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data/files/A000A/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000A",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1AK4",
|
| 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",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"1AK4"
|
| 27 |
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],
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| 28 |
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"FORCED_REFERENCES": null,
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| 29 |
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"REFERENCES": [
|
| 30 |
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"P62937",
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| 31 |
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"P12497"
|
| 32 |
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],
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| 33 |
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"INPUT_LIGANDS": null,
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| 34 |
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"LIGANDS": [],
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| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMY",
|
| 38 |
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"MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Peptidyl-prolyl cis-trans isomerase A",
|
| 43 |
+
"Peptidyl-prolyl cis-trans isomerase A, N-terminally processed",
|
| 44 |
+
"PPIase cyclophilin-type",
|
| 45 |
+
"Gag-Pol polyprotein",
|
| 46 |
+
"Capsid protein p24",
|
| 47 |
+
"Interaction with human PPIA/CYPA and NUP153",
|
| 48 |
+
"Dimerization/Multimerization of capsid protein p24",
|
| 49 |
+
"Cleavage; by viral protease",
|
| 50 |
+
"Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA"
|
| 51 |
+
],
|
| 52 |
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"FRAMESTEP": 0.1,
|
| 53 |
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"TIMESTEP": 2,
|
| 54 |
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"TEMP": 310,
|
| 55 |
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"ENSEMBLE": "NPT",
|
| 56 |
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"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
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],
|
| 59 |
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"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
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"SYSTATS": 4763,
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| 62 |
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"SYSTRES": 310,
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| 63 |
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"PROTATS": 4763,
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| 64 |
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"PROTRES": 310,
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| 65 |
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"NUCLATS": 0,
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| 66 |
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"NUCLRES": 0,
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| 67 |
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"LIPIATS": 0,
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| 68 |
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"LIPIRES": 0,
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| 69 |
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"CARBATS": 0,
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| 70 |
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"CARBRES": 0,
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| 71 |
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"SOLVATS": 0,
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| 72 |
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"SOLVRES": 0,
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| 73 |
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"COUNCAT": 0,
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| 74 |
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"COUNANI": 0,
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| 75 |
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"COUNION": 0,
|
| 76 |
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"INTERACTIONS": [
|
| 77 |
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{
|
| 78 |
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"name": "protein-protein interaction B-A",
|
| 79 |
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"agent_1": "protein B",
|
| 80 |
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"agent_2": "protein A",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
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"type": "protein-protein"
|
| 84 |
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}
|
| 85 |
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],
|
| 86 |
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"PBC_SELECTION": null,
|
| 87 |
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"CHAINNAMES": null,
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| 88 |
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"MEMBRANES": null,
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| 89 |
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"CUSTOMS": null,
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| 90 |
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"ORIENTATION": null,
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| 91 |
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"PTM": [],
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| 92 |
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"MULTIMERIC": null,
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| 93 |
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"COLLECTIONS": "dynarepo",
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| 94 |
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"WARNINGS": [],
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| 95 |
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"BOXSIZEX": 10.6979,
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| 96 |
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"BOXSIZEY": 10.6979,
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| 97 |
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"BOXSIZEZ": 7.58653,
