| 190 |
+
"mdIndex": 0,
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+
"mdNumber": 1,
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| 192 |
+
"refframe": 1,
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| 193 |
+
"internalId": "6843240bfc290ddc3d6d4fa0",
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| 194 |
+
"creationDate": "2025-06-06T17:23:23.000Z",
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+
"identifier": "A00AJ"
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+
}
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data/files/A00AJ/records.jsonl
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|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AK",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6BB4",
|
| 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 |
+
"6BB4"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DOX7",
|
| 31 |
+
"P84751",
|
| 32 |
+
"P10636"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"IVYKSPV",
|
| 39 |
+
"QVQLQQSDAELVKPGASVKISCKASGYTFTDRTIHWVKQRPEQGLEWIGYIYPGDDSTKYNDMFKAKATLTADKSSNTAYMQLNSLTSDDSAVYFCARRGTMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD",
|
| 40 |
+
"DVQMIQSPSSLSASLGDIVTMTCQASQDTSINLNWFQQKPGKAPKLLIYGASNLEDGVPSRFSGSRYGTDFTLTISSLEDEDMATYFCLQHTYLPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Immunoglobulin kappa light chain",
|
| 45 |
+
"Ig-like 1",
|
| 46 |
+
"Ig-like 2",
|
| 47 |
+
"Variable (V) domain, involved in antigen recognition",
|
| 48 |
+
"Constant (C) domain",
|
| 49 |
+
"Ig heavy chain Mem5",
|
| 50 |
+
"Ig-like 1",
|
| 51 |
+
"Ig-like 2",
|
| 52 |
+
"D segment",
|
| 53 |
+
"JH2 segment",
|
| 54 |
+
"Microtubule-associated protein tau",
|
| 55 |
+
"Disordered",
|
| 56 |
+
"Not glycated"
|
| 57 |
+
],
|
| 58 |
+
"FRAMESTEP": 0.1,
|
| 59 |
+
"TIMESTEP": 2,
|
| 60 |
+
"TEMP": 310,
|
| 61 |
+
"ENSEMBLE": "NPT",
|
| 62 |
+
"FF": [
|
| 63 |
+
"CHARMM36m"
|
| 64 |
+
],
|
| 65 |
+
"WAT": "TIP3P",
|
| 66 |
+
"BOXTYPE": "Dodecahedron",
|
| 67 |
+
"SYSTATS": 6566,
|
| 68 |
+
"SYSTRES": 434,
|
| 69 |
+
"PROTATS": 6566,
|
| 70 |
+
"PROTRES": 434,
|
| 71 |
+
"NUCLATS": 0,
|
| 72 |
+
"NUCLRES": 0,
|
| 73 |
+
"LIPIATS": 0,
|
| 74 |
+
"LIPIRES": 0,
|
| 75 |
+
"CARBATS": 0,
|
| 76 |
+
"CARBRES": 0,
|
| 77 |
+
"SOLVATS": 0,
|
| 78 |
+
"SOLVRES": 0,
|
| 79 |
+
"COUNCAT": 0,
|
| 80 |
+
"COUNANI": 0,
|
| 81 |
+
"COUNION": 0,
|
| 82 |
+
"INTERACTIONS": [
|
| 83 |
+
{
|
| 84 |
+
"name": "chain A-chain B interaction",
|
| 85 |
+
"agent_1": "chain A",
|
| 86 |
+
"agent_2": "chain B",
|
| 87 |
+
"selection_1": "chain A",
|
| 88 |
+
"selection_2": "chain B",
|
| 89 |
+
"type": "protein-protein"
|
| 90 |
+
},
|
| 91 |
+
{
|
| 92 |
+
"name": "chain A-chain C interaction",
|
| 93 |
+
"agent_1": "chain A",
|
| 94 |
+
"agent_2": "chain C",
|
| 95 |
+
"selection_1": "chain A",
|
| 96 |
+
"selection_2": "chain C",
|
| 97 |
+
"type": "protein-protein"
|
| 98 |
+
},
|
| 99 |
+
{
|
| 100 |
+
"name": "chain B-chain C interaction",
|
| 101 |
+
"agent_1": "chain B",
|
| 102 |
+
"agent_2": "chain C",
|
| 103 |
+
"selection_1": "chain B",
|
| 104 |
+
"selection_2": "chain C",
|
| 105 |
+
"type": "protein-protein"
|
| 106 |
+
}
|
| 107 |
+
],
|
| 108 |
+
"PBC_SELECTION": null,
|
| 109 |
+
"CHAINNAMES": null,
|
| 110 |
+
"MEMBRANES": null,
|
| 111 |
+
"CUSTOMS": null,
|
| 112 |
+
"ORIENTATION": null,
|
| 113 |
+
"PTM": [],
|
| 114 |
+
"MULTIMERIC": null,
|
| 115 |
+
"COLLECTIONS": "dynarepo",
|
| 116 |
+
"WARNINGS": [],
|
| 117 |
+
"BOXSIZEX": 10.3056,
|
| 118 |
+
"BOXSIZEY": 10.3056,
|
| 119 |
+
"BOXSIZEZ": 7.33106,
|
| 120 |
+
"mdName": "replica 1",
|
| 121 |
+
"mdAtoms": 6566,
|
| 122 |
+
"mdFrames": 5001
|
| 123 |
+
},
|
| 124 |
+
"mds": [
|
| 125 |
+
"replica 1",
|
| 126 |
+
"replica 2",
|
| 127 |
+
"replica 3"
|
| 128 |
+
],
|
| 129 |
+
"mdref": 0,
|
| 130 |
+
"files": [
|
| 131 |
+
"topology.tpr",
|
| 132 |
+
"screenshot.jpg",
|
| 133 |
+
"trajectory.bin",
|
| 134 |
+
"pca_trajectory_01.bin",
|
| 135 |
+
"pca_trajectory_02.bin",
|
| 136 |
+
"pca_trajectory_03.bin",
|
| 137 |
+
"pca_trajectory_04.bin",
|
| 138 |
+
"structure.pdb",
|
| 139 |
+
"trajectory.xtc",
|
| 140 |
+
"clusters_00_screenshot_00.jpg",
|
| 141 |
+
"clusters_00_screenshot_01.jpg",
|
| 142 |
+
"clusters_00_screenshot_02.jpg",
|
| 143 |
+
"clusters_00_screenshot_03.jpg",
|
| 144 |
+
"clusters_00_screenshot_04.jpg",
|
| 145 |
+
"clusters_00_screenshot_05.jpg",
|
| 146 |
+
"clusters_00_screenshot_06.jpg",
|
| 147 |
+
"clusters_00_screenshot_07.jpg",
|
| 148 |
+
"clusters_00_screenshot_08.jpg",
|
| 149 |
+
"clusters_00_screenshot_09.jpg",
|
| 150 |
+
"clusters_00_screenshot_10.jpg",
|
| 151 |
+
"clusters_00_screenshot_11.jpg",
|
| 152 |
+
"clusters_00_screenshot_12.jpg",
|
| 153 |
+
"clusters_00_screenshot_13.jpg",
|
| 154 |
+
"clusters_00_screenshot_14.jpg",
|
| 155 |
+
"clusters_00_screenshot_15.jpg",
|
| 156 |
+
"clusters_00_screenshot_16.jpg",
|
| 157 |
+
"clusters_00_screenshot_17.jpg",
|
