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A000U/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000U",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1GCQ",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"1GCQ"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P62993",
|
| 31 |
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"P27870"
|
| 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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"TYVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPVNR",
|
| 38 |
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"STYVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPV",
|
| 39 |
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"GSHMPKMEVFQEYYGIPPPPGAFGPFLRLNPGDIVELTKAEAEHNWWEGRNTATNEVGWFPCNRVHPYV"
|
| 40 |
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],
|
| 41 |
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"NUCLSEQ": [],
|
| 42 |
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"DOMAINS": [
|
| 43 |
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"Growth factor receptor-bound protein 2",
|
| 44 |
+
"SH3 2",
|
| 45 |
+
"Proto-oncogene vav",
|
| 46 |
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"SH3 1"
|
| 47 |
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],
|
| 48 |
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"FRAMESTEP": 0.1,
|
| 49 |
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"TIMESTEP": 2,
|
| 50 |
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"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
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"FF": [
|
| 53 |
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"CHARMM36m"
|
| 54 |
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],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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"BOXTYPE": "Dodecahedron",
|
| 57 |
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"SYSTATS": 2832,
|
| 58 |
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"SYSTRES": 182,
|
| 59 |
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"PROTATS": 2832,
|
| 60 |
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"PROTRES": 182,
|
| 61 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
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| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
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| 65 |
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"CARBATS": 0,
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| 66 |
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"CARBRES": 0,
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| 67 |
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"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
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"COUNCAT": 0,
|
| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
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{
|
| 74 |
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"name": "protein-protein interaction C-B",
|
| 75 |
+
"agent_1": "protein C",
|
| 76 |
+
"agent_2": "protein B",
|
| 77 |
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"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
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"type": "protein-protein"
|
| 80 |
+
},
|
| 81 |
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{
|
| 82 |
+
"name": "protein-protein interaction C-A",
|
| 83 |
+
"agent_1": "protein C",
|
| 84 |
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"agent_2": "protein A",
|
| 85 |
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"selection_1": "chain A",
|
| 86 |
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"selection_2": "chain C",
|
| 87 |
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"type": "protein-protein"
|
| 88 |
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},
|
| 89 |
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{
|
| 90 |
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"name": "protein-protein interaction B-A",
|
| 91 |
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"agent_1": "protein B",
|
| 92 |
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"agent_2": "protein A",
|
| 93 |
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"selection_1": "chain B",
|
| 94 |
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"selection_2": "chain C",
|
| 95 |
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"type": "protein-protein"
|
| 96 |
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}
|
| 97 |
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],
|
| 98 |
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"PBC_SELECTION": null,
|
| 99 |
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"CHAINNAMES": null,
|
| 100 |
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"MEMBRANES": null,
|
| 101 |
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"CUSTOMS": null,
|
| 102 |
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"ORIENTATION": null,
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| 103 |
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"PTM": [],
|
| 104 |
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"MULTIMERIC": null,
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| 105 |
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"COLLECTIONS": "dynarepo",
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| 106 |
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"WARNINGS": [],
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| 107 |
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"BOXSIZEX": 8.83195,
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| 108 |
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"BOXSIZEY": 8.83195,
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| 109 |
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"BOXSIZEZ": 6.20451,
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| 110 |
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"mdName": "replica 1",
|
| 111 |
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"mdAtoms": 2832,
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| 112 |
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"mdFrames": 5001
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| 113 |
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},
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| 114 |
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"mds": [
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| 115 |
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"replica 1",
|
| 116 |
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"replica 2",
|
| 117 |
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"replica 3"
|
| 118 |
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],
|
| 119 |
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"mdref": 0,
|
| 120 |
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"files": [
|
| 121 |
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"topology.tpr",
|
| 122 |
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"screenshot.jpg",
|
| 123 |
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"trajectory.bin",
|
| 124 |
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"pca_trajectory_01.bin",
|
| 125 |
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"pca_trajectory_02.bin",
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| 126 |
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| 127 |
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| 128 |
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"pca_trajectory_05.bin",
|
| 129 |
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"pca_trajectory_06.bin",
|
| 130 |
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"structure.pdb",
|
| 131 |
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"trajectory.xtc",
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| 132 |
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"clusters_00_screenshot_00.jpg",
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| 133 |
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| 134 |
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| 135 |
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| 139 |
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],
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"analyses": [
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"clusters",
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| 225 |
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| 226 |
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"rgyr",
|
| 227 |
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|
| 228 |
+
"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": "683f2afac496a23309feadf5",
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"creationDate": "2025-06-03T17:03:54.000Z",
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"identifier": "A000U"
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}
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| 1 |
+
{
|
| 2 |
+
"accession": "A000W",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1GPW",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1GPW"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9X0C6",
|
| 31 |
+
"Q9X0C8"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"MLAKRIIACLNVKDGRVVKGTNFENLRDSGDPVELGKFYSEIGIDELVFLDITASVEKRKTMLELVEKVAEQIDIPFTVGGGIHDFETASELILRGADKVSINTAAVENPSLITQIAQTFGSQAVVVAIDAKRVDGEFMVFTYSGKKNTGILLRDWVVEVEKRGAGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFREIDVRELKEYLKKHGVNVRLEGL",
|
| 38 |
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"MRIGIISVGPGNIMNLYRGVKRASENFEDVSIELVESPRNDLYDLLFIPGVGHFGEGMRRLRENDLIDFVRKHVEDERYVVGVCLGMQLLFEESEEAPGVKGLSLIEGNVVKLRSRRLPHMGWNEVIFKDTFPNGYYYFVHTYRAVCEEEHVLGTTEYDGEIFPSAVRKGRILGFQFHPEKSSKIGRKLLEKVIECSLSRR"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Imidazole glycerol phosphate synthase subunit HisF",
|
| 43 |
+
"Imidazole glycerol phosphate synthase subunit HisH",
|
| 44 |
+
"Glutamine amidotransferase type-1"
|
| 45 |
+
],
|
| 46 |
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"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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"SYSTRES": 454,
|
| 57 |
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|
| 58 |
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|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
+
"name": "protein-protein interaction A-B",
|
| 73 |
+
"agent_1": "protein A",
|
| 74 |
+
"agent_2": "protein B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
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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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"BOXSIZEZ": 7.64251,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 7197,
|
| 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 |
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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 |
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"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
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"pca_trajectory_11.bin",
|
| 117 |
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"pca_trajectory_12.bin",
|
| 118 |
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"pca_trajectory_13.bin",
|
| 119 |
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"pca_trajectory_14.bin",
|
| 120 |
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"pca_trajectory_15.bin",
|
| 121 |
+
"pca_trajectory_16.bin",
|
| 122 |
+
"structure.pdb",
|
| 123 |
+
"trajectory.xtc",
|
| 124 |
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"clusters_00_screenshot_00.jpg",
|
| 125 |
+
"clusters_00_screenshot_01.jpg",
|
| 126 |
+
"clusters_00_screenshot_02.jpg",
|
| 127 |
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"clusters_00_screenshot_03.jpg",
|
| 128 |
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"clusters_00_screenshot_04.jpg",
|
| 129 |
+
"clusters_00_screenshot_05.jpg",
|
| 130 |
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"clusters_00_screenshot_06.jpg",
|
| 131 |
+
"clusters_00_screenshot_07.jpg",
|
| 132 |
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"clusters_00_screenshot_08.jpg",
|
| 133 |
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"clusters_00_screenshot_09.jpg",
|
| 134 |
+
"clusters_00_screenshot_10.jpg",
|
| 135 |
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"clusters_00_screenshot_11.jpg",
|
| 136 |
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"clusters_00_screenshot_12.jpg",
|
| 137 |
+
"clusters_00_screenshot_13.jpg",
|
| 138 |
+
"clusters_00_screenshot_14.jpg",
|
| 139 |
+
"clusters_00_screenshot_15.jpg",
|
| 140 |
+
"clusters_00_screenshot_16.jpg",
|
| 141 |
+
"clusters_00_screenshot_17.jpg",
|
| 142 |
+
"clusters_00_screenshot_18.jpg",
|
| 143 |
+
"clusters_00_screenshot_19.jpg",
|
| 144 |
+
"clusters_01_screenshot_00.jpg",
|
| 145 |
+
"clusters_01_screenshot_01.jpg",
|
| 146 |
+
"clusters_01_screenshot_02.jpg",
|
| 147 |
+
"clusters_01_screenshot_03.jpg",
|
| 148 |
+
"clusters_01_screenshot_04.jpg",
|
| 149 |
+
"clusters_01_screenshot_05.jpg",
|
| 150 |
+
"clusters_01_screenshot_06.jpg",
|
| 151 |
+
"clusters_01_screenshot_07.jpg",
|
| 152 |
+
"clusters_01_screenshot_08.jpg",
|
| 153 |
+
"clusters_01_screenshot_09.jpg",
|
| 154 |
+
"clusters_01_screenshot_10.jpg",
|
| 155 |
+
"clusters_01_screenshot_11.jpg",
|
| 156 |
+
"clusters_01_screenshot_12.jpg",
|
| 157 |
+
"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
+
"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"clusters_01_screenshot_17.jpg",
|
| 162 |
+
"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"pocket_01.pdb",
|
| 164 |
+
"pocket_02.pdb",
|
| 165 |
+
"pocket_03.pdb",
|
| 166 |
+
"pocket_04.pdb",
|
| 167 |
+
"pocket_05.pdb",
|
| 168 |
+
"pocket_06.pdb",
|
| 169 |
+
"pocket_07.pdb",
|
| 170 |
+
"pocket_08.pdb",
|
| 171 |
+
"pocket_09.pdb",
|
| 172 |
+
"pocket_10.pdb"
|
| 173 |
+
],
|
| 174 |
+
"analyses": [
|
| 175 |
+
"clusters",
|
| 176 |
+
"clusters-00",
|
| 177 |
+
"clusters-01",
|
| 178 |
+
"dist-perres",
|
| 179 |
+
"energies",
|
| 180 |
+
"fluctuation",
|
| 181 |
+
"hbonds",
|
| 182 |
+
"interactions",
|
| 183 |
+
"pca",
|
| 184 |
+
"pockets",
|
| 185 |
+
"rgyr",
|
| 186 |
+
"rmsd-pairwise",
|
| 187 |
+
"rmsd-perres",
|
| 188 |
+
"rmsds",
|
| 189 |
+
"sasa",
|
| 190 |
+
"tmscores"
|
| 191 |
+
],
|
| 192 |
+
"mdIndex": 0,
|
| 193 |
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"mdNumber": 1,
|
| 194 |
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"refframe": 0,
|
| 195 |
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"internalId": "683f2e5c987902477d54c5b4",
|
| 196 |
+
"creationDate": "2025-06-03T17:18:20.000Z",
|
| 197 |
+
"identifier": "A000W"
|
| 198 |
+
}
|
A000W/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000W", "accession": "A000W", "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 1GPW", "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": ["1GPW"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9X0C6", "Q9X0C8"], 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|
A001C/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A001C",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1LFD",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1LFD"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q03386",
|
| 31 |
+
"P01112"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GDCCIIRVSLDVDNGNMYKSILVTSQDKAPTVIRKAMDKHNLDEDEPEDYELLQIISEDHKLKIPENANVFYAMNSAANYDFILKKR",
|
| 38 |
+
"MTEYKLVVVGAGGVGKSALTIQLIQNHFVDKYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ral guanine nucleotide dissociation stimulator",
|
| 43 |
+
"Ras-associating",
|
| 44 |
+
"GTPase HRas",
|
| 45 |
+
"GTPase HRas, N-terminally processed",
|
| 46 |
+
"Hypervariable region",
|
| 47 |
+
"Effector region"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 4036,
|
| 59 |
+
"SYSTRES": 254,
|
| 60 |
+
"PROTATS": 4036,
|
| 61 |
+
"PROTRES": 254,
|
| 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 |
+
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|
| 84 |
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"CHAINNAMES": null,
|
| 85 |
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"MEMBRANES": null,
|
| 86 |
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|
| 87 |
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"ORIENTATION": null,
|
| 88 |
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|
| 89 |
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"MULTIMERIC": null,
|
| 90 |
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"COLLECTIONS": "dynarepo",
|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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"mdName": "replica 1",
|
| 96 |
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|
| 97 |
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"mdFrames": 5001
|
| 98 |
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},
|
| 99 |
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"mds": [
|
| 100 |
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"replica 1",
|
| 101 |
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"replica 2",
|
| 102 |
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"replica 3"
|
| 103 |
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|
| 104 |
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"mdref": 0,
|
| 105 |
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"files": [
|
| 106 |
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"topology.tpr",
|
| 107 |
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"screenshot.jpg",
|
| 108 |
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"trajectory.bin",
|
| 109 |
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"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 |
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"pca_trajectory_06.bin",
|
| 115 |
+
"pca_trajectory_07.bin",
|
| 116 |
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"pca_trajectory_08.bin",