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| 98 |
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"mdName": "replica 1",
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| 99 |
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"mdAtoms": 4763,
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| 100 |
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"mdFrames": 5001
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| 101 |
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},
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| 102 |
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"mds": [
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| 103 |
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"replica 1",
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| 104 |
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"replica 2",
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| 105 |
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"replica 3"
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| 106 |
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],
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| 107 |
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"mdref": 0,
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| 108 |
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"files": [
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| 109 |
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"topology.tpr",
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| 110 |
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"screenshot.jpg",
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| 111 |
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"trajectory.bin",
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| 112 |
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"pca_trajectory_01.bin",
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| 113 |
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| 115 |
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| 116 |
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| 118 |
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| 119 |
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"structure.pdb",
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| 120 |
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"trajectory.xtc",
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| 121 |
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"clusters_00_screenshot_00.jpg",
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| 122 |
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| 132 |
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| 136 |
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| 137 |
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| 138 |
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| 139 |
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| 140 |
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| 141 |
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| 142 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 163 |
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"pocket_01.pdb"
|
| 164 |
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],
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| 165 |
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"analyses": [
|
| 166 |
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"clusters",
|
| 167 |
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"clusters-00",
|
| 168 |
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"clusters-01",
|
| 169 |
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"dist-perres",
|
| 170 |
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"energies",
|
| 171 |
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"fluctuation",
|
| 172 |
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"hbonds",
|
| 173 |
+
"interactions",
|
| 174 |
+
"pca",
|
| 175 |
+
"pockets",
|
| 176 |
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"rgyr",
|
| 177 |
+
"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
+
"rmsds",
|
| 180 |
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"sasa",
|
| 181 |
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"tmscores"
|
| 182 |
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],
|
| 183 |
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"mdIndex": 0,
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| 184 |
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"mdNumber": 1,
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| 185 |
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"refframe": 0,
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| 186 |
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"internalId": "683efc9b8959c0a482394c98",
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| 187 |
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"creationDate": "2025-06-03T13:46:03.000Z",
|
| 188 |
+
"identifier": "A000A"
|
| 189 |
+
}
|
data/files/A000A/records.jsonl
ADDED
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data/files/A000B/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000B",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1AKJ",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1AKJ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P04439",
|
| 31 |
+
"P61769",
|
| 32 |
+
"P01732"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"SQFRVSPLDRTWNLGETVELKCQVLLSNPTSGCSWLFQPRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLGDTFVLTLSDFRRENEGYYFCSALSNSIMYFSHFVPVFLPA",
|
| 39 |
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"QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM",
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| 40 |
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"ILKEPVHGV",
|
| 41 |
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| 42 |
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| 44 |
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| 46 |
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| 47 |
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| 48 |
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| 49 |
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| 50 |
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| 51 |
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| 52 |
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| 53 |