| 158 |
+
"clusters_00_screenshot_18.jpg",
|
| 159 |
+
"clusters_00_screenshot_19.jpg",
|
| 160 |
+
"clusters_01_screenshot_00.jpg",
|
| 161 |
+
"clusters_01_screenshot_01.jpg",
|
| 162 |
+
"clusters_01_screenshot_02.jpg",
|
| 163 |
+
"clusters_01_screenshot_03.jpg",
|
| 164 |
+
"clusters_01_screenshot_04.jpg",
|
| 165 |
+
"clusters_01_screenshot_05.jpg",
|
| 166 |
+
"clusters_01_screenshot_06.jpg",
|
| 167 |
+
"clusters_01_screenshot_07.jpg",
|
| 168 |
+
"clusters_01_screenshot_08.jpg",
|
| 169 |
+
"clusters_01_screenshot_09.jpg",
|
| 170 |
+
"clusters_01_screenshot_10.jpg",
|
| 171 |
+
"clusters_01_screenshot_11.jpg",
|
| 172 |
+
"clusters_01_screenshot_12.jpg",
|
| 173 |
+
"clusters_01_screenshot_13.jpg",
|
| 174 |
+
"clusters_01_screenshot_14.jpg",
|
| 175 |
+
"clusters_01_screenshot_15.jpg",
|
| 176 |
+
"clusters_01_screenshot_16.jpg",
|
| 177 |
+
"clusters_01_screenshot_17.jpg",
|
| 178 |
+
"clusters_01_screenshot_18.jpg",
|
| 179 |
+
"clusters_01_screenshot_19.jpg",
|
| 180 |
+
"clusters_02_screenshot_00.jpg",
|
| 181 |
+
"clusters_02_screenshot_01.jpg",
|
| 182 |
+
"clusters_02_screenshot_02.jpg",
|
| 183 |
+
"clusters_02_screenshot_03.jpg",
|
| 184 |
+
"clusters_02_screenshot_04.jpg",
|
| 185 |
+
"clusters_02_screenshot_05.jpg",
|
| 186 |
+
"clusters_02_screenshot_06.jpg",
|
| 187 |
+
"clusters_02_screenshot_07.jpg",
|
| 188 |
+
"clusters_02_screenshot_08.jpg",
|
| 189 |
+
"clusters_02_screenshot_09.jpg",
|
| 190 |
+
"clusters_02_screenshot_10.jpg",
|
| 191 |
+
"clusters_02_screenshot_11.jpg",
|
| 192 |
+
"clusters_02_screenshot_12.jpg",
|
| 193 |
+
"clusters_02_screenshot_13.jpg",
|
| 194 |
+
"clusters_02_screenshot_14.jpg",
|
| 195 |
+
"clusters_02_screenshot_15.jpg",
|
| 196 |
+
"clusters_02_screenshot_16.jpg",
|
| 197 |
+
"clusters_02_screenshot_17.jpg",
|
| 198 |
+
"clusters_02_screenshot_18.jpg",
|
| 199 |
+
"clusters_02_screenshot_19.jpg",
|
| 200 |
+
"clusters_02_screenshot_20.jpg",
|
| 201 |
+
"clusters_02_screenshot_21.jpg",
|
| 202 |
+
"clusters_03_screenshot_00.jpg",
|
| 203 |
+
"clusters_03_screenshot_01.jpg",
|
| 204 |
+
"clusters_03_screenshot_02.jpg",
|
| 205 |
+
"clusters_03_screenshot_03.jpg",
|
| 206 |
+
"clusters_03_screenshot_04.jpg",
|
| 207 |
+
"clusters_03_screenshot_05.jpg",
|
| 208 |
+
"clusters_03_screenshot_06.jpg",
|
| 209 |
+
"clusters_03_screenshot_07.jpg",
|
| 210 |
+
"clusters_03_screenshot_08.jpg",
|
| 211 |
+
"clusters_03_screenshot_09.jpg",
|
| 212 |
+
"clusters_03_screenshot_10.jpg",
|
| 213 |
+
"clusters_03_screenshot_11.jpg",
|
| 214 |
+
"clusters_03_screenshot_12.jpg",
|
| 215 |
+
"clusters_03_screenshot_13.jpg",
|
| 216 |
+
"clusters_03_screenshot_14.jpg",
|
| 217 |
+
"clusters_03_screenshot_15.jpg",
|
| 218 |
+
"clusters_03_screenshot_16.jpg",
|
| 219 |
+
"clusters_03_screenshot_17.jpg",
|
| 220 |
+
"clusters_03_screenshot_18.jpg",
|
| 221 |
+
"clusters_03_screenshot_19.jpg",
|
| 222 |
+
"clusters_03_screenshot_20.jpg",
|
| 223 |
+
"pocket_01.pdb",
|
| 224 |
+
"pocket_02.pdb",
|
| 225 |
+
"pocket_03.pdb",
|
| 226 |
+
"pocket_04.pdb",
|
| 227 |
+
"pocket_05.pdb",
|
| 228 |
+
"pocket_06.pdb",
|
| 229 |
+
"pocket_07.pdb",
|
| 230 |
+
"pocket_08.pdb",
|
| 231 |
+
"pocket_09.pdb",
|
| 232 |
+
"pocket_10.pdb"
|
| 233 |
+
],
|
| 234 |
+
"analyses": [
|
| 235 |
+
"clusters",
|
| 236 |
+
"clusters-00",
|
| 237 |
+
"clusters-01",
|
| 238 |
+
"clusters-02",
|
| 239 |
+
"clusters-03",
|
| 240 |
+
"dist-perres",
|
| 241 |
+
"energies",
|
| 242 |
+
"fluctuation",
|
| 243 |
+
"hbonds",
|
| 244 |
+
"interactions",
|
| 245 |
+
"pca",
|
| 246 |
+
"pockets",
|
| 247 |
+
"rgyr",
|
| 248 |
+
"rmsd-pairwise",
|
| 249 |
+
"rmsd-perres",
|
| 250 |
+
"rmsds",
|
| 251 |
+
"sasa",
|
| 252 |
+
"tmscores"
|
| 253 |
+
],
|
| 254 |
+
"mdIndex": 0,
|
| 255 |
+
"mdNumber": 1,
|
| 256 |
+
"refframe": 0,
|
| 257 |
+
"internalId": "6843293bc426b874af45c633",
|
| 258 |
+
"creationDate": "2025-06-06T17:45:31.000Z",
|
| 259 |
+
"identifier": "A00AK"
|
| 260 |
+
}
|
data/files/A00AK/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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| 1 |
+
{
|
| 2 |
+
"accession": "A00AL",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6BX5",
|
| 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 |
+
"6BX5"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q6J5N4",
|
| 31 |
+
"P02751"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MIKSLFAVIIGGSVGCTLRWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTALAYFLRQPHLDPFWKLMITTGLCGGLSTFSTFSVEVFALLQAGNYIWALTSVLVHVIGSLIMTALGFFIITILF",
|
| 38 |
+
"SVSSVPTKLEVVAATPTSLLISWDAPAVTVIFYVITYGETGGNSPVQEFTVPGSKSTATISGLKPGVDYTITVYATYYASNSGWYEYGSPISINYRT"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Fibronectin",
|
| 43 |
+
"Fibronectin type-III 10",
|
| 44 |
+
"Fibronectin type-III 11",
|
| 45 |
+
"Cell-attachment",
|
| 46 |
+
"Cell attachment site"
|
| 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": 3418,
|
| 58 |
+
"SYSTRES": 222,
|
| 59 |