|
| 117 |
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"pca_trajectory_09.bin",
|
| 118 |
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"pca_trajectory_10.bin",
|
| 119 |
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"pca_trajectory_11.bin",
|
| 120 |
+
"pca_trajectory_12.bin",
|
| 121 |
+
"pca_trajectory_13.bin",
|
| 122 |
+
"pca_trajectory_14.bin",
|
| 123 |
+
"structure.pdb",
|
| 124 |
+
"trajectory.xtc",
|
| 125 |
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"clusters_00_screenshot_00.jpg",
|
| 126 |
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"clusters_00_screenshot_01.jpg",
|
| 127 |
+
"clusters_00_screenshot_02.jpg",
|
| 128 |
+
"clusters_00_screenshot_03.jpg",
|
| 129 |
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"clusters_00_screenshot_04.jpg",
|
| 130 |
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"clusters_00_screenshot_05.jpg",
|
| 131 |
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"clusters_00_screenshot_06.jpg",
|
| 132 |
+
"clusters_00_screenshot_07.jpg",
|
| 133 |
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"clusters_00_screenshot_08.jpg",
|
| 134 |
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"clusters_00_screenshot_09.jpg",
|
| 135 |
+
"clusters_00_screenshot_10.jpg",
|
| 136 |
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"clusters_00_screenshot_11.jpg",
|
| 137 |
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"clusters_00_screenshot_12.jpg",
|
| 138 |
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"clusters_00_screenshot_13.jpg",
|
| 139 |
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"clusters_00_screenshot_14.jpg",
|
| 140 |
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"clusters_00_screenshot_15.jpg",
|
| 141 |
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"clusters_00_screenshot_16.jpg",
|
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+
"clusters_00_screenshot_17.jpg",
|
| 143 |
+
"clusters_00_screenshot_18.jpg",
|
| 144 |
+
"clusters_00_screenshot_19.jpg",
|
| 145 |
+
"clusters_01_screenshot_00.jpg",
|
| 146 |
+
"clusters_01_screenshot_01.jpg",
|
| 147 |
+
"clusters_01_screenshot_02.jpg",
|
| 148 |
+
"clusters_01_screenshot_03.jpg",
|
| 149 |
+
"clusters_01_screenshot_04.jpg",
|
| 150 |
+
"clusters_01_screenshot_05.jpg",
|
| 151 |
+
"clusters_01_screenshot_06.jpg",
|
| 152 |
+
"clusters_01_screenshot_07.jpg",
|
| 153 |
+
"clusters_01_screenshot_08.jpg",
|
| 154 |
+
"clusters_01_screenshot_09.jpg",
|
| 155 |
+
"clusters_01_screenshot_10.jpg",
|
| 156 |
+
"clusters_01_screenshot_11.jpg",
|
| 157 |
+
"clusters_01_screenshot_12.jpg",
|
| 158 |
+
"clusters_01_screenshot_13.jpg",
|
| 159 |
+
"clusters_01_screenshot_14.jpg",
|
| 160 |
+
"clusters_01_screenshot_15.jpg",
|
| 161 |
+
"clusters_01_screenshot_16.jpg",
|
| 162 |
+
"clusters_01_screenshot_17.jpg",
|
| 163 |
+
"clusters_01_screenshot_18.jpg",
|
| 164 |
+
"clusters_01_screenshot_19.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb"
|
| 173 |
+
],
|
| 174 |
+
"analyses": [
|
| 175 |
+
"clusters",
|
| 176 |
+
"clusters-00",
|
| 177 |
+
"clusters-01",
|
| 178 |
+
"dist-perres",
|
| 179 |
+
"energies",
|
| 180 |
+
"fluctuation",
|
| 181 |
+
"hbonds",
|
| 182 |
+
"interactions",
|
| 183 |
+
"pca",
|
| 184 |
+
"pockets",
|
| 185 |
+
"rgyr",
|
| 186 |
+
"rmsd-pairwise",
|
| 187 |
+
"rmsd-perres",
|
| 188 |
+
"rmsds",
|
| 189 |
+
"sasa",
|
| 190 |
+
"tmscores"
|
| 191 |
+
],
|
| 192 |
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"mdIndex": 0,
|
| 193 |
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"mdNumber": 1,
|
| 194 |
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"refframe": 1,
|
| 195 |
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"internalId": "683f4c87fe3dce5cc8b2a884",
|
| 196 |
+
"creationDate": "2025-06-03T19:27:03.000Z",
|
| 197 |
+
"identifier": "A001C"
|
| 198 |
+
}
|
A001C/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
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|
A002F/project.json
ADDED
|
@@ -0,0 +1,192 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A002F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1XQS",
|
| 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 |
+
"1XQS"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9NZL4",
|
| 31 |
+
"P0DMV8"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"RGEVEQMKSCLRVLSQPMPPTAGEAEQAADQQEREGALELLADLCENMDNAADFCQLSGMHLLVGRYLEAGAAGLRWRAAQLIGTCSQNVAAIQEQVLGLGALRKLLRLLDRDACDTVRVKALFAISCLVREQEAGLLQFLRLDGFSVLMRAMQQQVQKLKVKSAFLLQNLLVGHPEHKGTLCSMGMVQQLVALVRTEHSPFHEHVLGALCSLVTDFPQGVRECREPELGLEELLRHRCQLLQQHEEYQEELEFCEKLLQTCFS",
|
| 38 |
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"ERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Hsp70-binding protein 1",
|
| 43 |
+
"Heat shock 70 kDa protein 1A",
|
| 44 |
+
"Nucleotide-binding domain (NBD)"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 6783,
|
| 56 |
+
"SYSTRES": 429,
|
| 57 |
+
"PROTATS": 6783,
|
| 58 |
+
"PROTRES": 429,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 11.0148,
|
| 90 |
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"BOXSIZEY": 11.0148,
|
| 91 |
+
"BOXSIZEZ": 7.73571,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 6783,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"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 |
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"pca_trajectory_05.bin",
|
| 111 |
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"pca_trajectory_06.bin",
|
| 112 |
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"pca_trajectory_07.bin",
|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
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"structure.pdb",
|
| 115 |
+
"trajectory.xtc",
|
| 116 |
+
"clusters_00_screenshot_00.jpg",
|
| 117 |
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"clusters_00_screenshot_01.jpg",
|
| 118 |
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"clusters_00_screenshot_02.jpg",
|
| 119 |
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"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 |
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"clusters_00_screenshot_09.jpg",
|
| 126 |
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"clusters_00_screenshot_10.jpg",
|
| 127 |
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"clusters_00_screenshot_11.jpg",
|
| 128 |
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"clusters_00_screenshot_12.jpg",
|
| 129 |
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"clusters_00_screenshot_13.jpg",
|
| 130 |
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"clusters_00_screenshot_14.jpg",
|
| 131 |
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"clusters_00_screenshot_15.jpg",
|
| 132 |
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"clusters_00_screenshot_16.jpg",
|
| 133 |
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"clusters_00_screenshot_17.jpg",
|
| 134 |
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"clusters_00_screenshot_18.jpg",
|
| 135 |
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"clusters_00_screenshot_19.jpg",
|
| 136 |
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"clusters_00_screenshot_20.jpg",
|
| 137 |
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"clusters_01_screenshot_00.jpg",
|
| 138 |
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"clusters_01_screenshot_01.jpg",
|
| 139 |
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"clusters_01_screenshot_02.jpg",
|
| 140 |
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"clusters_01_screenshot_03.jpg",
|
| 141 |
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"clusters_01_screenshot_04.jpg",
|
| 142 |
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"clusters_01_screenshot_05.jpg",
|
| 143 |
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"clusters_01_screenshot_06.jpg",
|
| 144 |
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"clusters_01_screenshot_07.jpg",
|
| 145 |
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"clusters_01_screenshot_08.jpg",
|
| 146 |
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"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 |
+
"clusters_01_screenshot_20.jpg",
|
| 158 |
+
"clusters_01_screenshot_21.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 |
+
],
|
| 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 |
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"mdNumber": 1,
|
| 188 |
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"refframe": 0,
|
| 189 |
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"internalId": "683f8b9943a9d19eee6f9bd1",
|
| 190 |
+
"creationDate": "2025-06-03T23:56:09.000Z",
|
| 191 |
+
"identifier": "A002F"
|
| 192 |
+
}
|
A002F/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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A0040/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A0040",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2W8B",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"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 |
+
"2W8B"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0A855",
|
| 31 |
+
"P0A912"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"QNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYL",
|
| 38 |
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"EVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPSLAPNGTMVLYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tol-Pal system protein TolB",
|
| 43 |
+
"TolA box",
|
| 44 |
+
"Peptidoglycan-associated lipoprotein",
|
| 45 |
+
"OmpA-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 |
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|
| 57 |
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"SYSTRES": 517,
|
| 58 |
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"PROTATS": 7767,
|
| 59 |
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"PROTRES": 517,
|
| 60 |
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|
| 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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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
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"COUNANI": 0,
|
| 70 |
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"COUNION": 0,
|
| 71 |
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"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
+
"CHAINNAMES": null,
|
| 83 |
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"MEMBRANES": null,
|
| 84 |
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"CUSTOMS": null,
|
| 85 |
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"ORIENTATION": null,
|
| 86 |
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"PTM": [],
|
| 87 |
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"MULTIMERIC": null,
|
| 88 |
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"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 11.7628,
|
| 91 |
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"BOXSIZEY": 11.7628,
|
| 92 |
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"BOXSIZEZ": 8.31858,
|
| 93 |
+
"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 7767,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
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"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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"topology.tpr",
|
| 105 |
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"screenshot.jpg",
|
| 106 |
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"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 |
+
"structure.pdb",
|
| 117 |
+
"trajectory.xtc",
|
| 118 |
+
"clusters_00_screenshot_00.jpg",
|
| 119 |
+
"clusters_00_screenshot_01.jpg",
|
| 120 |
+
"clusters_00_screenshot_02.jpg",
|
| 121 |
+
"clusters_00_screenshot_03.jpg",
|
| 122 |
+
"clusters_00_screenshot_04.jpg",
|
| 123 |
+
"clusters_00_screenshot_05.jpg",
|
| 124 |
+
"clusters_00_screenshot_06.jpg",
|
| 125 |
+
"clusters_00_screenshot_07.jpg",
|
| 126 |
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"clusters_00_screenshot_08.jpg",
|
| 127 |
+
"clusters_00_screenshot_09.jpg",
|
| 128 |
+
"clusters_00_screenshot_10.jpg",
|
| 129 |
+
"clusters_00_screenshot_11.jpg",
|
| 130 |
+
"clusters_00_screenshot_12.jpg",
|
| 131 |
+
"clusters_00_screenshot_13.jpg",
|
| 132 |
+
"clusters_00_screenshot_14.jpg",
|
| 133 |
+
"clusters_00_screenshot_15.jpg",
|
| 134 |
+
"clusters_00_screenshot_16.jpg",
|
| 135 |
+
"clusters_00_screenshot_17.jpg",
|
| 136 |
+
"clusters_00_screenshot_18.jpg",
|
| 137 |
+
"clusters_00_screenshot_19.jpg",
|
| 138 |
+
"clusters_00_screenshot_20.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 |
+
"mdIndex": 0,
|
| 189 |
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"mdNumber": 1,
|
| 190 |
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"refframe": 0,
|
| 191 |
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"internalId": "68409dcb8a2553024048ca37",
|
| 192 |
+
"creationDate": "2025-06-04T19:26:03.000Z",
|
| 193 |
+
"identifier": "A0040"
|
| 194 |
+
}
|
A0040/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0040", "accession": "A0040", "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 2W8B", "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": ["2W8B"], "FORCED_REFERENCES": null, "REFERENCES": ["P0A855", "P0A912"], 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|
A0042/project.json
ADDED
|
@@ -0,0 +1,192 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0042",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 2WO3",
|
| 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 |
+
"2WO3"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P54764",
|
| 31 |
+
"O43921"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TGEVTLLDSRSVQGELGWIASPLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDCNSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNTEIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKR",
|
| 38 |
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"NSDRYAVYWNRSNPRFHAGAGDDGGGYTVEVSINDYLDIYCPHYGAPLPPAERMEHYVLYMVNGEGHASCDHRQRGFKRWECNRPAAPGGPLKFSEKFQLFTPFSLGFEFRPGHEYYYISATPPNAVDRPCLRLKVYVRPTQ"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ephrin type-A receptor 4",
|
| 43 |
+
"Eph LBD",
|
| 44 |
+
"Ephrin-A2",
|
| 45 |
+
"Ephrin RBD"
|
| 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": 5040,
|
| 57 |
+
"SYSTRES": 318,
|
| 58 |
+
"PROTATS": 5040,
|
| 59 |
+
"PROTRES": 318,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
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"CARBATS": 0,
|
| 65 |
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"CARBRES": 0,
|
| 66 |
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"SOLVATS": 0,
|
| 67 |
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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
+
"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 |
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"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
+
"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 9.54765,
|
| 91 |
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"BOXSIZEY": 9.54765,
|
| 92 |
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"BOXSIZEZ": 6.72566,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 5040,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
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"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
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],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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"topology.tpr",
|
| 105 |
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"screenshot.jpg",
|
| 106 |
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"trajectory.bin",
|
| 107 |
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"pca_trajectory_01.bin",
|
| 108 |
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"pca_trajectory_02.bin",
|
| 109 |
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|
| 110 |
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"pca_trajectory_04.bin",
|
| 111 |
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"pca_trajectory_05.bin",
|
| 112 |
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|
| 113 |
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"pca_trajectory_07.bin",
|
| 114 |
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|
| 115 |
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|
| 116 |
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|
| 117 |
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|
| 118 |
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|
| 119 |
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"structure.pdb",
|
| 120 |
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"trajectory.xtc",
|
| 121 |
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"clusters_00_screenshot_00.jpg",
|
| 122 |
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"clusters_00_screenshot_01.jpg",
|
| 123 |
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"clusters_00_screenshot_02.jpg",
|
| 124 |
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"clusters_00_screenshot_03.jpg",
|
| 125 |
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"clusters_00_screenshot_04.jpg",
|
| 126 |
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"clusters_00_screenshot_05.jpg",
|
| 127 |
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"clusters_00_screenshot_06.jpg",
|
| 128 |
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"clusters_00_screenshot_07.jpg",
|
| 129 |
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"clusters_00_screenshot_08.jpg",
|
| 130 |
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"clusters_00_screenshot_09.jpg",
|
| 131 |
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"clusters_00_screenshot_10.jpg",
|
| 132 |
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"clusters_00_screenshot_11.jpg",
|
| 133 |
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"clusters_00_screenshot_12.jpg",
|
| 134 |
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"clusters_00_screenshot_13.jpg",