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| 54 |
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|
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|
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"identifier": "A000B"
|
| 377 |
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}
|
data/files/A000B/records.jsonl
ADDED
|
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|
data/files/A000C/project.json
ADDED
|
@@ -0,0 +1,201 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000C",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1AVA",
|
| 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 |
+
"1AVA"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P04063",
|
| 31 |
+
"P07596"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI",
|
| 38 |
+
"ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Alpha-amylase type B isozyme",
|
| 43 |
+
"Transition state stabilizer",
|
| 44 |
+
"Alpha-amylase/subtilisin inhibitor",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Reactive bond"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 8969,
|
| 58 |
+
"SYSTRES": 584,
|
| 59 |
+
"PROTATS": 8969,
|
| 60 |
+
"PROTRES": 584,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "protein-protein interaction A-B",
|
| 75 |
+
"agent_1": "protein A",
|
| 76 |
+
"agent_2": "protein B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 10.5469,
|
| 92 |
+
"BOXSIZEY": 10.5469,
|
| 93 |
+
"BOXSIZEZ": 7.48757,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 8969,
|
| 96 |
+
"mdFrames": 5001
|
| 97 |
+
},
|
| 98 |
+
"mds": [
|
| 99 |
+
"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
+
"mdref": 0,
|
| 104 |
+
"files": [
|
| 105 |
+
"topology.tpr",
|
| 106 |
+
"screenshot.jpg",
|
| 107 |
+
"trajectory.bin",
|
| 108 |
+
"pca_trajectory_01.bin",
|
| 109 |
+
"pca_trajectory_02.bin",
|
| 110 |
+
"pca_trajectory_03.bin",
|
| 111 |
+
"pca_trajectory_04.bin",
|
| 112 |
+
"pca_trajectory_05.bin",
|
| 113 |
+
"pca_trajectory_06.bin",
|
| 114 |
+
"pca_trajectory_07.bin",
|
| 115 |
+
"pca_trajectory_08.bin",
|
| 116 |
+
"pca_trajectory_09.bin",
|
| 117 |
+
"pca_trajectory_10.bin",
|
| 118 |
+
"pca_trajectory_11.bin",
|
| 119 |
+
"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.bin",
|
| 121 |
+
"pca_trajectory_14.bin",
|
| 122 |
+
"structure.pdb",
|
| 123 |
+
"trajectory.xtc",
|
| 124 |
+
"clusters_00_screenshot_00.jpg",
|
| 125 |
+
"clusters_00_screenshot_01.jpg",
|
| 126 |
+
"clusters_00_screenshot_02.jpg",
|
| 127 |
+
"clusters_00_screenshot_03.jpg",
|
| 128 |
+
"clusters_00_screenshot_04.jpg",
|
| 129 |
+
"clusters_00_screenshot_05.jpg",
|
| 130 |
+
"clusters_00_screenshot_06.jpg",
|
| 131 |
+
"clusters_00_screenshot_07.jpg",
|
| 132 |
+
"clusters_00_screenshot_08.jpg",
|
| 133 |
+
"clusters_00_screenshot_09.jpg",
|
| 134 |
+
"clusters_00_screenshot_10.jpg",
|
| 135 |
+
"clusters_00_screenshot_11.jpg",
|
| 136 |
+
"clusters_00_screenshot_12.jpg",
|
| 137 |
+
"clusters_00_screenshot_13.jpg",
|
| 138 |
+
"clusters_00_screenshot_14.jpg",
|
| 139 |
+
"clusters_00_screenshot_15.jpg",
|
| 140 |
+
"clusters_00_screenshot_16.jpg",
|
| 141 |
+
"clusters_00_screenshot_17.jpg",
|
| 142 |
+
"clusters_00_screenshot_18.jpg",
|
| 143 |
+
"clusters_00_screenshot_19.jpg",
|
| 144 |
+
"clusters_00_screenshot_20.jpg",
|
| 145 |
+
"clusters_00_screenshot_21.jpg",
|
| 146 |
+
"clusters_01_screenshot_00.jpg",
|
| 147 |
+
"clusters_01_screenshot_01.jpg",
|
| 148 |
+
"clusters_01_screenshot_02.jpg",
|
| 149 |
+
"clusters_01_screenshot_03.jpg",
|
| 150 |
+
"clusters_01_screenshot_04.jpg",
|
| 151 |
+
"clusters_01_screenshot_05.jpg",
|
| 152 |
+
"clusters_01_screenshot_06.jpg",
|
| 153 |
+
"clusters_01_screenshot_07.jpg",
|
| 154 |
+
"clusters_01_screenshot_08.jpg",
|
| 155 |
+
"clusters_01_screenshot_09.jpg",
|
| 156 |
+
"clusters_01_screenshot_10.jpg",
|
| 157 |
+
"clusters_01_screenshot_11.jpg",
|
| 158 |
+
"clusters_01_screenshot_12.jpg",
|
| 159 |
+
"clusters_01_screenshot_13.jpg",
|
| 160 |
+
"clusters_01_screenshot_14.jpg",
|
| 161 |
+
"clusters_01_screenshot_15.jpg",
|
| 162 |
+
"clusters_01_screenshot_16.jpg",
|
| 163 |
+
"clusters_01_screenshot_17.jpg",
|
| 164 |
+
"clusters_01_screenshot_18.jpg",
|
| 165 |
+
"clusters_01_screenshot_19.jpg",
|
| 166 |
+
"pocket_01.pdb",
|
| 167 |
+
"pocket_02.pdb",
|
| 168 |
+
"pocket_03.pdb",
|
| 169 |
+
"pocket_04.pdb",
|
| 170 |
+
"pocket_05.pdb",
|
| 171 |
+
"pocket_06.pdb",
|
| 172 |
+
"pocket_07.pdb",
|
| 173 |
+
"pocket_08.pdb",
|
| 174 |
+
"pocket_09.pdb",
|
| 175 |
+
"pocket_10.pdb"
|
| 176 |
+
],
|
| 177 |
+
"analyses": [
|
| 178 |
+
"clusters",
|
| 179 |
+
"clusters-00",
|
| 180 |
+
"clusters-01",
|
| 181 |
+
"dist-perres",
|
| 182 |
+
"energies",
|
| 183 |
+
"fluctuation",
|
| 184 |
+
"hbonds",
|
| 185 |
+
"interactions",
|
| 186 |
+
"pca",
|
| 187 |
+
"pockets",
|
| 188 |
+
"rgyr",
|
| 189 |
+
"rmsd-pairwise",
|
| 190 |
+
"rmsd-perres",
|
| 191 |
+
"rmsds",
|
| 192 |
+
"sasa",
|
| 193 |
+
"tmscores"
|
| 194 |
+
],
|
| 195 |
+
"mdIndex": 0,
|
| 196 |
+
"mdNumber": 1,
|
| 197 |
+
"refframe": 0,
|
| 198 |
+
"internalId": "683efeec19836add5539898f",
|
| 199 |
+
"creationDate": "2025-06-03T13:55:56.000Z",
|
| 200 |
+
"identifier": "A000C"
|
| 201 |
+
}
|
data/files/A000C/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000C", "accession": "A000C", "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 1AVA", "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": ["1AVA"], "FORCED_REFERENCES": null, "REFERENCES": ["P04063", "P07596"], 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data/files/A000D/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000D",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1AY7",
|
| 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 |
+
"1AY7"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P05798",
|
| 31 |
+
"P11540"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC",
|
| 38 |
+
"KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Guanyl-specific ribonuclease Sa",
|
| 43 |
+
"Barstar"
|
| 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": 2875,
|
| 55 |
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"SYSTRES": 185,
|
| 56 |
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"PROTATS": 2875,
|
| 57 |
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"PROTRES": 185,
|
| 58 |
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"NUCLATS": 0,
|
| 59 |
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"NUCLRES": 0,
|
| 60 |