+
"PROTATS": 3418,
|
| 60 |
+
"PROTRES": 222,
|
| 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": 11.2753,
|
| 92 |
+
"BOXSIZEY": 11.2753,
|
| 93 |
+
"BOXSIZEZ": 7.95183,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 3418,
|
| 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 |
+
"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_01_screenshot_00.jpg",
|
| 138 |
+
"clusters_01_screenshot_01.jpg",
|
| 139 |
+
"clusters_01_screenshot_02.jpg",
|
| 140 |
+
"clusters_01_screenshot_03.jpg",
|
| 141 |
+
"clusters_01_screenshot_04.jpg",
|
| 142 |
+
"clusters_01_screenshot_05.jpg",
|
| 143 |
+
"clusters_01_screenshot_06.jpg",
|
| 144 |
+
"clusters_01_screenshot_07.jpg",
|
| 145 |
+
"clusters_01_screenshot_08.jpg",
|
| 146 |
+
"clusters_01_screenshot_09.jpg",
|
| 147 |
+
"clusters_01_screenshot_10.jpg",
|
| 148 |
+
"clusters_01_screenshot_11.jpg",
|
| 149 |
+
"clusters_01_screenshot_12.jpg",
|
| 150 |
+
"clusters_01_screenshot_13.jpg",
|
| 151 |
+
"clusters_01_screenshot_14.jpg",
|
| 152 |
+
"clusters_01_screenshot_15.jpg",
|
| 153 |
+
"clusters_01_screenshot_16.jpg",
|
| 154 |
+
"clusters_01_screenshot_17.jpg",
|
| 155 |
+
"clusters_01_screenshot_18.jpg",
|
| 156 |
+
"clusters_01_screenshot_19.jpg"
|
| 157 |
+
],
|
| 158 |
+
"analyses": [
|
| 159 |
+
"clusters",
|
| 160 |
+
"clusters-00",
|
| 161 |
+
"clusters-01",
|
| 162 |
+
"dist-perres",
|
| 163 |
+
"energies",
|
| 164 |
+
"fluctuation",
|
| 165 |
+
"hbonds",
|
| 166 |
+
"interactions",
|
| 167 |
+
"pca",
|
| 168 |
+
"rgyr",
|
| 169 |
+
"rmsd-pairwise",
|
| 170 |
+
"rmsd-perres",
|
| 171 |
+
"rmsds",
|
| 172 |
+
"sasa",
|
| 173 |
+
"tmscores"
|
| 174 |
+
],
|
| 175 |
+
"mdIndex": 0,
|
| 176 |
+
"mdNumber": 1,
|
| 177 |
+
"refframe": 0,
|
| 178 |
+
"internalId": "68432cd7b929f0c3de89b45e",
|
| 179 |
+
"creationDate": "2025-06-06T18:00:55.000Z",
|
| 180 |
+
"identifier": "A00AL"
|
| 181 |
+
}
|
data/files/A00AL/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00AL", "accession": "A00AL", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 6BX5", "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": ["6BX5"], "FORCED_REFERENCES": null, "REFERENCES": ["Q6J5N4", "P02751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MIKSLFAVIIGGSVGCTLRWLLSTKFNSLFPNLPPGTLVVNLLAGLIIGTALAYFLRQPHLDPFWKLMITTGLCGGLSTFSTFSVEVFALLQAGNYIWALTSVLVHVIGSLIMTALGFFIITILF", "SVSSVPTKLEVVAATPTSLLISWDAPAVTVIFYVITYGETGGNSPVQEFTVPGSKSTATISGLKPGVDYTITVYATYYASNSGWYEYGSPISINYRT"], "NUCLSEQ": [], "DOMAINS": ["Fibronectin", "Fibronectin type-III 10", "Fibronectin type-III 11", "Cell-attachment", "Cell attachment site"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3418, "SYSTRES": 222, "PROTATS": 3418, "PROTRES": 222, "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": 11.2753, "BOXSIZEY": 11.2753, "BOXSIZEZ": 7.95183, "mdName": "replica 1", "mdAtoms": 3418, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A00AL/files/topology.tpr", "length": 1336268, "contentType": "application/octet-stream", "metadata": {"project": "68432cd7b929f0c3de89b45e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A00AL/files/screenshot.jpg", "length": 16171, "contentType": "application/octet-stream", "metadata": {"project": "68432cd7b929f0c3de89b45e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A00AL/files/trajectory.bin", "length": 205121016, "contentType": "application/octet-stream", "metadata": {"project": "68432cd7b929f0c3de89b45e", "md": 0, "frames": 5001, "atoms": 3418}}, {"name": "pca_trajectory_01.bin", "downloadUrl": 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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00AM",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6C48",
|
| 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 |
+
"6C48"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q5TKA1",
|
| 31 |
+
"P10244",
|
| 32 |
+
"Q52LA3"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"METLGGFPVEFLIQVTRLSKILMIKKEHIKKLREMNTEAEKLKSYSMPISIEFQRRYATIVLELEQLNKDLNKVLHKVQQYCYE",
|
| 39 |
+
"RDDIDMLKELGSLTTANLMEKVRGLQNLAYQLGLDESREMTRGKFLNILEKPKK",
|
| 40 |
+
"SAWKTVACGGTRDQLFMQEKARQLLGRL"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Protein lin-9 homolog",
|
| 45 |
+
"Myb-related protein B",
|
| 46 |
+
"Protein lin-52 homolog"
|
| 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": 2792,
|
| 58 |
+
"SYSTRES": 166,
|
| 59 |
+
"PROTATS": 2792,
|
| 60 |
+
"PROTRES": 166,
|
| 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 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain B-chain C interaction",
|
| 91 |
+
"agent_1": "chain B",
|
| 92 |
+
"agent_2": "chain C",
|
| 93 |
+
"selection_1": "chain B",
|
| 94 |
+
"selection_2": "chain C",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
}
|
| 97 |
+
],
|
| 98 |
+
"PBC_SELECTION": null,
|
| 99 |
+
"CHAINNAMES": null,
|
| 100 |
+
"MEMBRANES": null,
|
| 101 |
+
"CUSTOMS": null,
|
| 102 |
+
"ORIENTATION": null,
|
| 103 |
+
"PTM": [],