|
| 135 |
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"clusters_00_screenshot_14.jpg",
|
| 136 |
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"clusters_00_screenshot_15.jpg",
|
| 137 |
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"clusters_00_screenshot_16.jpg",
|
| 138 |
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"clusters_00_screenshot_17.jpg",
|
| 139 |
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"clusters_00_screenshot_18.jpg",
|
| 140 |
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"clusters_00_screenshot_19.jpg",
|
| 141 |
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"clusters_01_screenshot_00.jpg",
|
| 142 |
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"clusters_01_screenshot_01.jpg",
|
| 143 |
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"clusters_01_screenshot_02.jpg",
|
| 144 |
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"clusters_01_screenshot_03.jpg",
|
| 145 |
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"clusters_01_screenshot_04.jpg",
|
| 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 |
+
"clusters_01_screenshot_11.jpg",
|
| 153 |
+
"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 |
+
"pocket_05.pdb",
|
| 166 |
+
"pocket_06.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 |
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"rmsd-perres",
|
| 182 |
+
"rmsds",
|
| 183 |
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"sasa",
|
| 184 |
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"tmscores"
|
| 185 |
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],
|
| 186 |
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"mdIndex": 0,
|
| 187 |
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"mdNumber": 1,
|
| 188 |
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"refframe": 0,
|
| 189 |
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"internalId": "6840a260ba0364e14d82393b",
|
| 190 |
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"creationDate": "2025-06-04T19:45:36.000Z",
|
| 191 |
+
"identifier": "A0042"
|
| 192 |
+
}
|
A0042/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
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A005Q/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A005Q",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3ONL",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
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|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
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|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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|
| 34 |
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|
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|
| 36 |
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|
| 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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"ENTH",
|
| 45 |
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"Disordered",
|
| 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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|
| 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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| 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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"name": "chain A-chain B interaction",
|
| 75 |
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|
| 76 |
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|
| 77 |
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"selection_1": "chain A",
|
| 78 |
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"selection_2": "chain B",
|
| 79 |
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"type": "protein-protein"
|
| 80 |
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},
|
| 81 |
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{
|
| 82 |
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"name": "chain A-chain C interaction",
|
| 83 |
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|
| 84 |
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|
| 85 |
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"selection_1": "chain A",
|
| 86 |
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"selection_2": "chain C",
|
| 87 |
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"type": "protein-protein"
|
| 88 |
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}
|
| 89 |
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],
|
| 90 |
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|
| 91 |
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| 92 |
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|
| 93 |
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| 94 |
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| 95 |
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| 96 |
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|
| 98 |
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|
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|
| 105 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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],
|
| 111 |
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"mdref": 0,
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| 112 |
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"files": [
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| 113 |
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| 116 |
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|
| 117 |
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| 118 |
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| 119 |
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|
| 120 |
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| 121 |
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| 122 |
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|
| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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| 132 |
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| 133 |
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|
| 134 |
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|
| 135 |
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| 136 |
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|
| 137 |
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|
| 138 |
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"clusters_00_screenshot_07.jpg",
|
| 139 |
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|
| 140 |
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"clusters_00_screenshot_09.jpg",
|
| 141 |
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"clusters_00_screenshot_10.jpg",
|
| 142 |
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"clusters_00_screenshot_11.jpg",
|
| 143 |
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"clusters_00_screenshot_12.jpg",
|
| 144 |
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"clusters_00_screenshot_13.jpg",
|
| 145 |
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"clusters_00_screenshot_14.jpg",
|
| 146 |
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|
| 147 |
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|
| 148 |
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"clusters_00_screenshot_17.jpg",
|
| 149 |
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"clusters_01_screenshot_00.jpg",
|
| 150 |
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"clusters_01_screenshot_01.jpg",
|
| 151 |
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"clusters_01_screenshot_02.jpg",
|
| 152 |
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"clusters_01_screenshot_03.jpg",
|
| 153 |
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|
| 154 |
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|
| 155 |
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| 156 |
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| 157 |
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| 158 |
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| 159 |
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| 160 |
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| 161 |
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|
| 162 |
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| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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|
| 167 |
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|
| 168 |
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|
| 169 |
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|
| 170 |
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|
| 171 |
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| 172 |
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|
| 173 |
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| 176 |
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| 179 |
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| 180 |
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|
| 181 |
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"clusters_02_screenshot_13.jpg",
|
| 182 |
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"clusters_02_screenshot_14.jpg",
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| 183 |
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|
| 184 |
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"clusters_02_screenshot_16.jpg",
|
| 185 |
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"clusters_02_screenshot_17.jpg",
|
| 186 |
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"clusters_02_screenshot_18.jpg",
|
| 187 |
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"pocket_01.pdb",
|
| 188 |
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"pocket_02.pdb",
|
| 189 |
+
"pocket_03.pdb",
|
| 190 |
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"pocket_04.pdb",
|
| 191 |
+
"pocket_05.pdb",
|
| 192 |
+
"pocket_06.pdb",
|
| 193 |
+
"pocket_07.pdb",
|
| 194 |
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"pocket_08.pdb",
|
| 195 |
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"pocket_09.pdb"
|
| 196 |
+
],
|
| 197 |
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"analyses": [
|
| 198 |
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"clusters",
|
| 199 |
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"clusters-00",
|
| 200 |
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"clusters-01",
|
| 201 |
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"clusters-02",
|
| 202 |
+
"dist-perres",
|
| 203 |
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"energies",
|
| 204 |
+
"fluctuation",
|
| 205 |
+
"hbonds",
|
| 206 |
+
"interactions",
|
| 207 |
+
"pca",
|
| 208 |
+
"pockets",
|
| 209 |
+
"rgyr",
|
| 210 |
+
"rmsd-pairwise",
|
| 211 |
+
"rmsd-perres",
|
| 212 |
+
"rmsds",
|
| 213 |
+
"sasa",
|
| 214 |
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"tmscores"
|
| 215 |
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],
|
| 216 |
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"mdIndex": 0,
|
| 217 |
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|
| 218 |
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|
| 219 |
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"internalId": "6841321239c46d9de5877a38",
|
| 220 |
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"creationDate": "2025-06-05T05:58:42.000Z",
|
| 221 |
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"identifier": "A005Q"
|
| 222 |
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}
|
A005Q/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005Q", "accession": "A005Q", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 3ONL", "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": ["3ONL"], "FORCED_REFERENCES": null, "REFERENCES": ["P47160", 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|
A005X/project.json
ADDED
|
@@ -0,0 +1,198 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005X",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3QQ8",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"3QQ8"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P55072",
|
| 31 |
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"Q9UNN5"
|
| 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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"DDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEG",
|
| 38 |
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"AEPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAK"
|
| 39 |
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],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Transitional endoplasmic reticulum ATPase",
|
| 43 |
+
"FAS-associated factor 1",
|
| 44 |
+
"UBX"
|
| 45 |
+
],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 4199,
|
| 56 |
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"SYSTRES": 257,
|
| 57 |
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"PROTATS": 4199,
|
| 58 |
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"PROTRES": 257,
|
| 59 |
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"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
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"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
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"PBC_SELECTION": null,
|
| 81 |
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"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [
|
| 89 |
+
{
|
| 90 |
+
"tag": "intrajrity",
|
| 91 |
+
"message": "RMSD check has failed: there may be sudden jumps along the trajectory"
|
| 92 |
+
}
|
| 93 |
+
],
|
| 94 |
+
"BOXSIZEX": 8.86977,
|
| 95 |
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"BOXSIZEY": 8.86977,
|
| 96 |
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"BOXSIZEZ": 6.27268,
|
| 97 |
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"mdName": "replica 1",
|
| 98 |
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"mdAtoms": 4199,
|
| 99 |
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"mdFrames": 5001
|
| 100 |
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},
|
| 101 |
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"mds": [
|
| 102 |
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"replica 1",
|
| 103 |
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"replica 2",
|
| 104 |
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"replica 3"
|
| 105 |
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],
|
| 106 |
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"mdref": 0,
|
| 107 |
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"files": [
|
| 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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|
| 114 |
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"pca_trajectory_04.bin",
|
| 115 |
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|
| 116 |
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|
| 117 |
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|
| 118 |
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|
| 119 |
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"pca_trajectory_09.bin",
|
| 120 |
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"structure.pdb",
|
| 121 |
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"trajectory.xtc",
|
| 122 |
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"clusters_00_screenshot_00.jpg",
|
| 123 |
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"clusters_00_screenshot_01.jpg",
|
| 124 |
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"clusters_00_screenshot_02.jpg",
|
| 125 |
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"clusters_00_screenshot_03.jpg",
|
| 126 |
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"clusters_00_screenshot_04.jpg",
|
| 127 |
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"clusters_00_screenshot_05.jpg",
|
| 128 |
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"clusters_00_screenshot_06.jpg",
|
| 129 |
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"clusters_00_screenshot_07.jpg",
|
| 130 |
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"clusters_00_screenshot_08.jpg",
|
| 131 |
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"clusters_00_screenshot_09.jpg",
|
| 132 |
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"clusters_00_screenshot_10.jpg",
|
| 133 |
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"clusters_00_screenshot_11.jpg",
|
| 134 |
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"clusters_00_screenshot_12.jpg",
|
| 135 |
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"clusters_00_screenshot_13.jpg",
|
| 136 |
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"clusters_00_screenshot_14.jpg",
|
| 137 |
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"clusters_00_screenshot_15.jpg",
|
| 138 |
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"clusters_00_screenshot_16.jpg",
|
| 139 |
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"clusters_00_screenshot_17.jpg",
|
| 140 |
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"clusters_00_screenshot_18.jpg",
|
| 141 |
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"clusters_00_screenshot_19.jpg",
|
| 142 |
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"clusters_01_screenshot_00.jpg",
|
| 143 |
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"clusters_01_screenshot_01.jpg",
|
| 144 |
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"clusters_01_screenshot_02.jpg",
|
| 145 |
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"clusters_01_screenshot_03.jpg",
|
| 146 |
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"clusters_01_screenshot_04.jpg",
|
| 147 |
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"clusters_01_screenshot_05.jpg",
|
| 148 |
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"clusters_01_screenshot_06.jpg",
|
| 149 |
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"clusters_01_screenshot_07.jpg",
|
| 150 |
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"clusters_01_screenshot_08.jpg",
|
| 151 |