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"LIPIATS": 0,
|
| 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 |
+
"SOLVRES": 0,
|
| 66 |
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"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "protein-protein interaction B-A",
|
| 72 |
+
"agent_1": "protein B",
|
| 73 |
+
"agent_2": "protein A",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
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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 |
+
"MULTIMERIC": null,
|
| 86 |
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"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
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"BOXSIZEX": 8.14692,
|
| 89 |
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"BOXSIZEY": 8.14692,
|
| 90 |
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"BOXSIZEZ": 5.75583,
|
| 91 |
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"mdName": "replica 1",
|
| 92 |
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"mdAtoms": 2875,
|
| 93 |
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"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
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"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 |
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"pca_trajectory_09.bin",
|
| 114 |
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"pca_trajectory_10.bin",
|
| 115 |
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"pca_trajectory_11.bin",
|
| 116 |
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"pca_trajectory_12.bin",
|
| 117 |
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"pca_trajectory_13.bin",
|
| 118 |
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"pca_trajectory_14.bin",
|
| 119 |
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"pca_trajectory_15.bin",
|
| 120 |
+
"pca_trajectory_16.bin",
|
| 121 |
+
"pca_trajectory_17.bin",
|
| 122 |
+
"structure.pdb",
|
| 123 |
+
"trajectory.xtc",
|
| 124 |
+
"clusters_00_screenshot_00.jpg",
|
| 125 |
+
"clusters_00_screenshot_01.jpg",
|
| 126 |
+
"clusters_00_screenshot_02.jpg",
|
| 127 |
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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 |
+
"clusters_00_screenshot_08.jpg",
|
| 133 |
+
"clusters_00_screenshot_09.jpg",
|
| 134 |
+
"clusters_00_screenshot_10.jpg",
|
| 135 |
+
"clusters_00_screenshot_11.jpg",
|
| 136 |
+
"clusters_00_screenshot_12.jpg",
|
| 137 |
+
"clusters_00_screenshot_13.jpg",
|
| 138 |
+
"clusters_00_screenshot_14.jpg",
|
| 139 |
+
"clusters_00_screenshot_15.jpg",
|
| 140 |
+
"clusters_00_screenshot_16.jpg",
|
| 141 |
+
"clusters_00_screenshot_17.jpg",
|
| 142 |
+
"clusters_00_screenshot_18.jpg",
|
| 143 |
+
"clusters_00_screenshot_19.jpg",
|
| 144 |
+
"clusters_01_screenshot_00.jpg",
|
| 145 |
+
"clusters_01_screenshot_01.jpg",
|
| 146 |
+
"clusters_01_screenshot_02.jpg",
|
| 147 |
+
"clusters_01_screenshot_03.jpg",
|
| 148 |
+
"clusters_01_screenshot_04.jpg",
|
| 149 |
+
"clusters_01_screenshot_05.jpg",
|
| 150 |
+
"clusters_01_screenshot_06.jpg",
|
| 151 |
+
"clusters_01_screenshot_07.jpg",
|
| 152 |
+
"clusters_01_screenshot_08.jpg",
|
| 153 |
+
"clusters_01_screenshot_09.jpg",
|
| 154 |
+
"clusters_01_screenshot_10.jpg",
|
| 155 |
+
"clusters_01_screenshot_11.jpg",
|
| 156 |
+
"clusters_01_screenshot_12.jpg",
|
| 157 |
+
"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
+
"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb",
|
| 165 |
+
"pocket_05.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 |
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"mdNumber": 1,
|
| 187 |
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"refframe": 0,
|
| 188 |
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"internalId": "683f0058acc0a79ac6ea66e7",
|
| 189 |
+
"creationDate": "2025-06-03T14:02:00.000Z",
|
| 190 |
+
"identifier": "A000D"
|
| 191 |
+
}
|
data/files/A000D/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
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| 1 |
+
{"project_identifier": "A000D", "accession": "A000D", "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 1AY7", "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": ["1AY7"], "FORCED_REFERENCES": null, "REFERENCES": ["P05798", "P11540"], 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| 1 |
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{
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| 2 |
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"accession": "A000E",
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| 3 |
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| 4 |
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"metadata": {
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| 5 |
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"NAME": "Dynarepo 1B2S",
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| 6 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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| 10 |
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],
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{
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"name": "protein-protein interaction B-A",
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| 73 |
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| 167 |
+
"hbonds",
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| 168 |
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"interactions",
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| 169 |
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"pca",
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"pockets",
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| 171 |
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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": "683f00d236a1ef4572241e03",
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"creationDate": "2025-06-03T14:04:02.000Z",
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"identifier": "A000E"
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}
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data/files/A000E/records.jsonl
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data/files/A000F/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1B6C",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"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 |
+
"1B6C"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"P62942",