|
| 104 |
+
"MULTIMERIC": null,
|
| 105 |
+
"COLLECTIONS": "dynarepo",
|
| 106 |
+
"WARNINGS": [],
|
| 107 |
+
"BOXSIZEX": 9.19717,
|
| 108 |
+
"BOXSIZEY": 9.19717,
|
| 109 |
+
"BOXSIZEZ": 6.52234,
|
| 110 |
+
"mdName": "replica 1",
|
| 111 |
+
"mdAtoms": 2792,
|
| 112 |
+
"mdFrames": 5001
|
| 113 |
+
},
|
| 114 |
+
"mds": [
|
| 115 |
+
"replica 1",
|
| 116 |
+
"replica 2",
|
| 117 |
+
"replica 3"
|
| 118 |
+
],
|
| 119 |
+
"mdref": 0,
|
| 120 |
+
"files": [
|
| 121 |
+
"topology.tpr",
|
| 122 |
+
"screenshot.jpg",
|
| 123 |
+
"trajectory.bin",
|
| 124 |
+
"pca_trajectory_01.bin",
|
| 125 |
+
"pca_trajectory_02.bin",
|
| 126 |
+
"pca_trajectory_03.bin",
|
| 127 |
+
"pca_trajectory_04.bin",
|
| 128 |
+
"pca_trajectory_05.bin",
|
| 129 |
+
"pca_trajectory_06.bin",
|
| 130 |
+
"pca_trajectory_07.bin",
|
| 131 |
+
"pca_trajectory_08.bin",
|
| 132 |
+
"pca_trajectory_09.bin",
|
| 133 |
+
"pca_trajectory_10.bin",
|
| 134 |
+
"pca_trajectory_11.bin",
|
| 135 |
+
"pca_trajectory_12.bin",
|
| 136 |
+
"pca_trajectory_13.bin",
|
| 137 |
+
"pca_trajectory_14.bin",
|
| 138 |
+
"pca_trajectory_15.bin",
|
| 139 |
+
"structure.pdb",
|
| 140 |
+
"trajectory.xtc",
|
| 141 |
+
"clusters_00_screenshot_00.jpg",
|
| 142 |
+
"clusters_00_screenshot_01.jpg",
|
| 143 |
+
"clusters_00_screenshot_02.jpg",
|
| 144 |
+
"clusters_00_screenshot_03.jpg",
|
| 145 |
+
"clusters_00_screenshot_04.jpg",
|
| 146 |
+
"clusters_00_screenshot_05.jpg",
|
| 147 |
+
"clusters_00_screenshot_06.jpg",
|
| 148 |
+
"clusters_00_screenshot_07.jpg",
|
| 149 |
+
"clusters_00_screenshot_08.jpg",
|
| 150 |
+
"clusters_00_screenshot_09.jpg",
|
| 151 |
+
"clusters_00_screenshot_10.jpg",
|
| 152 |
+
"clusters_00_screenshot_11.jpg",
|
| 153 |
+
"clusters_00_screenshot_12.jpg",
|
| 154 |
+
"clusters_00_screenshot_13.jpg",
|
| 155 |
+
"clusters_00_screenshot_14.jpg",
|
| 156 |
+
"clusters_00_screenshot_15.jpg",
|
| 157 |
+
"clusters_00_screenshot_16.jpg",
|
| 158 |
+
"clusters_00_screenshot_17.jpg",
|
| 159 |
+
"clusters_00_screenshot_18.jpg",
|
| 160 |
+
"clusters_00_screenshot_19.jpg",
|
| 161 |
+
"clusters_00_screenshot_20.jpg",
|
| 162 |
+
"clusters_00_screenshot_21.jpg",
|
| 163 |
+
"clusters_01_screenshot_00.jpg",
|
| 164 |
+
"clusters_01_screenshot_01.jpg",
|
| 165 |
+
"clusters_01_screenshot_02.jpg",
|
| 166 |
+
"clusters_01_screenshot_03.jpg",
|
| 167 |
+
"clusters_01_screenshot_04.jpg",
|
| 168 |
+
"clusters_01_screenshot_05.jpg",
|
| 169 |
+
"clusters_01_screenshot_06.jpg",
|
| 170 |
+
"clusters_01_screenshot_07.jpg",
|
| 171 |
+
"clusters_01_screenshot_08.jpg",
|
| 172 |
+
"clusters_01_screenshot_09.jpg",
|
| 173 |
+
"clusters_01_screenshot_10.jpg",
|
| 174 |
+
"clusters_01_screenshot_11.jpg",
|
| 175 |
+
"clusters_01_screenshot_12.jpg",
|
| 176 |
+
"clusters_01_screenshot_13.jpg",
|
| 177 |
+
"clusters_01_screenshot_14.jpg",
|
| 178 |
+
"clusters_01_screenshot_15.jpg",
|
| 179 |
+
"clusters_01_screenshot_16.jpg",
|
| 180 |
+
"clusters_01_screenshot_17.jpg",
|
| 181 |
+
"clusters_01_screenshot_18.jpg",
|
| 182 |
+
"clusters_01_screenshot_19.jpg",
|
| 183 |
+
"clusters_02_screenshot_00.jpg",
|
| 184 |
+
"clusters_02_screenshot_01.jpg",
|
| 185 |
+
"clusters_02_screenshot_02.jpg",
|
| 186 |
+
"clusters_02_screenshot_03.jpg",
|
| 187 |
+
"clusters_02_screenshot_04.jpg",
|
| 188 |
+
"clusters_02_screenshot_05.jpg",
|
| 189 |
+
"clusters_02_screenshot_06.jpg",
|
| 190 |
+
"clusters_02_screenshot_07.jpg",
|
| 191 |
+
"clusters_02_screenshot_08.jpg",
|
| 192 |
+
"clusters_02_screenshot_09.jpg",
|
| 193 |
+
"clusters_02_screenshot_10.jpg",
|
| 194 |
+
"clusters_02_screenshot_11.jpg",
|
| 195 |
+
"clusters_02_screenshot_12.jpg",
|
| 196 |
+
"clusters_02_screenshot_13.jpg",
|
| 197 |
+
"clusters_02_screenshot_14.jpg",
|
| 198 |
+
"clusters_02_screenshot_15.jpg",
|
| 199 |
+
"clusters_02_screenshot_16.jpg",
|
| 200 |
+
"clusters_02_screenshot_17.jpg",
|
| 201 |
+
"clusters_03_screenshot_00.jpg",
|
| 202 |
+
"clusters_03_screenshot_01.jpg",
|
| 203 |
+
"clusters_03_screenshot_02.jpg",
|
| 204 |
+
"clusters_03_screenshot_03.jpg",
|
| 205 |
+
"clusters_03_screenshot_04.jpg",
|
| 206 |
+
"clusters_03_screenshot_05.jpg",
|
| 207 |
+
"clusters_03_screenshot_06.jpg",
|
| 208 |
+
"clusters_03_screenshot_07.jpg",
|
| 209 |
+
"clusters_03_screenshot_08.jpg",
|
| 210 |
+
"clusters_03_screenshot_09.jpg",
|
| 211 |
+
"clusters_03_screenshot_10.jpg",
|
| 212 |
+
"clusters_03_screenshot_11.jpg",
|
| 213 |
+
"clusters_03_screenshot_12.jpg",
|
| 214 |
+
"clusters_03_screenshot_13.jpg",
|
| 215 |
+
"clusters_03_screenshot_14.jpg",
|
| 216 |
+
"clusters_03_screenshot_15.jpg",
|
| 217 |
+
"clusters_03_screenshot_16.jpg",
|
| 218 |
+
"clusters_03_screenshot_17.jpg",
|
| 219 |
+
"clusters_03_screenshot_18.jpg",
|
| 220 |
+
"clusters_03_screenshot_19.jpg",
|
| 221 |
+
"pocket_01.pdb",
|
| 222 |
+
"pocket_02.pdb",
|
| 223 |
+
"pocket_03.pdb"
|
| 224 |
+
],
|
| 225 |
+
"analyses": [
|
| 226 |
+
"clusters",
|
| 227 |
+
"clusters-00",
|