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"clusters_01_screenshot_09.jpg",
|
| 152 |
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"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
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"clusters_01_screenshot_12.jpg",
|
| 155 |
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"clusters_01_screenshot_13.jpg",
|
| 156 |
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"clusters_01_screenshot_14.jpg",
|
| 157 |
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"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
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"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.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 |
+
"pocket_07.pdb",
|
| 169 |
+
"pocket_08.pdb",
|
| 170 |
+
"pocket_09.pdb",
|
| 171 |
+
"pocket_10.pdb"
|
| 172 |
+
],
|
| 173 |
+
"analyses": [
|
| 174 |
+
"mem-map",
|
| 175 |
+
"clusters",
|
| 176 |
+
"clusters-00",
|
| 177 |
+
"clusters-01",
|
| 178 |
+
"dist-perres",
|
| 179 |
+
"energies",
|
| 180 |
+
"fluctuation",
|
| 181 |
+
"hbonds",
|
| 182 |
+
"interactions",
|
| 183 |
+
"pca",
|
| 184 |
+
"pockets",
|
| 185 |
+
"rgyr",
|
| 186 |
+
"rmsd-pairwise",
|
| 187 |
+
"rmsd-perres",
|
| 188 |
+
"rmsds",
|
| 189 |
+
"sasa",
|
| 190 |
+
"tmscores"
|
| 191 |
+
],
|
| 192 |
+
"mdIndex": 0,
|
| 193 |
+
"mdNumber": 1,
|
| 194 |
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"refframe": 0,
|
| 195 |
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"internalId": "6841404592cef1dced7e2d2c",
|
| 196 |
+
"creationDate": "2025-06-05T06:59:17.000Z",
|
| 197 |
+
"identifier": "A005X"
|
| 198 |
+
}
|
A005X/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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A0065/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A0065",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3TZ1",
|
| 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 |
+
"3TZ1"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q27428",
|
| 31 |
+
"Q7M3Y3"
|
| 32 |
+
],
|
| 33 |
+
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|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"LDERELKEAFRVLDKEKKGVIKVDVLRWILKSLGDELTEDEIENMIAETDTDGSGTVDYEEFKCLMMSSDA",
|
| 38 |
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"GLSPEKKKMLKKLIMQKAAEDLAN"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"EF-hand",
|
| 43 |
+
"Troponin I",
|
| 44 |
+
"Disordered"
|
| 45 |
+
],
|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
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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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"name": "chain A-chain B interaction",
|
| 73 |
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"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
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"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
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"type": "protein-protein"
|
| 78 |
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}
|
| 79 |
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],
|
| 80 |
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|
| 81 |
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|
| 82 |
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|
| 83 |
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|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
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|
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| 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 |
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"pca_trajectory_05.bin",
|
| 111 |
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"pca_trajectory_06.bin",
|
| 112 |
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"pca_trajectory_07.bin",
|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
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"pca_trajectory_09.bin",
|
| 115 |
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"pca_trajectory_10.bin",
|
| 116 |
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"pca_trajectory_11.bin",
|
| 117 |
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"pca_trajectory_12.bin",
|
| 118 |
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"pca_trajectory_13.bin",
|
| 119 |
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"pca_trajectory_14.bin",
|
| 120 |
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"pca_trajectory_15.bin",
|
| 121 |
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"structure.pdb",
|
| 122 |
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"trajectory.xtc",
|
| 123 |
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"clusters_00_screenshot_00.jpg",
|
| 124 |
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"clusters_00_screenshot_01.jpg",
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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"clusters_00_screenshot_06.jpg",
|
| 130 |
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"clusters_00_screenshot_07.jpg",
|
| 131 |
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|
| 132 |
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"clusters_00_screenshot_09.jpg",
|
| 133 |
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"clusters_00_screenshot_10.jpg",
|
| 134 |
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"clusters_00_screenshot_11.jpg",
|
| 135 |
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"clusters_00_screenshot_12.jpg",
|
| 136 |
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"clusters_00_screenshot_13.jpg",
|
| 137 |
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"clusters_00_screenshot_14.jpg",
|
| 138 |
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"clusters_00_screenshot_15.jpg",
|
| 139 |
+
"clusters_00_screenshot_16.jpg",
|
| 140 |
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"clusters_00_screenshot_17.jpg",
|
| 141 |
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"clusters_00_screenshot_18.jpg",
|
| 142 |
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"clusters_01_screenshot_00.jpg",
|
| 143 |
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"clusters_01_screenshot_01.jpg",
|
| 144 |
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"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
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"clusters_01_screenshot_04.jpg",
|
| 147 |
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"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
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"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
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"clusters_01_screenshot_11.jpg",
|
| 154 |
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"clusters_01_screenshot_12.jpg",
|
| 155 |
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"clusters_01_screenshot_13.jpg",
|
| 156 |
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"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.jpg",
|
| 162 |
+
"pocket_01.pdb",
|
| 163 |
+
"pocket_02.pdb"
|
| 164 |
+
],
|
| 165 |
+
"analyses": [
|
| 166 |
+
"clusters",
|
| 167 |
+
"clusters-00",
|
| 168 |
+
"clusters-01",
|
| 169 |
+
"dist-perres",
|
| 170 |
+
"energies",
|
| 171 |
+
"fluctuation",
|
| 172 |
+
"hbonds",
|
| 173 |
+
"interactions",
|
| 174 |
+
"pca",
|
| 175 |
+
"pockets",
|
| 176 |
+
"rgyr",
|
| 177 |
+
"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
+
"rmsds",
|
| 180 |
+
"sasa",
|
| 181 |
+
"tmscores"
|
| 182 |
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],
|
| 183 |
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"mdIndex": 0,
|
| 184 |
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"mdNumber": 1,
|
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|
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|
| 187 |
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"creationDate": "2025-06-05T08:22:16.000Z",
|
| 188 |
+
"identifier": "A0065"
|
| 189 |
+
}
|
A0065/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
{"project_identifier": "A0065", "accession": "A0065", "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 3TZ1", "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": ["3TZ1"], "FORCED_REFERENCES": null, "REFERENCES": ["Q27428", "Q7M3Y3"], 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| 3 |
+
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| 1 |
+
{
|
| 2 |
+
"accession": "A0069",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3UZ0",
|
| 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 |
+
"3UZ0"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P49785",
|
| 31 |
+
"P71044"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"NVAMPVVDSENVSVVKKFYETDAAKEEKEAALVTYNNTYSLSKGIDLAEKDGKDFDVSASLSGTVVKAEKDPVLGYVVEVEHADGLSTVYQSLSEVSVEQGDKVKQNQVIGKSGKNLYSEDSGNHVHFEIRKDGVAMNPLNFM",
|
| 38 |
+
"DLFTTYRLDLEDARSKEREELNAIVSSDDATAKEKSEAYDKMTALSEVEGTEKQLETLIKTQGYEDALVNAEGDKINITVKSDKHSKSKATAIIDLVAKEIKTMKDVAVTFEPS"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Stage III sporulation protein AH",
|
| 43 |
+
"Stage II sporulation protein Q"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
"SYSTATS": 3943,
|
| 55 |
+
"SYSTRES": 257,
|
| 56 |
+
"PROTATS": 3943,
|
| 57 |
+
"PROTRES": 257,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
+
"SOLVRES": 0,
|
| 66 |
+
"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
+
"MEMBRANES": null,
|
| 82 |
+
"CUSTOMS": null,
|
| 83 |
+
"ORIENTATION": null,
|
| 84 |
+
"PTM": [],
|
| 85 |
+
"MULTIMERIC": null,
|
| 86 |
+
"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
+
"BOXSIZEX": 9.8305,
|
| 89 |
+
"BOXSIZEY": 9.8305,
|
| 90 |
+
"BOXSIZEZ": 6.95536,
|
| 91 |
+
"mdName": "replica 1",
|
| 92 |
+
"mdAtoms": 3943,
|
| 93 |
+
"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
+
"mdref": 0,
|
| 101 |
+
"files": [
|
| 102 |
+
"topology.tpr",
|
| 103 |
+
"screenshot.jpg",
|
| 104 |
+
"trajectory.bin",
|
| 105 |
+
"pca_trajectory_01.bin",
|
| 106 |
+
"pca_trajectory_02.bin",
|
| 107 |
+
"pca_trajectory_03.bin",
|
| 108 |
+
"pca_trajectory_04.bin",
|
| 109 |
+
"pca_trajectory_05.bin",
|
| 110 |
+
"pca_trajectory_06.bin",
|
| 111 |
+
"pca_trajectory_07.bin",
|
| 112 |
+
"pca_trajectory_08.bin",
|
| 113 |
+
"pca_trajectory_09.bin",
|
| 114 |
+
"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 |
+
"clusters_00_screenshot_04.jpg",
|
| 121 |
+
"clusters_00_screenshot_05.jpg",
|
| 122 |
+
"clusters_00_screenshot_06.jpg",
|
| 123 |
+
"clusters_00_screenshot_07.jpg",
|
| 124 |
+
"clusters_00_screenshot_08.jpg",
|
| 125 |
+
"clusters_00_screenshot_09.jpg",
|
| 126 |
+
"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_00_screenshot_20.jpg",
|
| 137 |
+
"clusters_00_screenshot_21.jpg",
|
| 138 |
+
"clusters_01_screenshot_00.jpg",
|
| 139 |
+
"clusters_01_screenshot_01.jpg",
|
| 140 |
+
"clusters_01_screenshot_02.jpg",
|
| 141 |
+
"clusters_01_screenshot_03.jpg",
|
| 142 |
+
"clusters_01_screenshot_04.jpg",
|
| 143 |
+
"clusters_01_screenshot_05.jpg",
|
| 144 |
+
"clusters_01_screenshot_06.jpg",
|
| 145 |
+
"clusters_01_screenshot_07.jpg",
|
| 146 |
+
"clusters_01_screenshot_08.jpg",
|
| 147 |
+
"clusters_01_screenshot_09.jpg",
|
| 148 |
+
"clusters_01_screenshot_10.jpg",
|
| 149 |
+
"clusters_01_screenshot_11.jpg",
|
| 150 |
+
"clusters_01_screenshot_12.jpg",
|
| 151 |
+
"clusters_01_screenshot_13.jpg",
|
| 152 |
+
"clusters_01_screenshot_14.jpg",
|
| 153 |
+
"clusters_01_screenshot_15.jpg",
|
| 154 |
+
"clusters_01_screenshot_16.jpg",
|
| 155 |
+
"clusters_01_screenshot_17.jpg",
|
| 156 |
+
"clusters_01_screenshot_18.jpg",
|
| 157 |
+
"clusters_01_screenshot_19.jpg",
|
| 158 |
+
"clusters_01_screenshot_20.jpg",
|
| 159 |
+
"clusters_01_screenshot_21.jpg",
|
| 160 |
+
"pocket_01.pdb",
|
| 161 |
+
"pocket_02.pdb",
|
| 162 |
+
"pocket_03.pdb",
|
| 163 |
+
"pocket_04.pdb",
|
| 164 |
+
"pocket_05.pdb",
|
| 165 |
+
"pocket_06.pdb"
|
| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
+
"clusters",
|
| 169 |
+
"clusters-00",
|
| 170 |
+
"clusters-01",
|
| 171 |
+
"dist-perres",
|
| 172 |
+
"energies",
|
| 173 |
+
"fluctuation",
|
| 174 |
+
"hbonds",
|
| 175 |
+
"interactions",
|
| 176 |
+
"pca",
|
| 177 |
+
"pockets",
|
| 178 |
+
"rgyr",
|
| 179 |
+
"rmsd-pairwise",
|
| 180 |
+
"rmsd-perres",
|
| 181 |
+
"rmsds",
|
| 182 |
+
"sasa",
|
| 183 |
+
"tmscores"
|
| 184 |
+
],
|
| 185 |
+
"mdIndex": 0,
|
| 186 |
+
"mdNumber": 1,
|
| 187 |
+
"refframe": 0,
|
| 188 |
+
"internalId": "68415b3b4812e9330164fa7c",
|
| 189 |
+
"creationDate": "2025-06-05T08:54:19.000Z",
|
| 190 |
+
"identifier": "A0069"
|
| 191 |
+
}
|
A0069/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0069", "accession": "A0069", "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 3UZ0", "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": ["3UZ0"], "FORCED_REFERENCES": null, "REFERENCES": ["P49785", "P71044"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["NVAMPVVDSENVSVVKKFYETDAAKEEKEAALVTYNNTYSLSKGIDLAEKDGKDFDVSASLSGTVVKAEKDPVLGYVVEVEHADGLSTVYQSLSEVSVEQGDKVKQNQVIGKSGKNLYSEDSGNHVHFEIRKDGVAMNPLNFM", "DLFTTYRLDLEDARSKEREELNAIVSSDDATAKEKSEAYDKMTALSEVEGTEKQLETLIKTQGYEDALVNAEGDKINITVKSDKHSKSKATAIIDLVAKEIKTMKDVAVTFEPS"], "NUCLSEQ": [], "DOMAINS": ["Stage III sporulation protein AH", "Stage II sporulation protein Q"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3943, "SYSTRES": 257, "PROTATS": 3943, "PROTRES": 257, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.8305, "BOXSIZEY": 9.8305, "BOXSIZEZ": 6.95536, "mdName": "replica 1", "mdAtoms": 3943, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0069/files/topology.tpr", "length": 1392260, "contentType": "application/octet-stream", "metadata": {"project": "68415b3b4812e9330164fa7c", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0069/files/screenshot.jpg", "length": 21120, "contentType": "application/octet-stream", "metadata": {"project": "68415b3b4812e9330164fa7c", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0069/files/trajectory.bin", "length": 236627316, "contentType": "application/octet-stream", "metadata": {"project": "68415b3b4812e9330164fa7c", "md": 0, "frames": 5001, "atoms": 3943}}, {"name": "pca_trajectory_01.bin", "downloadUrl": 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|
A0076/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0076",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4FAO",
|
| 6 |
+
"DESCRIPTION": "Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Author Omid Mokhtari",
|
| 9 |
+
"Author Hamed Khakzad",
|
| 10 |
+
"Author Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"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": [
|
| 25 |
+
{
|
| 26 |
+
"name": "Link_name",
|
| 27 |
+
"url": "www.link-name.org"
|
| 28 |
+
}
|
| 29 |
+
],
|
| 30 |
+
"PDBIDS": [
|
| 31 |
+
"4FAO"
|
| 32 |
+
],
|
| 33 |
+
"FORCED_REFERENCES": null,
|
| 34 |
+
"REFERENCES": [
|
| 35 |
+
"Q9UK05",
|
| 36 |
+
"P37023",
|
| 37 |
+
"Q13705"
|
| 38 |
+
],
|
| 39 |
+
"INPUT_LIGANDS": null,
|
| 40 |
+
"LIGANDS": [],
|
| 41 |
+
"LIGANDNAMES": null,
|
| 42 |
+
"PROTSEQ": [
|
| 43 |
+
"PLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSL",
|
| 44 |
+
"SHCQKTSLRVNFEDIGWDSWIIAPKEYEAYECKGGCFFPLADDVTPTKHAIVQTLVHLKFPTKVGKACCVPTKLSPISVLYKDDMGVPTLKYHYEGMSVAECGCR",
|
| 45 |
+
"PLVTCTCESPHCKGPTCRGAWCTVVLVREEGRHPQEHRGCGNLHRELCRGRPTEFVNHYCCDSHLCNHNVSLVLE",
|
| 46 |
+
"RECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLP"
|
| 47 |
+
],
|
| 48 |
+
"NUCLSEQ": [],
|
| 49 |
+
"DOMAINS": [
|
| 50 |
+
"Growth/differentiation factor 2",
|
| 51 |
+
"Interaction with ENG",
|
| 52 |
+
"Activin receptor type-1-like",
|
| 53 |
+
"Mediates specificity for BMP ligand",
|
| 54 |
+
"Activin receptor type-2B"
|
| 55 |
+
],
|
| 56 |
+
"FRAMESTEP": 0.02,
|
| 57 |
+
"TIMESTEP": 5000,
|
| 58 |
+
"TEMP": 310,
|
| 59 |
+
"ENSEMBLE": "NPT",
|
| 60 |
+
"FF": [
|
| 61 |
+
"CHARMM36m"
|
| 62 |
+
],
|
| 63 |
+
"WAT": "TIP3P",
|
| 64 |
+
"BOXTYPE": "Dodecahedron",
|
| 65 |
+
"SYSTATS": 8342,
|
| 66 |
+
"SYSTRES": 539,
|
| 67 |
+
"PROTATS": 8342,
|
| 68 |
+
"PROTRES": 539,
|
| 69 |
+
"NUCLATS": 0,
|
| 70 |
+
"NUCLRES": 0,
|
| 71 |
+
"LIPIATS": 0,
|
| 72 |
+
"LIPIRES": 0,
|
| 73 |
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|
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|
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|
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|
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|
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|
| 91 |
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|
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|
| 93 |
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|
| 95 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 114 |
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|
| 115 |
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|
| 116 |
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|
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|
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|
| 119 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 333 |
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| 334 |
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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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|
| 343 |
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|
| 344 |
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],
|
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|
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"clusters",
|
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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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|
| 360 |
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|
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|
| 362 |
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|
| 363 |
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|
| 364 |
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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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"creationDate": "2025-06-05T19:28:07.000Z",