|
| 31 |
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"P36897"
|
| 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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"TTLKDLIYDMTTSGSGSGLPLLVQRTIARTIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEG",
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| 38 |
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"GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Peptidyl-prolyl cis-trans isomerase FKBP1A",
|
| 43 |
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"PPIase FKBP-type",
|
| 44 |
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"TGF-beta receptor type-1",
|
| 45 |
+
"GS",
|
| 46 |
+
"Protein kinase",
|
| 47 |
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"FKBP1A-binding"
|
| 48 |
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],
|
| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
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"TIMESTEP": 2,
|
| 51 |
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"TEMP": 310,
|
| 52 |
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"ENSEMBLE": "NPT",
|
| 53 |
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"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
|
| 58 |
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"SYSTATS": 6875,
|
| 59 |
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"SYSTRES": 433,
|
| 60 |
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"PROTATS": 6875,
|
| 61 |
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"PROTRES": 433,
|
| 62 |
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"NUCLATS": 0,
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| 63 |
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"NUCLRES": 0,
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| 64 |
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"LIPIATS": 0,
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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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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
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"name": "protein-protein interaction A-B",
|
| 76 |
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"agent_1": "protein A",
|
| 77 |
+
"agent_2": "protein B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
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"type": "protein-protein"
|
| 81 |
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}
|
| 82 |
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],
|
| 83 |
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"PBC_SELECTION": null,
|
| 84 |
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"CHAINNAMES": null,
|
| 85 |
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"MEMBRANES": null,
|
| 86 |
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"CUSTOMS": null,
|
| 87 |
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"ORIENTATION": null,
|
| 88 |
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"PTM": [],
|
| 89 |
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"MULTIMERIC": null,
|
| 90 |
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"COLLECTIONS": "dynarepo",
|
| 91 |
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"WARNINGS": [],
|
| 92 |
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"BOXSIZEX": 11.3557,
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| 93 |
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"BOXSIZEY": 11.3557,
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| 94 |
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"BOXSIZEZ": 8.02029,
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| 95 |
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"mdName": "replica 1",
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| 96 |
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"mdAtoms": 6875,
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| 97 |
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| 98 |
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},
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| 99 |
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"mds": [
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| 100 |
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"replica 1",
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| 101 |
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"replica 2",
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| 102 |
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| 103 |
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],
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| 104 |
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"mdref": 0,
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| 105 |
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"files": [
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| 106 |
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| 107 |
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| 109 |
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| 110 |
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"pca_trajectory_12.bin",
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"pca_trajectory_14.bin",
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"structure.pdb",
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"trajectory.xtc",
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"clusters_00_screenshot_17.jpg",
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"clusters_00_screenshot_18.jpg",
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"clusters_00_screenshot_19.jpg",
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"clusters_00_screenshot_20.jpg",
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"clusters_00_screenshot_21.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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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb",
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"pocket_08.pdb",
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+
"pocket_09.pdb",
|
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"pocket_10.pdb"
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| 177 |
+
],
|
| 178 |
+
"analyses": [
|
| 179 |
+
"clusters",
|
| 180 |
+
"clusters-00",
|
| 181 |
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"clusters-01",
|
| 182 |