| 228 |
+
"clusters-01",
|
| 229 |
+
"clusters-02",
|
| 230 |
+
"clusters-03",
|
| 231 |
+
"dist-perres",
|
| 232 |
+
"energies",
|
| 233 |
+
"fluctuation",
|
| 234 |
+
"hbonds",
|
| 235 |
+
"interactions",
|
| 236 |
+
"pca",
|
| 237 |
+
"pockets",
|
| 238 |
+
"rgyr",
|
| 239 |
+
"rmsd-pairwise",
|
| 240 |
+
"rmsd-perres",
|
| 241 |
+
"rmsds",
|
| 242 |
+
"sasa",
|
| 243 |
+
"tmscores"
|
| 244 |
+
],
|
| 245 |
+
"mdIndex": 0,
|
| 246 |
+
"mdNumber": 1,
|
| 247 |
+
"refframe": 0,
|
| 248 |
+
"internalId": "68432e3a4843165481b90409",
|
| 249 |
+
"creationDate": "2025-06-06T18:06:50.000Z",
|
| 250 |
+
"identifier": "A00AM"
|
| 251 |
+
}
|
data/files/A00AM/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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| 3 |
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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 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"6CO2"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q96DE0",
|
| 31 |
+
"Q12888"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GAKRLELGEALALGSGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHLTEGPHRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAREQLLEALQDLGLL",
|
| 38 |
+
"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 |
+
"SYSTRES": 478,
|
| 60 |
+
"PROTATS": 7509,
|
| 61 |
+
"PROTRES": 478,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
+
"CARBATS": 0,
|
| 67 |
+
"CARBRES": 0,
|
| 68 |
+
"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"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 |
+
"agent_2": "chain C",
|
| 94 |
+
"selection_1": "chain B",
|
| 95 |
+
"selection_2": "chain C",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
}
|
| 98 |
+
],
|
| 99 |
+
"PBC_SELECTION": null,
|
| 100 |
+
"CHAINNAMES": null,
|
| 101 |
+
"MEMBRANES": null,
|
| 102 |
+
"CUSTOMS": null,
|
| 103 |
+
"ORIENTATION": null,
|
| 104 |
+
"PTM": [],
|
| 105 |
+
"MULTIMERIC": null,
|
| 106 |
+
"COLLECTIONS": "dynarepo",
|
| 107 |
+
"WARNINGS": [],
|
| 108 |
+
"BOXSIZEX": 11.6008,
|
| 109 |
+
"BOXSIZEY": 11.6008,
|
| 110 |
+
"BOXSIZEZ": 8.23039,
|
| 111 |
+
"mdName": "replica 1",
|
| 112 |
+
"mdAtoms": 7509,
|
| 113 |
+
"mdFrames": 5001
|
| 114 |
+
},
|
| 115 |
+
"mds": [
|
| 116 |
+
"replica 1",
|
| 117 |
+
"replica 2",
|
| 118 |
+
"replica 3"
|
| 119 |
+
],
|
| 120 |
+
"mdref": 0,
|
| 121 |
+
"files": [
|
| 122 |
+
"topology.tpr",
|
| 123 |
+
"screenshot.jpg",
|
| 124 |
+
"trajectory.bin",
|
| 125 |
+
"pca_trajectory_01.bin",
|
| 126 |
+
"pca_trajectory_02.bin",
|
| 127 |
+
"pca_trajectory_03.bin",
|
| 128 |
+
"pca_trajectory_04.bin",
|
| 129 |
+
"pca_trajectory_05.bin",
|
| 130 |
+
"pca_trajectory_06.bin",
|
| 131 |
+
"pca_trajectory_07.bin",
|
| 132 |
+
"pca_trajectory_08.bin",
|
| 133 |
+
"pca_trajectory_09.bin",
|
| 134 |
+
"pca_trajectory_10.bin",
|
| 135 |
+
"pca_trajectory_11.bin",
|
| 136 |
+
"structure.pdb",
|
| 137 |
+
"trajectory.xtc",
|
| 138 |
+
"clusters_00_screenshot_00.jpg",
|
| 139 |
+
"clusters_00_screenshot_01.jpg",
|
| 140 |
+
"clusters_00_screenshot_02.jpg",
|
| 141 |
+
"clusters_00_screenshot_03.jpg",
|
| 142 |
+
"clusters_00_screenshot_04.jpg",
|
| 143 |
+
"clusters_00_screenshot_05.jpg",
|
| 144 |
+
"clusters_00_screenshot_06.jpg",
|
| 145 |
+
"clusters_00_screenshot_07.jpg",
|
| 146 |
+
"clusters_00_screenshot_08.jpg",
|
| 147 |
+
"clusters_00_screenshot_09.jpg",
|
| 148 |
+
"clusters_00_screenshot_10.jpg",
|
| 149 |
+
"clusters_00_screenshot_11.jpg",
|
| 150 |
+
"clusters_00_screenshot_12.jpg",
|
| 151 |
+
"clusters_00_screenshot_13.jpg",
|
| 152 |
+
"clusters_00_screenshot_14.jpg",
|
| 153 |
+
"clusters_00_screenshot_15.jpg",
|
| 154 |
+
"clusters_00_screenshot_16.jpg",
|
| 155 |
+
"clusters_00_screenshot_17.jpg",
|
| 156 |
+
"clusters_00_screenshot_18.jpg",
|
| 157 |
+
"clusters_00_screenshot_19.jpg",
|
| 158 |
+
"clusters_01_screenshot_00.jpg",
|
| 159 |
+
"clusters_01_screenshot_01.jpg",
|
| 160 |
+
"clusters_01_screenshot_02.jpg",
|
| 161 |
+
"clusters_01_screenshot_03.jpg",
|
| 162 |
+
"clusters_01_screenshot_04.jpg",
|
| 163 |
+
"clusters_01_screenshot_05.jpg",
|
| 164 |
+
"clusters_01_screenshot_06.jpg",
|
| 165 |
+
"clusters_01_screenshot_07.jpg",
|
| 166 |
+
"clusters_01_screenshot_08.jpg",
|
| 167 |
+
"clusters_01_screenshot_09.jpg",
|
| 168 |
+
"clusters_01_screenshot_10.jpg",
|
| 169 |
+
"clusters_01_screenshot_11.jpg",
|
| 170 |
+
"clusters_01_screenshot_12.jpg",
|
| 171 |
+
"clusters_01_screenshot_13.jpg",
|
| 172 |
+
"clusters_01_screenshot_14.jpg",
|
| 173 |
+
"clusters_01_screenshot_15.jpg",
|
| 174 |
+
"clusters_01_screenshot_16.jpg",
|
| 175 |
+
"clusters_01_screenshot_17.jpg",
|
| 176 |
+
"clusters_01_screenshot_18.jpg",
|
| 177 |
+
"clusters_01_screenshot_19.jpg",
|
| 178 |
+
"clusters_02_screenshot_00.jpg",
|
| 179 |
+
"clusters_02_screenshot_01.jpg",
|
| 180 |
+
"clusters_02_screenshot_02.jpg",
|
| 181 |
+
"clusters_02_screenshot_03.jpg",
|
| 182 |
+