|
| 374 |
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"identifier": "A0076"
|
| 375 |
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}
|
A0076/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A007A/project.json
ADDED
|
@@ -0,0 +1,193 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A007A",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4GH7",
|
| 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 |
+
"4GH7"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P80188",
|
| 31 |
+
"P02751"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGKAGNHDLREDKDPRKMQATIYELKEDKSYNVTNVRFVHKKCNYRIWTFVPGSQPGEFTLGNIKSWPGLTSWLVRVVSTNYNQHAMVFFKRVYQNRELFEITLYGRTKELTNELKENFIRFSKSLGLPENHIVFPVPIDQCIDG",
|
| 38 |
+
"PLSPPTNLHLEANPDTGVLTVSWERSTTPDITGYRITTTPTNGQQGNSLEEVVHADQSSCTFDNLSPGLEYNVSVYTVKDDKESVPISDTIIPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQTAVPPPTDLRFTNIGPDTMRVTWAPPPSIDLTNFLVRYSPVKNEEDVAELSISPSDNAVVLTNLLPGTEYVVSVSSVYEQHESTPLRGRQKT"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Neutrophil gelatinase-associated lipocalin",
|
| 43 |
+
"Fibronectin",
|
| 44 |
+
"Fibronectin type-III 6",
|
| 45 |
+
"Fibronectin type-III 7",
|
| 46 |
+
"Fibronectin type-III 8; extra domain B",
|
| 47 |
+
"Fibronectin type-III 9",
|
| 48 |
+
"Cell-attachment"
|
| 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": 7003,
|
| 60 |
+
"SYSTRES": 449,
|
| 61 |
+
"PROTATS": 7003,
|
| 62 |
+
"PROTRES": 449,
|
| 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": 13.2703,
|
| 94 |
+
"BOXSIZEY": 13.2703,
|
| 95 |
+
"BOXSIZEZ": 9.38143,
|
| 96 |
+
"mdName": "replica 1",
|
| 97 |
+
"mdAtoms": 7003,
|
| 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 |
+
"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 |
+
"clusters_01_screenshot_19.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb",
|
| 165 |
+
"pocket_05.pdb",
|
| 166 |
+
"pocket_06.pdb",
|
| 167 |
+
"pocket_07.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 |
+
"mdNumber": 1,
|
| 189 |
+
"refframe": 0,
|
| 190 |
+
"internalId": "6841fd06bd689095d2a83be8",
|
| 191 |
+
"creationDate": "2025-06-05T20:24:38.000Z",
|
| 192 |
+
"identifier": "A007A"
|
| 193 |
+
}
|
A007A/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A007A", "accession": "A007A", "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 4GH7", "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": ["4GH7"], "FORCED_REFERENCES": null, "REFERENCES": ["P80188", "P02751"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["SDLIPAPPLSKVPLQQNFQDNQFHGKWYVVGKAGNHDLREDKDPRKMQATIYELKEDKSYNVTNVRFVHKKCNYRIWTFVPGSQPGEFTLGNIKSWPGLTSWLVRVVSTNYNQHAMVFFKRVYQNRELFEITLYGRTKELTNELKENFIRFSKSLGLPENHIVFPVPIDQCIDG", "PLSPPTNLHLEANPDTGVLTVSWERSTTPDITGYRITTTPTNGQQGNSLEEVVHADQSSCTFDNLSPGLEYNVSVYTVKDDKESVPISDTIIPEVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGIDYDISVITLINGGESAPTTLTQQTAVPPPTDLRFTNIGPDTMRVTWAPPPSIDLTNFLVRYSPVKNEEDVAELSISPSDNAVVLTNLLPGTEYVVSVSSVYEQHESTPLRGRQKT"], "NUCLSEQ": [], "DOMAINS": ["Neutrophil gelatinase-associated lipocalin", "Fibronectin", "Fibronectin type-III 6", "Fibronectin type-III 7", "Fibronectin type-III 8; extra domain B", "Fibronectin type-III 9", "Cell-attachment"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 7003, "SYSTRES": 449, "PROTATS": 7003, "PROTRES": 449, "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": 13.2703, "BOXSIZEY": 13.2703, "BOXSIZEZ": 9.38143, "mdName": "replica 1", "mdAtoms": 7003, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A007A/files/topology.tpr", "length": 2391848, "contentType": "application/octet-stream", "metadata": {"project": "6841fd06bd689095d2a83be8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A007A/files/screenshot.jpg", "length": 21101, "contentType": "application/octet-stream", "metadata": {"project": "6841fd06bd689095d2a83be8", 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A007B/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A007B",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4GN4",
|
| 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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"4GN4"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q8ZYM8",
|
| 31 |
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"P00698"
|
| 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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"AVYPKKTHWTAEITPNLHGSEVVVAGWVAHLGDYGRVKIVKVSDREGGAAVPVYLERGKTPDHLFKVFAELSREDVVVIKGIVEASEQYGSATGVEIFPSEIWILNKA",
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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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"Aspartate--tRNA(Asp) ligase",
|
| 43 |
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"Important for tRNA discrimination",
|
| 44 |
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"Lysozyme C",
|
| 45 |
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"C-type lysozyme"
|
| 46 |
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],
|
| 47 |
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"FRAMESTEP": 0.1,
|
| 48 |
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"TIMESTEP": 2,
|
| 49 |
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"TEMP": 310,
|
| 50 |
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"ENSEMBLE": "NPT",
|
| 51 |
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"FF": [
|
| 52 |
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"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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"WAT": "TIP3P",
|
| 55 |
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"BOXTYPE": "Dodecahedron",
|
| 56 |
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"SYSTATS": 3641,
|
| 57 |
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"SYSTRES": 237,
|
| 58 |
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"PROTATS": 3641,
|
| 59 |
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"PROTRES": 237,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
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| 62 |
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"LIPIATS": 0,
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| 63 |
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"LIPIRES": 0,
|
| 64 |
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|
| 65 |
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"CARBRES": 0,
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| 66 |
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"SOLVATS": 0,
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| 67 |
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"SOLVRES": 0,
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| 68 |
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"COUNCAT": 0,
|
| 69 |
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"COUNANI": 0,
|
| 70 |
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"COUNION": 0,
|
| 71 |
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"INTERACTIONS": [
|
| 72 |
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{
|
| 73 |
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"name": "chain A-chain B interaction",
|
| 74 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
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],
|
| 81 |
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"PBC_SELECTION": null,
|
| 82 |
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"CHAINNAMES": null,
|
| 83 |
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"MEMBRANES": null,
|
| 84 |
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|
| 85 |
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|
| 86 |
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"PTM": [],
|
| 87 |
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"MULTIMERIC": null,
|
| 88 |
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"COLLECTIONS": "dynarepo",
|
| 89 |
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"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 9.26387,
|
| 91 |
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"BOXSIZEY": 9.26387,
|
| 92 |
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"BOXSIZEZ": 6.51721,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 3641,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
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"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
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],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
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| 104 |
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|
| 105 |
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|
| 106 |
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| 107 |
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|
| 108 |
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|
| 109 |
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| 111 |
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| 112 |
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| 114 |
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| 118 |
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|
| 119 |
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|
| 120 |
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| 121 |
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| 122 |
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"clusters_01_screenshot_13.jpg",
|
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"clusters_01_screenshot_14.jpg",
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"clusters_01_screenshot_15.jpg",
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"clusters_01_screenshot_16.jpg",
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"clusters_01_screenshot_17.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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| 161 |
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"pocket_03.pdb"
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| 162 |
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],
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| 163 |
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"analyses": [
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| 164 |
+
"clusters",
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| 165 |
+
"clusters-00",
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| 166 |
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"clusters-01",
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| 167 |
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"dist-perres",
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| 168 |
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"energies",
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| 169 |
+
"fluctuation",
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| 170 |
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"hbonds",
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| 171 |
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"interactions",
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| 172 |
+
"pca",
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| 173 |
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"pockets",
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| 174 |
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"rgyr",
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| 175 |
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"rmsd-pairwise",
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| 176 |
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"rmsd-perres",
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"rmsds",
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| 178 |
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"sasa",
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| 179 |
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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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| 183 |
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"refframe": 0,
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| 184 |
+
"internalId": "6841ff69ab6888b288f8db97",
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"creationDate": "2025-06-05T20:34:49.000Z",
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"identifier": "A007B"
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}
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A007B/records.jsonl
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|
A007E/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A007E",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4HEP",
|
| 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 |
+
"4HEP"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9G096",
|
| 31 |
+
"P01764"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"VQLVESGGGLVQPGGSLRLSCEASGFSFDDYAIGWFRQAPGKEREGVSYISMSDGRTYVADSVTGRFTISSDNAKNTVYLQMNSLKLEDTAVYYCAAGRFVTFGSAWSFVGGGPYGIDYWGKGTLVTVSS",
|
| 38 |
+
"ASIKKVYRGMKNGAETINDDLEAINSELTSGGNVVHKTGDETIAGKKTFTGNVEVNGSLTLPTKSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Lower baseplate protein N-terminal",
|
| 43 |
+
"Receptor-binding protein of phage tail base-plate Siphoviridae head",
|
| 44 |
+
"Immunoglobulin heavy variable 3-23",
|
| 45 |
+
"Ig-like",
|
| 46 |
+
"Framework-1",
|
| 47 |
+
"Complementarity-determining-1",
|
| 48 |
+
"Framework-2",
|
| 49 |
+
"Complementarity-determining-2",
|
| 50 |
+
"Framework-3",
|
| 51 |
+
"Complementarity-determining-3"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
+
"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 4286,
|
| 63 |
+
"SYSTRES": 292,
|
| 64 |
+
"PROTATS": 4286,
|
| 65 |
+
"PROTRES": 292,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "chain A-chain B interaction",
|
| 80 |
+
"agent_1": "chain A",
|
| 81 |
+
"agent_2": "chain B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
}
|
| 86 |
+
],
|
| 87 |
+
"PBC_SELECTION": null,
|
| 88 |
+
"CHAINNAMES": null,
|
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| 91 |
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| 114 |
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| 124 |
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|
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|
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|
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|
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|
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|
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|
| 157 |
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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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|
| 168 |
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|
| 169 |
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],
|
| 170 |
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"analyses": [
|
| 171 |
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|
| 172 |
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|
| 173 |
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"clusters-01",
|
| 174 |
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"dist-perres",
|
| 175 |
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"energies",
|
| 176 |
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"fluctuation",
|
| 177 |
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"hbonds",
|
| 178 |
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"interactions",
|
| 179 |
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"pca",
|
| 180 |
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"rgyr",
|
| 181 |
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"rmsd-pairwise",
|
| 182 |
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"rmsd-perres",
|
| 183 |
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"rmsds",
|
| 184 |
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"sasa",
|
| 185 |
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"tmscores"
|
| 186 |
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|
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|
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|
| 192 |
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"identifier": "A007E"
|
| 193 |
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}
|
A007E/records.jsonl
ADDED
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| 1 |
+
{
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"accession": "A007L",
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"published": true,
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+
"metadata": {
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| 5 |
+
"NAME": "Dynarepo 4K1R",
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| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
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+
"AUTHORS": [
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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 |
+
"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 |
+
"4K1R"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9P371",
|
| 31 |
+
"P0CG48"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
|
| 38 |
+
"TFKIHAYTEGGKPLRTIYLPKLLKKVFLDVVKPNTKKNLETCGILCGKLRQNAFFITHLVIPLQEATSDTCGTTDEASLFEFQDKHNLLTLGWIHTHPTQTCFMSSVDLHTHCSYQLMLPEAIAIVMAPSKNTSGIFRLLDPEGLQTIVKXRKPGLFHPHEGKVYTMVAQPGHVREINSKLQVVDLRVK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"AMSH-like protease sst2",
|
| 43 |
+
"MPN",
|
| 44 |
+
"JAMM motif",
|
| 45 |
+
"Indirect zinc-binding",
|
| 46 |
+
"Ubiquitin",
|
| 47 |
+
"Ubiquitin-like 1",
|
| 48 |
+
"Ubiquitin-like 2",
|
| 49 |
+
"Interacts with activating enzyme",
|
| 50 |
+
"Essential for function"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 4276,
|
| 62 |
+
"SYSTRES": 266,
|
| 63 |
+
"PROTATS": 4276,
|
| 64 |
+
"PROTRES": 266,
|
| 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 |
+
"PBC_SELECTION": null,
|
| 87 |
+
"CHAINNAMES": null,
|
| 88 |
+
"MEMBRANES": null,
|
| 89 |
+
"CUSTOMS": null,
|
| 90 |
+
"ORIENTATION": null,
|
| 91 |
+
"PTM": [],
|
| 92 |
+