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"dist-perres",
|
| 183 |
+
"energies",
|
| 184 |
+
"fluctuation",
|
| 185 |
+
"hbonds",
|
| 186 |
+
"interactions",
|
| 187 |
+
"pca",
|
| 188 |
+
"pockets",
|
| 189 |
+
"rgyr",
|
| 190 |
+
"rmsd-pairwise",
|
| 191 |
+
"rmsd-perres",
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"rmsds",
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+
"sasa",
|
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"tmscores"
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],
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"mdIndex": 0,
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+
"mdNumber": 1,
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"refframe": 1,
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+
"internalId": "683f015a0c8f2012a132bdfb",
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+
"creationDate": "2025-06-03T14:06:18.000Z",
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+
"identifier": "A000F"
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+
}
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data/files/A000F/records.jsonl
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data/files/A000G/project.json
ADDED
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
| 11 |
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| 12 |
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| 13 |
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|
| 14 |
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| 16 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 24 |
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| 29 |
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| 30 |
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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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| 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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| 71 |
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{
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| 72 |
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| 73 |
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| 74 |
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| 75 |
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| 76 |
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| 77 |
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| 78 |
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data/files/A000H/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000H",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1DFJ",
|
| 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 |
+
"1DFJ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P61823",
|
| 31 |
+
"P10775"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MNLDIHCEQLSDARWTELLPLLQQYEVVRLDDCGLTEEHCKDIGSALRANPSLTELCLRTNELGDAGVHLVLQGLQSPTCKIQKLSLQNCSLTEAGCGVLPSTLRSLPTLRELHLSDNPLGDAGLRLLCEGLLDPQCHLEKLQLEYCRLTAASCEPLASVLRATRALKELTVSNNDIGEAGARVLGQGLADSACQLETLRLENCGLTPANCKDLCGIVASQASLRELDLGSNGLGDAGIAELCPGLLSPASRLKTLWLWECDITASGCRDLCRVLQAKETLKELSLAGNKLGDEGARLLCESLLQPGCQLESLWVKSCSLTAACCQHVSLMLTQNKHLLELQLSSNKLGDSGIQELCQALSQPGTTLRVLCLGDCEVTNSGCSSLASLLLANRSLRELDLSNNCVGDPGVLQLLGSLEQPGCALEQLVLYDTYWTEEVEDRLQALEGSKPGLRVIS",
|
| 38 |
+
"KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ribonuclease pancreatic",
|
| 43 |
+
"Ribonuclease inhibitor"
|
| 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": 8726,
|
| 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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"NUCLRES": 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 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "protein-protein interaction A-B",
|
| 72 |
+
"agent_1": "protein A",
|
| 73 |
+
"agent_2": "protein 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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|
| 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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|
| 88 |
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|
| 89 |
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|
| 90 |
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"BOXSIZEZ": 7.02764,
|
| 91 |
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"mdName": "replica 1",
|
| 92 |
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"mdAtoms": 8726,
|
| 93 |
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"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
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"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"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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"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 |
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"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 |
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"pca_trajectory_08.bin",
|
| 113 |
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"pca_trajectory_09.bin",
|
| 114 |
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"pca_trajectory_10.bin",
|
| 115 |
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"pca_trajectory_11.bin",
|
| 116 |
+
"pca_trajectory_12.bin",
|
| 117 |
+
"pca_trajectory_13.bin",
|
| 118 |
+
"structure.pdb",
|
| 119 |
+
"trajectory.xtc",
|
| 120 |
+
"clusters_00_screenshot_00.jpg",
|
| 121 |
+
"clusters_00_screenshot_01.jpg",
|
| 122 |
+
"clusters_00_screenshot_02.jpg",
|
| 123 |
+
"clusters_00_screenshot_03.jpg",
|
| 124 |
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"clusters_00_screenshot_04.jpg",
|
| 125 |
+
"clusters_00_screenshot_05.jpg",
|
| 126 |
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"clusters_00_screenshot_06.jpg",
|
| 127 |
+
"clusters_00_screenshot_07.jpg",
|
| 128 |
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"clusters_00_screenshot_08.jpg",
|
| 129 |
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"clusters_00_screenshot_09.jpg",
|
| 130 |
+
"clusters_00_screenshot_10.jpg",
|
| 131 |
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"clusters_00_screenshot_11.jpg",
|
| 132 |
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"clusters_00_screenshot_12.jpg",
|
| 133 |
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"clusters_00_screenshot_13.jpg",
|
| 134 |
+
"clusters_00_screenshot_14.jpg",
|
| 135 |