"clusters_02_screenshot_04.jpg",
|
| 183 |
+
"clusters_02_screenshot_05.jpg",
|
| 184 |
+
"clusters_02_screenshot_06.jpg",
|
| 185 |
+
"clusters_02_screenshot_07.jpg",
|
| 186 |
+
"clusters_02_screenshot_08.jpg",
|
| 187 |
+
"clusters_02_screenshot_09.jpg",
|
| 188 |
+
"clusters_02_screenshot_10.jpg",
|
| 189 |
+
"clusters_02_screenshot_11.jpg",
|
| 190 |
+
"clusters_02_screenshot_12.jpg",
|
| 191 |
+
"clusters_02_screenshot_13.jpg",
|
| 192 |
+
"clusters_02_screenshot_14.jpg",
|
| 193 |
+
"clusters_02_screenshot_15.jpg",
|
| 194 |
+
"clusters_02_screenshot_16.jpg",
|
| 195 |
+
"clusters_02_screenshot_17.jpg",
|
| 196 |
+
"clusters_02_screenshot_18.jpg",
|
| 197 |
+
"clusters_02_screenshot_19.jpg",
|
| 198 |
+
"clusters_03_screenshot_00.jpg",
|
| 199 |
+
"clusters_03_screenshot_01.jpg",
|
| 200 |
+
"clusters_03_screenshot_02.jpg",
|
| 201 |
+
"clusters_03_screenshot_03.jpg",
|
| 202 |
+
"clusters_03_screenshot_04.jpg",
|
| 203 |
+
"clusters_03_screenshot_05.jpg",
|
| 204 |
+
"clusters_03_screenshot_06.jpg",
|
| 205 |
+
"clusters_03_screenshot_07.jpg",
|
| 206 |
+
"clusters_03_screenshot_08.jpg",
|
| 207 |
+
"clusters_03_screenshot_09.jpg",
|
| 208 |
+
"clusters_03_screenshot_10.jpg",
|
| 209 |
+
"clusters_03_screenshot_11.jpg",
|
| 210 |
+
"clusters_03_screenshot_12.jpg",
|
| 211 |
+
"clusters_03_screenshot_13.jpg",
|
| 212 |
+
"clusters_03_screenshot_14.jpg",
|
| 213 |
+
"clusters_03_screenshot_15.jpg",
|
| 214 |
+
"clusters_03_screenshot_16.jpg",
|
| 215 |
+
"clusters_03_screenshot_17.jpg",
|
| 216 |
+
"clusters_03_screenshot_18.jpg",
|
| 217 |
+
"clusters_03_screenshot_19.jpg",
|
| 218 |
+
"clusters_03_screenshot_20.jpg",
|
| 219 |
+
"clusters_03_screenshot_21.jpg",
|
| 220 |
+
"pocket_01.pdb",
|
| 221 |
+
"pocket_02.pdb",
|
| 222 |
+
"pocket_03.pdb",
|
| 223 |
+
"pocket_04.pdb",
|
| 224 |
+
"pocket_05.pdb",
|
| 225 |
+
"pocket_06.pdb"
|
| 226 |
+
],
|
| 227 |
+
"analyses": [
|
| 228 |
+
"clusters",
|
| 229 |
+
"clusters-00",
|
| 230 |
+
"clusters-01",
|
| 231 |
+
"clusters-02",
|
| 232 |
+
"clusters-03",
|
| 233 |
+
"dist-perres",
|
| 234 |
+
"energies",
|
| 235 |
+
"fluctuation",
|
| 236 |
+
"hbonds",
|
| 237 |
+
"interactions",
|
| 238 |
+
"pca",
|
| 239 |
+
"pockets",
|
| 240 |
+
"rgyr",
|
| 241 |
+
"rmsd-pairwise",
|
| 242 |
+
"rmsd-perres",
|
| 243 |
+
"rmsds",
|
| 244 |
+
"sasa",
|
| 245 |
+
"tmscores"
|
| 246 |
+
],
|
| 247 |
+
"mdIndex": 0,
|
| 248 |
+
"mdNumber": 1,
|
| 249 |
+
"refframe": 0,
|
| 250 |
+
"internalId": "68433049b96ba5f83fd5f931",
|
| 251 |
+
"creationDate": "2025-06-06T18:15:37.000Z",
|
| 252 |
+
"identifier": "A00AN"
|
| 253 |
+
}
|
data/files/A00AN/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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data/files/A00AO/project.json
ADDED
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@@ -0,0 +1,197 @@
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| 1 |
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{
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| 2 |
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"accession": "A00AO",
|
| 3 |
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|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 6CWG",
|
| 6 |
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|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
|
| 15 |
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|
| 16 |
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|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
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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",
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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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"6CWG"
|
| 27 |
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],
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| 28 |
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|
| 29 |
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"REFERENCES": [
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| 30 |
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| 31 |
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"P01764"
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| 32 |
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],
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| 33 |
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| 39 |
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],
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| 40 |
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|
| 41 |
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|
| 42 |
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"Ricin A chain",
|
| 43 |
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"Immunoglobulin heavy variable 3-23",
|
| 44 |
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"Ig-like",
|
| 45 |