"MULTIMERIC": null,
|
| 93 |
+
"COLLECTIONS": "dynarepo",
|
| 94 |
+
"WARNINGS": [],
|
| 95 |
+
"BOXSIZEX": 8.47526,
|
| 96 |
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"BOXSIZEY": 8.47526,
|
| 97 |
+
"BOXSIZEZ": 5.99131,
|
| 98 |
+
"mdName": "replica 1",
|
| 99 |
+
"mdAtoms": 4276,
|
| 100 |
+
"mdFrames": 5001
|
| 101 |
+
},
|
| 102 |
+
"mds": [
|
| 103 |
+
"replica 1",
|
| 104 |
+
"replica 2",
|
| 105 |
+
"replica 3"
|
| 106 |
+
],
|
| 107 |
+
"mdref": 0,
|
| 108 |
+
"files": [
|
| 109 |
+
"topology.tpr",
|
| 110 |
+
"screenshot.jpg",
|
| 111 |
+
"trajectory.bin",
|
| 112 |
+
"pca_trajectory_01.bin",
|
| 113 |
+
"pca_trajectory_02.bin",
|
| 114 |
+
"pca_trajectory_03.bin",
|
| 115 |
+
"pca_trajectory_04.bin",
|
| 116 |
+
"pca_trajectory_05.bin",
|
| 117 |
+
"pca_trajectory_06.bin",
|
| 118 |
+
"pca_trajectory_07.bin",
|
| 119 |
+
"pca_trajectory_08.bin",
|
| 120 |
+
"pca_trajectory_09.bin",
|
| 121 |
+
"pca_trajectory_10.bin",
|
| 122 |
+
"pca_trajectory_11.bin",
|
| 123 |
+
"pca_trajectory_12.bin",
|
| 124 |
+
"pca_trajectory_13.bin",
|
| 125 |
+
"pca_trajectory_14.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_00_screenshot_20.jpg",
|
| 149 |
+
"clusters_00_screenshot_21.jpg",
|
| 150 |
+
"clusters_00_screenshot_22.jpg",
|
| 151 |
+
"clusters_01_screenshot_00.jpg",
|
| 152 |
+
"clusters_01_screenshot_01.jpg",
|
| 153 |
+
"clusters_01_screenshot_02.jpg",
|
| 154 |
+
"clusters_01_screenshot_03.jpg",
|
| 155 |
+
"clusters_01_screenshot_04.jpg",
|
| 156 |
+
"clusters_01_screenshot_05.jpg",
|
| 157 |
+
"clusters_01_screenshot_06.jpg",
|
| 158 |
+
"clusters_01_screenshot_07.jpg",
|
| 159 |
+
"clusters_01_screenshot_08.jpg",
|
| 160 |
+
"clusters_01_screenshot_09.jpg",
|
| 161 |
+
"clusters_01_screenshot_10.jpg",
|
| 162 |
+
"clusters_01_screenshot_11.jpg",
|
| 163 |
+
"clusters_01_screenshot_12.jpg",
|
| 164 |
+
"clusters_01_screenshot_13.jpg",
|
| 165 |
+
"clusters_01_screenshot_14.jpg",
|
| 166 |
+
"clusters_01_screenshot_15.jpg",
|
| 167 |
+
"clusters_01_screenshot_16.jpg",
|
| 168 |
+
"clusters_01_screenshot_17.jpg",
|
| 169 |
+
"clusters_01_screenshot_18.jpg",
|
| 170 |
+
"pocket_01.pdb",
|
| 171 |
+
"pocket_02.pdb",
|
| 172 |
+
"pocket_03.pdb",
|
| 173 |
+
"pocket_04.pdb",
|
| 174 |
+
"pocket_05.pdb",
|
| 175 |
+
"pocket_06.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": "684216a05f4214d459a864c4",
|
| 199 |
+
"creationDate": "2025-06-05T22:13:52.000Z",
|
| 200 |
+
"identifier": "A007L"
|
| 201 |
+
}
|
A007L/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A007L", "accession": "A007L", "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 4K1R", "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": ["4K1R"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9P371", "P0CG48"], 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|
A0084/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0084",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4NSO",
|
| 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 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"4NSO"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9KN42",
|
| 31 |
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"Q9KN41"
|
| 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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"IWPLGKTSEKYESAGRGPGVISTGNGDYGGASYGCYQMSSNLGVVQKYIQSSKFKEFFSGLNPATKEFNVVWQDIASRYPQEFREEQHQFIKRTHYDIQIGHLRGKGLLFEHNRAAVHDLIWSTSVQFGGRTNLIFNALNGQNMESMTDKDIIILVQDYKLVNTERLFKSSPSWWSDLKKRAVSEKKALLELEILEH",
|
| 38 |
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"TSGVHQKILVCIQNEIAKSETQIRNNISSKSIDYGFPDDFYSKQRLAIHEKCMLYINVGGQRGELLMNQCELSMLQGLDIYIQQYIEDVDNSLL"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Type VI secretion system spike protein VgrG3",
|
| 43 |
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"Antitoxin protein TsiV3"
|
| 44 |
+
],
|
| 45 |
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"FRAMESTEP": 0.1,
|
| 46 |
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"TIMESTEP": 2,
|
| 47 |
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"TEMP": 310,
|
| 48 |
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"ENSEMBLE": "NPT",
|
| 49 |
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"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
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],
|
| 52 |
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"WAT": "TIP3P",
|
| 53 |
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"BOXTYPE": "Dodecahedron",
|
| 54 |
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"SYSTATS": 4655,
|
| 55 |
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"SYSTRES": 291,
|
| 56 |
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"PROTATS": 4655,
|
| 57 |
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"PROTRES": 291,
|
| 58 |
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"NUCLATS": 0,
|
| 59 |
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"NUCLRES": 0,
|
| 60 |
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"LIPIATS": 0,
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| 61 |
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"LIPIRES": 0,
|
| 62 |
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"CARBATS": 0,
|
| 63 |
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"CARBRES": 0,
|
| 64 |
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"SOLVATS": 0,
|
| 65 |
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"SOLVRES": 0,
|
| 66 |
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"COUNCAT": 0,
|
| 67 |
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"COUNANI": 0,
|
| 68 |
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"COUNION": 0,
|
| 69 |
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"INTERACTIONS": [
|
| 70 |
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{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
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],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
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"CHAINNAMES": null,
|
| 81 |
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"MEMBRANES": null,
|
| 82 |
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"CUSTOMS": null,
|
| 83 |
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"ORIENTATION": null,
|
| 84 |
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"PTM": [],
|
| 85 |
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"MULTIMERIC": null,
|
| 86 |
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"COLLECTIONS": "dynarepo",
|
| 87 |
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"WARNINGS": [],
|
| 88 |
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"BOXSIZEX": 11.133,
|
| 89 |
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"BOXSIZEY": 11.133,
|
| 90 |
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"BOXSIZEZ": 7.8783,
|
| 91 |
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"mdName": "replica 1",
|
| 92 |
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"mdAtoms": 4655,
|
| 93 |
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"mdFrames": 5001
|
| 94 |
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},
|
| 95 |
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"mds": [
|
| 96 |
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"replica 1",
|
| 97 |
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"replica 2",
|
| 98 |
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"replica 3"
|
| 99 |
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],
|
| 100 |
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"mdref": 0,
|
| 101 |
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"files": [
|
| 102 |
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|
| 103 |
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|
| 104 |
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"trajectory.bin",
|
| 105 |
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"pca_trajectory_01.bin",
|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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|
| 114 |
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|
| 115 |
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|
| 116 |
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|
| 117 |
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|
| 118 |
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|
| 119 |
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"structure.pdb",
|
| 120 |
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"trajectory.xtc",
|
| 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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| 131 |
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| 132 |
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| 133 |
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"clusters_00_screenshot_12.jpg",
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"clusters_01_screenshot_00.jpg",
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"clusters_01_screenshot_01.jpg",
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"clusters_01_screenshot_02.jpg",
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"clusters_01_screenshot_03.jpg",
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"clusters_01_screenshot_04.jpg",
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"clusters_01_screenshot_05.jpg",
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"clusters_01_screenshot_06.jpg",
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"clusters_01_screenshot_07.jpg",
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"clusters_01_screenshot_08.jpg",
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"clusters_01_screenshot_09.jpg",
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"clusters_01_screenshot_10.jpg",
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"clusters_01_screenshot_11.jpg",
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"clusters_01_screenshot_12.jpg",
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"clusters_01_screenshot_13.jpg",
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"clusters_01_screenshot_14.jpg",
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"clusters_01_screenshot_15.jpg",
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"clusters_01_screenshot_16.jpg",
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"clusters_01_screenshot_17.jpg",
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"clusters_01_screenshot_18.jpg",
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"clusters_01_screenshot_19.jpg",
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"pocket_01.pdb",
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| 161 |
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"pocket_02.pdb",
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| 162 |
+
"pocket_03.pdb",
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+
"pocket_04.pdb",
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| 164 |
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"pocket_05.pdb",
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| 165 |
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"pocket_06.pdb"
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| 166 |
+
],
|
| 167 |
+
"analyses": [
|
| 168 |
+
"clusters",
|
| 169 |
+
"clusters-00",
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| 170 |
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"clusters-01",
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| 171 |
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"dist-perres",
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| 172 |
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"energies",
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| 173 |
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"fluctuation",
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| 174 |
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"hbonds",
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| 175 |
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"interactions",
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| 176 |
+
"pca",
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| 177 |
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "684237c771123b572a4463d5",
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"creationDate": "2025-06-06T00:35:19.000Z",
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"identifier": "A0084"
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}
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A0084/records.jsonl
ADDED
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|
A0094/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A0094",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5ET1",
|
| 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 |
+
"5ET1"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9ET47",
|
| 31 |
+
"Q1EG27"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"AMALEQALQAARRGDLDVLRSLHAAGLLGPSLRDSLDALPVHHAARSGKLHCLRYLVEEVALPAVSRARNGATPAHDAAATGYLSCLQWLLTQGGCRVQEKDNSGATVLHLAARFGHPDVVKWLLYQGGANSAITTDTGALPIHYAAAKGDLPSLKLLVGHYPEGVNAQTNNGATPLYLACQEGHLEVTKYLVQECSADPHLRAQDGMTPLHAAAQMGHNPVLVWLVSFADVSFSEQDHDGATAMHFAASRGHTKVLSWLLLHGAEISQDLWGGTPLHDAAENGELECCQILAVNGAGLDVRDHDGYTAADLAEFNGHTHCSRYLRTVQTL",
|
| 38 |
+
"RRRCQQPKMLSSPEDTMYYNQLN"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Espin",
|
| 43 |
+
"Myosin-IIIb",
|
| 44 |
+
"Disordered"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
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|
| 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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|
| 69 |
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|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
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|
| 81 |
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"CHAINNAMES": null,
|
| 82 |
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|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
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"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 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"pca_trajectory_13.bin",
|
| 119 |
+
"pca_trajectory_14.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
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"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.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 |
+
"pocket_07.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 |
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"mdNumber": 1,
|
| 190 |
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"refframe": 0,
|
| 191 |
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"internalId": "6842894afc7693a179f9e1d9",
|
| 192 |
+
"creationDate": "2025-06-06T06:23:06.000Z",
|
| 193 |
+
"identifier": "A0094"
|
| 194 |
+
}
|
A0094/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
{"project_identifier": "A0094", "accession": "A0094", "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 5ET1", "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": ["5ET1"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9ET47", "Q1EG27"], 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| 1 |
+
{
|
| 2 |
+
"accession": "A009J",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5KOF",
|
| 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 |
+
"5KOF"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
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"P0A953",
|
| 31 |
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"P0A6A8"
|
| 32 |
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],
|
| 33 |
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|
| 34 |
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| 36 |
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|
| 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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|
| 47 |
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|
| 48 |
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|
| 49 |
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| 50 |
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|
| 53 |
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|
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|
| 55 |
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|
| 56 |
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| 57 |
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| 58 |
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{
|
| 75 |
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|
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|
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|
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|
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| 81 |
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|
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|
| 84 |
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|
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|
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|
| 88 |
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|
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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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|
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|
| 96 |
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"type": "protein-protein"
|
| 97 |
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},
|
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{
|
| 99 |
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"name": "chain B-chain C interaction",
|
| 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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"type": "protein-protein"
|
| 105 |
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},
|
| 106 |
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{
|
| 107 |
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"name": "chain C-chain D interaction",
|
| 108 |
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"agent_1": "chain C",