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"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_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": "683f039946cbbc1b6661f0c9",
|
| 192 |
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"creationDate": "2025-06-03T14:15:53.000Z",
|
| 193 |
+
"identifier": "A000H"
|
| 194 |
+
}
|
data/files/A000H/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000H", "accession": "A000H", "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 1DFJ", "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": ["1DFJ"], "FORCED_REFERENCES": null, "REFERENCES": ["P61823", "P10775"], 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data/files/A000I/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000I",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1DP5",
|
| 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 |
+
"1DP5"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P07267",
|
| 31 |
+
"P01094"
|
| 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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"NTDQQKVSEIFQSSKEKLQGDAKVVSDAFMM",
|
| 38 |
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"GGHDVPLTNYLNAQYYTDITLGTPPQNFKVILDTGSSNLWVPSNECGSLACFLHSKYDHEASSSYKANGTEFAIQYGTGSLEGYISQDTLSIGDLTIPKQDFAEATSEPGLTFAFGKFDGILGLGYDTISVDKVVPPFYNAIQQDLLDEKRFAFYLGDTSKDTENGGEATFGGIDESKFKGDITWLPVRRKAYWEVKFEGIGLGDEYAELESHGAAIDTGTSLITLPSGLAEMINAEIGAKKGWTGQYTLDCNTRDNLPDLIFNFNGYNFTIGPYDYTLEVSGSCISAITPMDFPEPVGPLAIVGDAFLRKYYSIYDLGNNAVGLAKAI"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
+
"Saccharopepsin",
|
| 43 |
+
"Peptidase A1",
|
| 44 |
+
"Protease A inhibitor 3",
|
| 45 |
+
"Inhibitory domain",
|
| 46 |
+
"Disordered"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 5415,
|
| 58 |
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"SYSTRES": 360,
|
| 59 |
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"PROTATS": 5415,
|
| 60 |
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"PROTRES": 360,
|
| 61 |
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"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
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"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
|
| 68 |
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"SOLVRES": 0,
|
| 69 |
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"COUNCAT": 0,
|
| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
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{
|
| 74 |
+
"name": "protein-protein interaction A-B",
|
| 75 |
+
"agent_1": "protein A",
|
| 76 |
+
"agent_2": "protein B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
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"CHAINNAMES": null,
|
| 84 |
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"MEMBRANES": null,
|
| 85 |
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"CUSTOMS": null,
|
| 86 |
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"ORIENTATION": null,
|
| 87 |
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"PTM": [],
|
| 88 |
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"MULTIMERIC": null,
|
| 89 |
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"COLLECTIONS": "dynarepo",
|
| 90 |
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"WARNINGS": [],
|
| 91 |
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"BOXSIZEX": 8.89519,
|
| 92 |
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"BOXSIZEY": 8.89519,
|
| 93 |
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"BOXSIZEZ": 6.24575,
|
| 94 |
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"mdName": "replica 1",
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| 95 |
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"mdAtoms": 5415,
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| 96 |
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"mdFrames": 5001
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| 97 |
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},
|
| 98 |
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"mds": [
|
| 99 |
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"replica 1",
|
| 100 |
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"replica 2",
|
| 101 |
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"replica 3"
|
| 102 |
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],
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| 103 |
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"mdref": 0,
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| 104 |
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"files": [
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| 105 |
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| 108 |
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| 109 |
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|
| 110 |
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"pocket_01.pdb",
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"pocket_08.pdb",
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"pocket_09.pdb",
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"pocket_10.pdb"
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],
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"analyses": [
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"clusters",
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"clusters-00",
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"clusters-01",
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 1,
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"internalId": "683f04e0f25c90c47cca515a",
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"creationDate": "2025-06-03T14:21:20.000Z",
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"identifier": "A000I"
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}
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data/files/A000I/records.jsonl
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data/files/A000J/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A000J",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1E3U",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 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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"1E3U"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P14489"
|
| 31 |
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],
|
| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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| 36 |
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| 37 |