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|
| 46 |
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| 47 |
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| 48 |
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| 49 |
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| 50 |
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| 51 |
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],
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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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],
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| 59 |
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"WAT": "TIP3P",
|
| 60 |
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| 61 |
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| 62 |
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| 63 |
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| 74 |
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| 75 |
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| 76 |
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| 77 |
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{
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| 78 |
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"name": "chain A-chain B interaction",
|
| 79 |
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"agent_1": "chain A",
|
| 80 |
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"agent_2": "chain B",
|
| 81 |
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"selection_1": "chain A",
|
| 82 |
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"selection_2": "chain B",
|
| 83 |
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"type": "protein-protein"
|
| 84 |
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}
|
| 85 |
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],
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| 86 |
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| 87 |
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| 93 |
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| 94 |
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|
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|
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],
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"analyses": [
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],
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"mdIndex": 0,
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data/files/A00AP/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A00AP",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6D13",
|
| 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 |
+
"6D13"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0A6K1",
|
| 31 |
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"P0A776"
|
| 32 |
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],
|
| 33 |
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|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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"SMQFSKMHGLGNDFMVVDAVTQNVFFSPELIRRLADRHLGVGFDQLLVVEPPYDPELDFHYRIFNADGSEVAQCGNGARCFARFVRLKGLTNKRDIRVSTANGRMVLTVTDDDLVRVNMGEPNFEPSAVPFRANKAEKTYIMRAAEQTILCGVVSMGNPHCVIQVDDVDTAAVETLGPVLESHERFPERANIGFMQVVKREHIRLRVYERGAGETQACGSGACAAVAVGIQQGLLAEEVRVELPGGRLDIAWKGPGHPLYMTGPAVHVYDGFIHL",
|
| 38 |
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|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
+
"Diaminopimelate epimerase",
|
| 43 |
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"Could be important to modulate the pK values of the two catalytic cysteine residues",
|
| 44 |
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"Important for dimerization",
|
| 45 |
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"RNA pyrophosphohydrolase",
|
| 46 |
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"Nudix hydrolase",
|
| 47 |
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"Nudix box"
|
| 48 |
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],
|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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| 61 |
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|
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|
| 67 |
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|
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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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"agent_1": "chain A",
|
| 77 |
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"agent_2": "chain B",
|
| 78 |
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"selection_1": "chain A",
|
| 79 |
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"selection_2": "chain B",
|
| 80 |
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"type": "protein-protein"
|
| 81 |