|
| 109 |
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|
| 110 |
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"selection_1": "chain B",
|
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"selection_2": "chain D",
|
| 112 |
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"type": "protein-protein"
|
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}
|
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],
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|
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|
| 228 |
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| 230 |
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| 233 |
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| 234 |
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| 235 |
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| 237 |
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| 241 |
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| 243 |
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| 246 |
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|
| 248 |
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| 249 |
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|
| 250 |
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|
| 251 |
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|
| 252 |
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| 253 |
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|
| 254 |
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|
| 255 |
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|
| 256 |
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|
| 257 |
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|
| 258 |
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| 259 |
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|
| 260 |
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|
| 261 |
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| 262 |
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|
| 263 |
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|
| 264 |
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|
| 265 |
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|
| 266 |
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|
| 267 |
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|
| 268 |
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|
| 269 |
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|
| 270 |
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|
| 271 |
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|
| 272 |
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"clusters_05_screenshot_19.jpg",
|
| 273 |
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"pocket_01.pdb",
|
| 274 |
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"pocket_02.pdb",
|
| 275 |
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"pocket_03.pdb",
|
| 276 |
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"pocket_04.pdb",
|
| 277 |
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"pocket_05.pdb",
|
| 278 |
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"pocket_06.pdb",
|
| 279 |
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"pocket_07.pdb",
|
| 280 |
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"pocket_08.pdb",
|
| 281 |
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"pocket_09.pdb"
|
| 282 |
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],
|
| 283 |
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"analyses": [
|
| 284 |
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"clusters",
|
| 285 |
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"clusters-00",
|
| 286 |
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"clusters-01",
|
| 287 |
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"clusters-02",
|
| 288 |
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"clusters-03",
|
| 289 |
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"clusters-04",
|
| 290 |
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"clusters-05",
|
| 291 |
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"dist-perres",
|
| 292 |
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"energies",
|
| 293 |
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"fluctuation",
|
| 294 |
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"hbonds",
|
| 295 |
+
"interactions",
|
| 296 |
+
"pca",
|
| 297 |
+
"pockets",
|
| 298 |
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"rgyr",
|
| 299 |
+
"rmsd-pairwise",
|
| 300 |
+
"rmsd-perres",
|
| 301 |
+
"rmsds",
|
| 302 |
+
"sasa",
|
| 303 |
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"tmscores"
|
| 304 |
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],
|
| 305 |
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"mdIndex": 0,
|
| 306 |
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"mdNumber": 1,
|
| 307 |
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|
| 308 |
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"internalId": "6842aec23d5c09dca0ee53c7",
|
| 309 |
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"creationDate": "2025-06-06T09:02:58.000Z",
|
| 310 |
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"identifier": "A009J"
|
| 311 |
+
}
|
A009J/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
A009M/project.json
ADDED
|
@@ -0,0 +1,205 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A009M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 5L21",
|
| 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 |
+
"5L21"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DPI1",
|
| 31 |
+
"P01802"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"QVQLVESGGGLAQPGGSLRLSCEASGFGTWFRFDENTVNWYRQPPGKSREFDELVARYPKSGIVTYLDSVKGRFTISRDNAKKMAFLQMDNLKPEDTAVYYCNVGEFWGQGTQVTISSE",
|
| 38 |
+
"GPMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Botulinum neurotoxin type A",
|
| 43 |
+
"Botulinum neurotoxin A heavy chain",
|
| 44 |
+
"Translocation domain (TD)",
|
| 45 |
+
"N-terminus of receptor binding domain (N-RBD)",
|
| 46 |
+
"C-terminus of receptor binding domain (C-RBD)",
|
| 47 |
+
"Host ganglioside-binding motif",
|
| 48 |
+
"Ig heavy chain V-III region W3082",
|
| 49 |
+
"Ig-like"
|
| 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": 8830,
|
| 61 |
+
"SYSTRES": 547,
|
| 62 |
+
"PROTATS": 8830,
|
| 63 |
+
"PROTRES": 547,
|
| 64 |
+
"NUCLATS": 0,
|
| 65 |
+
"NUCLRES": 0,
|
| 66 |
+
"LIPIATS": 0,
|
| 67 |
+
"LIPIRES": 0,
|
| 68 |
+
"CARBATS": 0,
|
| 69 |
+
"CARBRES": 0,
|
| 70 |
+
"SOLVATS": 0,
|
| 71 |
+
"SOLVRES": 0,
|
| 72 |
+
"COUNCAT": 0,
|
| 73 |
+
"COUNANI": 0,
|
| 74 |
+
"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 |
+
"CHAINNAMES": null,
|
| 87 |
+
"MEMBRANES": null,
|
| 88 |
+
"CUSTOMS": null,
|
| 89 |
+
"ORIENTATION": null,
|
| 90 |
+
"PTM": [],
|
| 91 |
+
"MULTIMERIC": null,
|
| 92 |
+
"COLLECTIONS": "dynarepo",
|
| 93 |
+
"WARNINGS": [],
|
| 94 |
+
"BOXSIZEX": 10.768,
|
| 95 |
+
"BOXSIZEY": 10.768,
|
| 96 |
+
"BOXSIZEZ": 7.70354,
|
| 97 |
+
"mdName": "replica 1",
|
| 98 |
+
"mdAtoms": 8830,
|
| 99 |
+
"mdFrames": 5001
|
| 100 |
+
},
|
| 101 |
+
"mds": [
|
| 102 |
+
"replica 1",
|
| 103 |
+
"replica 2",
|
| 104 |
+
"replica 3"
|
| 105 |
+
],
|
| 106 |
+
"mdref": 0,
|
| 107 |
+
"files": [
|
| 108 |
+
"topology.tpr",
|
| 109 |
+
"screenshot.jpg",
|
| 110 |
+
"trajectory.bin",
|
| 111 |
+
"pca_trajectory_01.bin",
|
| 112 |
+
"pca_trajectory_02.bin",
|
| 113 |
+
"pca_trajectory_03.bin",
|
| 114 |
+
"pca_trajectory_04.bin",
|
| 115 |
+
"pca_trajectory_05.bin",
|
| 116 |
+
"pca_trajectory_06.bin",
|
| 117 |
+
"pca_trajectory_07.bin",
|
| 118 |
+
"pca_trajectory_08.bin",
|
| 119 |
+
"pca_trajectory_09.bin",
|
| 120 |
+
"pca_trajectory_10.bin",
|
| 121 |
+
"pca_trajectory_11.bin",
|
| 122 |
+
"pca_trajectory_12.bin",
|
| 123 |
+
"pca_trajectory_13.bin",
|
| 124 |
+
"pca_trajectory_14.bin",
|
| 125 |
+
"pca_trajectory_15.bin",
|
| 126 |
+
"pca_trajectory_16.bin",
|
| 127 |
+
"pca_trajectory_17.bin",
|
| 128 |
+
"structure.pdb",
|
| 129 |
+
"trajectory.xtc",
|
| 130 |
+
"clusters_00_screenshot_00.jpg",
|
| 131 |
+
"clusters_00_screenshot_01.jpg",
|
| 132 |
+
"clusters_00_screenshot_02.jpg",
|
| 133 |
+
"clusters_00_screenshot_03.jpg",
|
| 134 |
+
"clusters_00_screenshot_04.jpg",
|
| 135 |
+
"clusters_00_screenshot_05.jpg",
|
| 136 |
+
"clusters_00_screenshot_06.jpg",
|
| 137 |
+
"clusters_00_screenshot_07.jpg",
|
| 138 |
+
"clusters_00_screenshot_08.jpg",
|
| 139 |
+
"clusters_00_screenshot_09.jpg",
|
| 140 |
+
"clusters_00_screenshot_10.jpg",
|
| 141 |
+
"clusters_00_screenshot_11.jpg",
|
| 142 |
+
"clusters_00_screenshot_12.jpg",
|
| 143 |
+
"clusters_00_screenshot_13.jpg",
|
| 144 |
+
"clusters_00_screenshot_14.jpg",
|
| 145 |
+
"clusters_00_screenshot_15.jpg",
|
| 146 |
+
"clusters_00_screenshot_16.jpg",
|
| 147 |
+
"clusters_00_screenshot_17.jpg",
|
| 148 |
+
"clusters_00_screenshot_18.jpg",
|
| 149 |
+
"clusters_00_screenshot_19.jpg",
|
| 150 |
+
"clusters_01_screenshot_00.jpg",
|
| 151 |
+
"clusters_01_screenshot_01.jpg",
|
| 152 |
+
"clusters_01_screenshot_02.jpg",
|
| 153 |
+
"clusters_01_screenshot_03.jpg",
|
| 154 |
+
"clusters_01_screenshot_04.jpg",
|
| 155 |
+
"clusters_01_screenshot_05.jpg",
|
| 156 |
+
"clusters_01_screenshot_06.jpg",
|
| 157 |
+
"clusters_01_screenshot_07.jpg",
|
| 158 |
+
"clusters_01_screenshot_08.jpg",
|
| 159 |
+
"clusters_01_screenshot_09.jpg",
|
| 160 |
+
"clusters_01_screenshot_10.jpg",
|
| 161 |
+
"clusters_01_screenshot_11.jpg",
|
| 162 |
+
"clusters_01_screenshot_12.jpg",
|
| 163 |
+
"clusters_01_screenshot_13.jpg",
|
| 164 |
+
"clusters_01_screenshot_14.jpg",
|
| 165 |
+
"clusters_01_screenshot_15.jpg",
|
| 166 |
+
"clusters_01_screenshot_16.jpg",
|
| 167 |
+
"clusters_01_screenshot_17.jpg",
|
| 168 |
+
"clusters_01_screenshot_18.jpg",
|
| 169 |
+
"clusters_01_screenshot_19.jpg",
|
| 170 |
+
"pocket_01.pdb",
|
| 171 |
+
"pocket_02.pdb",
|
| 172 |
+
"pocket_03.pdb",
|
| 173 |
+
"pocket_04.pdb",
|
| 174 |
+
"pocket_05.pdb",
|
| 175 |
+
"pocket_06.pdb",
|
| 176 |
+
"pocket_07.pdb",
|
| 177 |
+
"pocket_08.pdb",
|
| 178 |
+
"pocket_09.pdb",
|
| 179 |
+
"pocket_10.pdb"
|
| 180 |
+
],
|
| 181 |
+
"analyses": [
|
| 182 |
+
"clusters",
|
| 183 |
+
"clusters-00",
|
| 184 |
+
"clusters-01",
|
| 185 |
+
"dist-perres",
|
| 186 |
+
"energies",
|
| 187 |
+
"fluctuation",
|
| 188 |
+
"hbonds",
|
| 189 |
+
"interactions",
|
| 190 |
+
"pca",
|
| 191 |
+
"pockets",
|
| 192 |
+
"rgyr",
|
| 193 |
+
"rmsd-pairwise",
|
| 194 |
+
"rmsd-perres",
|
| 195 |
+
"rmsds",
|
| 196 |
+
"sasa",
|
| 197 |
+
"tmscores"
|
| 198 |
+
],
|
| 199 |
+
"mdIndex": 0,
|
| 200 |
+
"mdNumber": 1,
|
| 201 |
+
"refframe": 0,
|
| 202 |
+
"internalId": "6842b945fbfb1e4c9a865ee1",
|
| 203 |
+
"creationDate": "2025-06-06T09:47:49.000Z",
|
| 204 |
+
"identifier": "A009M"
|
| 205 |
+
}
|
A009M/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A009M", "accession": "A009M", "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 5L21", "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": ["5L21"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DPI1", "P01802"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["QVQLVESGGGLAQPGGSLRLSCEASGFGTWFRFDENTVNWYRQPPGKSREFDELVARYPKSGIVTYLDSVKGRFTISRDNAKKMAFLQMDNLKPEDTAVYYCNVGEFWGQGTQVTISSE", "GPMNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGAKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPL"], "NUCLSEQ": [], "DOMAINS": ["Botulinum neurotoxin type A", "Botulinum neurotoxin A heavy chain", "Translocation domain (TD)", "N-terminus of receptor binding domain (N-RBD)", "C-terminus of receptor binding domain (C-RBD)", "Host ganglioside-binding motif", "Ig heavy chain V-III region W3082", "Ig-like"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 8830, "SYSTRES": 547, "PROTATS": 8830, "PROTRES": 547, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.768, "BOXSIZEY": 10.768, "BOXSIZEZ": 7.70354, "mdName": "replica 1", "mdAtoms": 8830, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A009M/files/topology.tpr", "length": 2681144, "contentType": "application/octet-stream", "metadata": {"project": "6842b945fbfb1e4c9a865ee1", "md": null}}, {"name": 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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"
|
| 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 |
+
"5YOY"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01375",
|
| 31 |
+
"P04433",
|
| 32 |
+
"P0DP02"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"RTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIALTS",
|
| 39 |
+
"QVQLVESGGGVVQPGRSLRLSCAASGFIFSSYAMHWVRQAPGNGLEWVAFMSYDGSNKKYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRGIAAGGNYYYYGMDVWGQGTTVTVS",
|
| 40 |
+
"EIVLTQSPATLSLSPGERATLSCRASQSVYSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPFTFGPGTKVDIK",
|
| 41 |
+
"QVQLVESGGGVVQPGRSLRLSCAASGFIFSSYAMHWVRQAPGNGLEWVAFMSYDGSNKKYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDRGIAAGGNYYYYGMDVWGQGTTVTVSS"
|
| 42 |
+
],
|
| 43 |
+
"NUCLSEQ": [],
|
| 44 |
+
"DOMAINS": [
|
| 45 |
+
"Tumor necrosis factor, membrane form",
|
| 46 |
+
"Tumor necrosis factor, soluble form",
|
| 47 |
+
"THD",
|
| 48 |
+
"Immunoglobulin kappa variable 3-11",
|
| 49 |
+
"Ig-like",
|
| 50 |
+
"Framework-1",
|
| 51 |
+
"Complementarity-determining-1",
|
| 52 |
+
"Framework-2",
|
| 53 |
+
"Complementarity-determining-2",
|
| 54 |
+
"Framework-3",
|
| 55 |
+
"Complementarity-determining-3",
|
| 56 |
+
"Immunoglobulin heavy variable 3-30-3",
|
| 57 |
+
"Ig-like",
|
| 58 |
+
"Framework-1",
|
| 59 |
+
"Complementarity-determining-1",
|
| 60 |
+
"Framework-2",
|
| 61 |
+
"Complementarity-determining-2",
|
| 62 |
+
"Framework-3",
|
| 63 |
+
"Complementarity-determining-3"
|
| 64 |
+
],
|
| 65 |
+
"FRAMESTEP": 0.1,
|
| 66 |
+
"TIMESTEP": 2,
|
| 67 |
+
"TEMP": 310,
|
| 68 |
+
"ENSEMBLE": "NPT",
|
| 69 |
+
"FF": [
|
| 70 |
+
"CHARMM36m"
|
| 71 |
+
],
|
| 72 |
+
"WAT": "TIP3P",
|
| 73 |
+
"BOXTYPE": "Dodecahedron",
|
| 74 |
+
"SYSTATS": 17830,
|
| 75 |
+
"SYSTRES": 1163,
|
| 76 |
+
"PROTATS": 17830,
|
| 77 |
+
"PROTRES": 1163,
|
| 78 |
+
"NUCLATS": 0,
|
| 79 |
+
"NUCLRES": 0,
|
| 80 |
+
"LIPIATS": 0,
|
| 81 |
+
"LIPIRES": 0,
|
| 82 |
+
"CARBATS": 0,
|
| 83 |
+
"CARBRES": 0,
|
| 84 |
+
"SOLVATS": 0,
|
| 85 |
+
"SOLVRES": 0,
|
| 86 |
+
"COUNCAT": 0,
|
| 87 |
+
"COUNANI": 0,
|
| 88 |
+
"COUNION": 0,
|
| 89 |
+
"INTERACTIONS": [
|
| 90 |
+
{
|
| 91 |
+
"name": "chain A-chain B interaction",
|
| 92 |
+
"agent_1": "chain A",
|
| 93 |
+
"agent_2": "chain B",
|
| 94 |
+
"selection_1": "chain A",
|
| 95 |
+
"selection_2": "chain B",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
},
|
| 98 |
+
{
|
| 99 |
+
"name": "chain A-chain C interaction",
|
| 100 |
+
"agent_1": "chain A",
|
| 101 |
+
"agent_2": "chain C",
|
| 102 |
+
"selection_1": "chain A",
|
| 103 |
+
"selection_2": "chain C",
|
| 104 |
+
"type": "protein-protein"
|
| 105 |
+
},
|
| 106 |
+
{
|
| 107 |
+
"name": "chain A-chain F interaction",
|
| 108 |
+
"agent_1": "chain A",
|
| 109 |
+
"agent_2": "chain F",
|
| 110 |
+
"selection_1": "chain A",
|
| 111 |
+
"selection_2": "chain D",
|
| 112 |
+
"type": "protein-protein"
|
| 113 |
+
},
|
| 114 |
+
{
|
| 115 |
+
"name": "chain A-chain G interaction",
|
| 116 |
+
"agent_1": "chain A",
|
| 117 |
+
"agent_2": "chain G",
|
| 118 |
+
"selection_1": "chain A",
|
| 119 |
+
"selection_2": "chain E",
|
| 120 |
+
"type": "protein-protein"
|
| 121 |
+
},
|
| 122 |
+
{
|
| 123 |
+
"name": "chain A-chain I interaction",
|
| 124 |
+
"agent_1": "chain A",
|
| 125 |
+
"agent_2": "chain I",
|
| 126 |
+
"selection_1": "chain A",
|
| 127 |
+
"selection_2": "chain F",
|
| 128 |
+
"type": "protein-protein"
|
| 129 |
+
},
|
| 130 |
+
{
|
| 131 |
+
"name": "chain B-chain C interaction",
|
| 132 |
+
"agent_1": "chain B",
|
| 133 |
+
"agent_2": "chain C",
|
| 134 |
+
"selection_1": "chain A",
|
| 135 |
+
"selection_2": "chain G",
|
| 136 |
+
"type": "protein-protein"
|
| 137 |
+
},
|
| 138 |
+
{
|
| 139 |
+
"name": "chain B-chain D interaction",
|
| 140 |
+
"agent_1": "chain B",
|
| 141 |
+
"agent_2": "chain D",
|
| 142 |
+
"selection_1": "chain A",
|
| 143 |
+
"selection_2": "chain H",
|
| 144 |
+
"type": "protein-protein"
|
| 145 |
+
},
|
| 146 |
+
{
|
| 147 |
+
"name": "chain B-chain G interaction",
|
| 148 |
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"clusters_14_screenshot_17.jpg",
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"clusters_14_screenshot_18.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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+
"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_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": [
|
| 546 |
+
"clusters",
|
| 547 |
+
"clusters-00",
|
| 548 |
+
"clusters-01",
|
| 549 |
+
"clusters-02",
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"clusters-03",
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"clusters-04",
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"clusters-05",
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+
"clusters-06",
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"clusters-07",
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"clusters-08",
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"clusters-09",
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"clusters-10",
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"clusters-11",
|
| 559 |
+
"clusters-12",
|
| 560 |
+
"clusters-13",
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| 561 |
+
"clusters-14",
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| 562 |
+
"dist-perres",
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| 563 |
+
"energies",
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| 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 |
+
"mdIndex": 0,
|
| 577 |
+
"mdNumber": 1,
|
| 578 |
+
"refframe": 3,
|
| 579 |
+
"internalId": "6843148e6d4af78e835ee5de",
|
| 580 |
+
"creationDate": "2025-06-06T16:17:18.000Z",
|
| 581 |
+
"identifier": "A00AE"
|
| 582 |
+
}
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{"project_identifier": "A00AZ", "accession": "A00AZ", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "clusters-02", "clusters-03", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 6H3T", "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": ["6H3T"], "FORCED_REFERENCES": null, "REFERENCES": 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| 1 |
+
{
|
| 2 |
+
"accession": "A00B2",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 6HUL",
|
| 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 |
+
"6HUL"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P50382",
|
| 31 |
+
"P50383"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"DEILPKYWYNIIPDLPKPLPPPRDPQGAYFSRIDLLRSILPKEVLRQQFTIERYIKIPEEVRDRYLSIGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLDVVLLHQSVIGQETITQLDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMMKR",
|
| 38 |
+
"GKMLVVYMTLGYPNVQSFKDFIIGAVENGADILELGIPPKYAKYDGPVIRKSYDKVKGLDIWPLIEDIRKDVGVPIIALTYLEDWVDQLENFLNMIKDVKLDGILFPDLLIDYIDDLDKIDGIIKNKGLKNVIFTSPSVPDLLIHKVSKISDLFLYYGVRPTTGVPIPVSVKQLINRVRNLVENKLIVGFGLSSESDLRDALSAGADGIAIGTVFIEEIERNGVKSAINLVKKFRAILDEY"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tryptophan synthase alpha chain",
|
| 43 |
+
"Tryptophan synthase beta chain 1"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
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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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"COUNION": 0,
|
| 69 |
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"INTERACTIONS": [
|
| 70 |
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{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
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"MEMBRANES": null,
|
| 82 |
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"CUSTOMS": null,
|
| 83 |
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|
| 84 |
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"PTM": [],
|
| 85 |
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"MULTIMERIC": null,
|
| 86 |
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"COLLECTIONS": "dynarepo",
|
| 87 |
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"WARNINGS": [],
|
| 88 |
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|
| 89 |
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"BOXSIZEY": 11.4152,
|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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"mdFrames": 5001
|
| 94 |
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},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
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"mdref": 0,
|
| 101 |
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"files": [
|
| 102 |
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"topology.tpr",
|
| 103 |
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"screenshot.jpg",
|
| 104 |
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"trajectory.bin",
|
| 105 |
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"pca_trajectory_01.bin",
|
| 106 |
+
"pca_trajectory_02.bin",
|
| 107 |
+
"pca_trajectory_03.bin",
|
| 108 |
+
"pca_trajectory_04.bin",
|
| 109 |
+
"pca_trajectory_05.bin",
|
| 110 |
+
"pca_trajectory_06.bin",
|
| 111 |
+
"pca_trajectory_07.bin",
|
| 112 |
+
"pca_trajectory_08.bin",
|
| 113 |
+
"pca_trajectory_09.bin",
|
| 114 |
+
"pca_trajectory_10.bin",
|
| 115 |
+
"pca_trajectory_11.bin",
|
| 116 |
+
"pca_trajectory_12.bin",
|
| 117 |
+
"pca_trajectory_13.bin",
|
| 118 |
+
"structure.pdb",
|
| 119 |
+
"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 |
+
"clusters_00_screenshot_03.jpg",
|
| 124 |
+
"clusters_00_screenshot_04.jpg",
|
| 125 |
+
"clusters_00_screenshot_05.jpg",
|
| 126 |
+
"clusters_00_screenshot_06.jpg",
|
| 127 |
+
"clusters_00_screenshot_07.jpg",
|
| 128 |
+
"clusters_00_screenshot_08.jpg",
|
| 129 |
+
"clusters_00_screenshot_09.jpg",
|
| 130 |
+
"clusters_00_screenshot_10.jpg",
|
| 131 |
+
"clusters_00_screenshot_11.jpg",
|
| 132 |
+
"clusters_00_screenshot_12.jpg",
|
| 133 |
+
"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 |
+
"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 |
+
"mdIndex": 0,
|
| 189 |
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"mdNumber": 1,
|
| 190 |
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"refframe": 1,
|
| 191 |
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"internalId": "684356a6b3d0988a22673631",
|
| 192 |
+
"creationDate": "2025-06-06T20:59:18.000Z",
|
| 193 |
+
"identifier": "A00B2"
|
| 194 |
+
}
|
A00B2/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00B2", "accession": "A00B2", "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 6HUL", "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": ["6HUL"], "FORCED_REFERENCES": null, "REFERENCES": ["P50382", "P50383"], 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A00BZ/project.json
ADDED
|
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| 1 |
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{
|
| 2 |
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"accession": "A00BZ",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 2I3T",
|
| 6 |
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"DESCRIPTION": "PPIs from test53, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
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| 26 |
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"2I3T"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P26449",
|
| 31 |
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"P47074"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
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| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
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| 37 |
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"MKPEKIDCNFKLIYCEDEESKGGRLEFSLEEVLAISRNVYKRV",
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| 38 |
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"MQIVQIEQAPKDYISDIKIIPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSLRYKHPLLCCNFIDNTDLQIYVGTVQGEILKVDLIGSPSFQALTNNEANLGICRICKYGDDKLIAASWDGLIEVIDPRNYGDGVIAVKNLNSNNTKVKNKIFTMDTNSSRLIVGMNNSQVQWFRLPLCEDDNGTIEESGLKYQIRDVALLPKEQEGYACSSIDGRVAVEFFDDQGDDYNSSKRFAFRCHRLNLKDTNLAYPVNSIEFSPRHKFLYTAGSDGIISCWNLQTRKKIKNFAKFNEDSVVKIACSDNILCLATSDDTFKTNAAIDQTIELNASSIYIIFDYE"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Spindle assembly checkpoint protein BUB3",
|
| 43 |
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"Spindle assembly checkpoint component MAD3",
|
| 44 |
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"Interaction with BUB3"
|
| 45 |
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],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 6083,
|
| 56 |
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"SYSTRES": 383,
|
| 57 |
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"PROTATS": 6083,
|
| 58 |
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"PROTRES": 383,
|
| 59 |
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"NUCLATS": 0,
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| 60 |
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"NUCLRES": 0,
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| 61 |
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"LIPIATS": 0,
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| 62 |
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| 63 |
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"CARBATS": 0,
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| 64 |
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| 65 |
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| 66 |
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| 67 |
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"COUNCAT": 0,
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| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
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"name": "chain A-chain B interaction",
|
| 73 |
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"agent_1": "chain A",
|
| 74 |
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"agent_2": "chain B",
|
| 75 |
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"selection_1": "chain A",
|
| 76 |
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"selection_2": "chain B",
|
| 77 |
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"type": "protein-protein"
|
| 78 |
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}
|
| 79 |
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],
|
| 80 |
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"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": [],
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| 86 |
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"MULTIMERIC": null,
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| 87 |
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"COLLECTIONS": "dynarepo",
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| 88 |
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"WARNINGS": [],
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| 89 |
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| 90 |
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| 91 |
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| 92 |
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| 93 |
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| 94 |
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| 95 |
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},
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| 96 |
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"mds": [
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| 97 |
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| 98 |
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| 99 |
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|
| 100 |
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| 101 |
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| 102 |
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| 103 |
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| 106 |
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| 107 |
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| 110 |
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| 120 |
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| 121 |
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| 122 |
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| 123 |
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| 124 |
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| 133 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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| 156 |
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| 157 |
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| 158 |
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|
| 159 |
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| 160 |
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|
| 161 |
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|
| 162 |
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"pocket_01.pdb",
|
| 163 |
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|
| 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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"pocket_08.pdb",
|
| 170 |
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|
| 171 |
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],
|
| 172 |
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"analyses": [
|
| 173 |
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|
| 174 |
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|
| 175 |
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|
| 176 |
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| 178 |
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|
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|
| 180 |
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|
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|
| 182 |
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|
| 183 |
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|
| 184 |
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|
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|
| 186 |
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|
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|
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],
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| 194 |
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"internalId": "686ba51efeffb82640ee5d78",
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"creationDate": "2025-07-07T10:44:46.000Z",
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"identifier": "A00BZ"
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| 1 |
+
{
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| 2 |
+
"accession": "A00D1",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1WDW",
|
| 6 |
+
"DESCRIPTION": "single chains from test53, 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 |
+
"1WDW"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q8U093"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"MWFGEFGGQYVPETLIEPLKELEKAYKRFKDDEEFNRQLNYYLKTWAGRPTPLYYAKRLTEKIGGAKIYLKREDLVHGGAHKTNNAIGQALLAKFMGKTRLIAETGAGQHGVATAMAGALLGMKVDIYMGAEDVERQKMNVFRMKLLGANVIPVNSGSRTLKDAINEALRDWVATFEYTHYLIGSVVGPHPYPTIVRDFQSVIGREAKAQILEAEGQLPDVIVACVGGGSNAMGIFYPFVNDKKVKLVGVEAGGKGLESGKHSASLNAGQVGVFHGMLSYFLQDEEGQIKPTHSIAPGLDYPGVGPEHAYLKKIQRAEYVTVTDEEALKAFHELSRTEGIIPALESAHAVAYAMKLAKEMSRDEIIIVNLSGRGDKDLDIVLKVS"
|
| 37 |
+
],
|
| 38 |
+
"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
+
"Tryptophan synthase beta chain 1"
|
| 41 |
+
],
|
| 42 |
+
"FRAMESTEP": 0.1,
|
| 43 |
+
"TIMESTEP": 2,
|
| 44 |
+
"TEMP": 310,
|
| 45 |
+
"ENSEMBLE": "NPT",
|
| 46 |
+
"FF": [
|
| 47 |
+
"CHARMM36m"
|
| 48 |
+
],
|
| 49 |
+
"WAT": "TIP3P",
|
| 50 |
+
"BOXTYPE": "Dodecahedron",
|
| 51 |
+
"SYSTATS": 5979,
|
| 52 |
+
"SYSTRES": 385,
|
| 53 |
+
"PROTATS": 5979,
|
| 54 |
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"PROTRES": 385,
|
| 55 |
+
"NUCLATS": 0,
|
| 56 |
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"NUCLRES": 0,
|
| 57 |
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"LIPIATS": 0,
|
| 58 |
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"LIPIRES": 0,
|
| 59 |
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"CARBATS": 0,
|
| 60 |
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"CARBRES": 0,
|
| 61 |
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"SOLVATS": 0,
|
| 62 |
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"SOLVRES": 0,
|
| 63 |
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"COUNCAT": 0,
|
| 64 |
+
"COUNANI": 0,
|
| 65 |
+
"COUNION": 0,
|
| 66 |
+
"INTERACTIONS": [],
|
| 67 |
+
"PBC_SELECTION": null,
|
| 68 |
+
"CHAINNAMES": null,
|
| 69 |
+
"MEMBRANES": null,
|
| 70 |
+
"CUSTOMS": null,
|
| 71 |
+
"ORIENTATION": null,
|
| 72 |
+
"PTM": [],
|
| 73 |
+
"MULTIMERIC": null,
|
| 74 |
+
"COLLECTIONS": "dynarepo",
|
| 75 |
+
"WARNINGS": [],
|
| 76 |
+
"BOXSIZEX": 8.64297,
|
| 77 |
+
"BOXSIZEY": 8.64297,
|
| 78 |
+
"BOXSIZEZ": 6.04907,
|
| 79 |
+
"mdName": "replica 1",
|
| 80 |
+
"mdAtoms": 5979,
|
| 81 |
+
"mdFrames": 5001
|
| 82 |
+
},
|
| 83 |
+
"mds": [
|
| 84 |
+
"replica 1",
|
| 85 |
+
"replica 2",
|
| 86 |
+
"replica 3"
|
| 87 |
+
],
|
| 88 |
+
"mdref": 0,
|
| 89 |
+
"files": [
|
| 90 |
+
"topology.tpr",
|
| 91 |
+
"screenshot.jpg",
|
| 92 |
+
"trajectory.bin",
|
| 93 |
+
"pca_trajectory_01.bin",
|
| 94 |
+
"pca_trajectory_02.bin",
|
| 95 |
+
"pca_trajectory_03.bin",
|
| 96 |
+
"pca_trajectory_04.bin",
|
| 97 |
+
"pca_trajectory_05.bin",
|
| 98 |
+
"pca_trajectory_06.bin",
|
| 99 |
+
"pca_trajectory_07.bin",
|
| 100 |
+
"pca_trajectory_08.bin",
|
| 101 |
+
"pca_trajectory_09.bin",
|
| 102 |
+
"pca_trajectory_10.bin",
|
| 103 |
+
"pca_trajectory_11.bin",
|
| 104 |
+
"pca_trajectory_12.bin",
|
| 105 |
+
"pca_trajectory_13.bin",
|
| 106 |
+
"pca_trajectory_14.bin",
|
| 107 |
+
"pca_trajectory_15.bin",
|
| 108 |
+
"structure.pdb",
|
| 109 |
+
"trajectory.xtc",
|
| 110 |
+
"clusters_00_screenshot_00.jpg",
|
| 111 |
+
"clusters_00_screenshot_01.jpg",
|
| 112 |
+
"clusters_00_screenshot_02.jpg",
|
| 113 |
+
"clusters_00_screenshot_03.jpg",
|
| 114 |
+
"clusters_00_screenshot_04.jpg",
|
| 115 |
+
"clusters_00_screenshot_05.jpg",
|
| 116 |
+
"clusters_00_screenshot_06.jpg",
|
| 117 |
+
"clusters_00_screenshot_07.jpg",
|
| 118 |
+
"clusters_00_screenshot_08.jpg",
|
| 119 |
+
"clusters_00_screenshot_09.jpg",
|
| 120 |
+
"clusters_00_screenshot_10.jpg",
|
| 121 |
+
"clusters_00_screenshot_11.jpg",
|
| 122 |
+
"clusters_00_screenshot_12.jpg",
|
| 123 |
+
"clusters_00_screenshot_13.jpg",
|
| 124 |
+
"clusters_00_screenshot_14.jpg",
|
| 125 |
+
"clusters_00_screenshot_15.jpg",
|
| 126 |
+
"clusters_00_screenshot_16.jpg",
|
| 127 |
+
"clusters_00_screenshot_17.jpg",
|
| 128 |
+
"pocket_01.pdb",
|
| 129 |
+
"pocket_02.pdb",
|
| 130 |
+
"pocket_03.pdb",
|
| 131 |
+
"pocket_04.pdb",
|
| 132 |
+
"pocket_05.pdb",
|
| 133 |
+
"pocket_06.pdb",
|
| 134 |
+
"pocket_07.pdb",
|
| 135 |
+
"pocket_08.pdb",
|
| 136 |
+
"pocket_09.pdb",
|
| 137 |
+
"pocket_10.pdb"
|
| 138 |
+
],
|
| 139 |
+
"analyses": [
|
| 140 |
+
"mem-map",
|
| 141 |
+
"clusters",
|
| 142 |
+
"clusters-00",
|
| 143 |
+
"fluctuation",
|
| 144 |
+
"pca",
|
| 145 |
+
"pockets",
|
| 146 |
+
"rgyr",
|
| 147 |
+
"rmsd-pairwise",
|
| 148 |
+
"rmsd-perres",
|
| 149 |
+
"rmsds",
|
| 150 |
+
"sasa",
|
| 151 |
+
"tmscores"
|
| 152 |
+
],
|
| 153 |
+
"updateDate": "2025-07-19T20:33:27.021Z",
|
| 154 |
+
"mdcount": 3,
|
| 155 |
+
"mdIndex": 0,
|
| 156 |
+
"mdNumber": 1,
|
| 157 |
+
"refframe": 0,
|
| 158 |
+
"internalId": "687b845a99fe6bdf85a95c8c",
|
| 159 |
+
"creationDate": "2025-07-19T11:41:14.000Z",
|
| 160 |
+
"identifier": "A00D1"
|
| 161 |
+
}
|
A00D1/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00D1", "accession": "A00D1", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1WDW", "DESCRIPTION": "single chains from test53, 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": ["1WDW"], "FORCED_REFERENCES": null, "REFERENCES": ["Q8U093"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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