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}
|
| 82 |
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],
|
| 83 |
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"PBC_SELECTION": null,
|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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| 93 |
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"replica 1",
|
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"replica 2",
|
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|
| 103 |
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],
|
| 104 |
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"mdref": 0,
|
| 105 |
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"files": [
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| 106 |
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|
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"screenshot.jpg",
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"trajectory.bin",
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| 109 |
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"pca_trajectory_01.bin",
|
| 110 |
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"pca_trajectory_02.bin",
|
| 111 |
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"pca_trajectory_03.bin",
|
| 112 |
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|
| 113 |
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|
| 114 |
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"pca_trajectory_06.bin",
|
| 115 |
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"pca_trajectory_07.bin",
|
| 116 |
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"pca_trajectory_08.bin",
|
| 117 |
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"pca_trajectory_09.bin",
|
| 118 |
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"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",
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| 137 |
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|
| 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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|
| 141 |
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|
| 142 |
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"clusters_01_screenshot_01.jpg",
|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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"clusters_01_screenshot_05.jpg",
|
| 147 |
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"clusters_01_screenshot_06.jpg",
|
| 148 |
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"clusters_01_screenshot_07.jpg",
|
| 149 |
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"clusters_01_screenshot_08.jpg",
|
| 150 |
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"clusters_01_screenshot_09.jpg",
|
| 151 |
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"clusters_01_screenshot_10.jpg",
|
| 152 |
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"clusters_01_screenshot_11.jpg",
|
| 153 |
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"clusters_01_screenshot_12.jpg",
|
| 154 |
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"clusters_01_screenshot_13.jpg",
|
| 155 |
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"clusters_01_screenshot_14.jpg",
|
| 156 |
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"clusters_01_screenshot_15.jpg",
|
| 157 |
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"clusters_01_screenshot_16.jpg",
|
| 158 |
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"clusters_01_screenshot_17.jpg",
|
| 159 |
+
"clusters_01_screenshot_18.jpg",
|
| 160 |
+
"clusters_01_screenshot_19.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb"
|
| 165 |
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],
|
| 166 |
+
"analyses": [
|
| 167 |
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"clusters",
|
| 168 |
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"clusters-00",
|
| 169 |
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"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 |
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"tmscores"
|
| 183 |
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],
|
| 184 |
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|
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|
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|
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"creationDate": "2025-06-06T18:37:52.000Z",
|
| 189 |
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"identifier": "A00AP"
|
| 190 |
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}
|
data/files/A00AP/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00AP", "accession": "A00AP", "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 6D13", "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": ["6D13"], "FORCED_REFERENCES": null, "REFERENCES": ["P0A6K1", "P0A776"], 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