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|
| 38 |
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],
|
| 39 |
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"NUCLSEQ": [],
|
| 40 |
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"DOMAINS": [
|
| 41 |
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"Beta-lactamase OXA-10"
|
| 42 |
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],
|
| 43 |
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"FRAMESTEP": 0.1,
|
| 44 |
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"TIMESTEP": 2,
|
| 45 |
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"TEMP": 310,
|
| 46 |
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"ENSEMBLE": "NPT",
|
| 47 |
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"FF": [
|
| 48 |
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"CHARMM36m"
|
| 49 |
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],
|
| 50 |
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"WAT": "TIP3P",
|
| 51 |
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"BOXTYPE": "Dodecahedron",
|
| 52 |
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"SYSTATS": 7716,
|
| 53 |
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"SYSTRES": 488,
|
| 54 |
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"PROTATS": 7716,
|
| 55 |
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"PROTRES": 488,
|
| 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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| 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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"INTERACTIONS": [
|
| 68 |
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{
|
| 69 |
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"name": "protein-protein interaction B-A",
|
| 70 |
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"agent_1": "protein B",
|
| 71 |
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"agent_2": "protein A",
|
| 72 |
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"selection_1": "chain A",
|
| 73 |
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"selection_2": "chain B",
|
| 74 |
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"type": "protein-protein"
|
| 75 |
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}
|
| 76 |
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],
|
| 77 |
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| 78 |
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| 79 |
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| 80 |
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| 81 |
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| 82 |
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| 83 |
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| 84 |
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"COLLECTIONS": "dynarepo",
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| 85 |
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"WARNINGS": [],
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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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| 92 |
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},
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| 93 |
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| 95 |
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| 96 |
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],
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"analyses": [
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| 174 |
+
"clusters-00",
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| 175 |
+
"clusters-01",
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| 176 |
+
"dist-perres",
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| 177 |
+
"energies",
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| 178 |
+
"fluctuation",
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| 179 |
+
"hbonds",
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| 180 |
+
"interactions",
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| 181 |
+
"pca",
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| 182 |
+
"pockets",
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| 183 |
+
"rgyr",
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| 184 |
+
"rmsd-pairwise",
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| 185 |
+
"rmsd-perres",
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| 186 |
+
"rmsds",
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| 187 |
+
"sasa",
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| 188 |
+
"tmscores"
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| 189 |
+
],
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| 190 |
+
"mdIndex": 0,
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| 191 |
+
"mdNumber": 1,
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| 192 |
+
"refframe": 0,
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| 193 |
+
"internalId": "683f1fbaa4df910e8af0c108",
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| 194 |
+
"creationDate": "2025-06-03T16:15:54.000Z",
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| 195 |
+
"identifier": "A000J"
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+
}
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data/files/A000J/records.jsonl
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| 1 |
+
{
|
| 2 |
+
"accession": "A000K",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1E6E",
|
| 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 |
+
"1E6E"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P08165",
|
| 31 |
+
"P00257"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"DKITVHFINRDGETLTTKGKIGDSLLDVVVQNNLDIDGFGACEGTLACSTCHLIFEQHIFEKLEAITDEENDMLDLAYGLTDRSRLGCQICLTKAMDNMTVRVPDAVSDARES",
|
| 38 |
+
"EQTPQICVVGSGPAGFYTAQHLLKHHSRAHVDIYEKQLVPFGLVRFGVAPDHPEVKNVINTFTQTARSDRCAFYGNVEVGRDVTVQELQDAYHAVVLSYGAEDHQALDIPGEELPGVFSARAFVGWYNGLPENRELAPDLSCDTAVILGQGNVALDVARILLTPPDHLEKTDITEAALGALRQSRVKTVWIVGRRGPLQVAFTIKELREMIQLPGTRPMLDPADFLGLQDRIKEAARPRKRLMELLLRTATEKPGVEEAARRASASRAWGLRFFRSPQQVLPSPDGRRAAGIRLAVTRLEGIGEATRAVPTGDVEDLPCGLVLSSIGYKSRPIDPSVPFDPKLGVVPNMEGRVVDVPGLYCSGWVKRGPTGVITTTMTDSFLTGQILLQDLKAGHLPSGPRPGSAFIKALLDSRGVWPVSFSDWEKLDAEEVSRGQASGKPREKLLDPQEMLRLLGH"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"NADPH:adrenodoxin oxidoreductase, mitochondrial",
|
| 43 |
+
"Adrenodoxin, mitochondrial",
|
| 44 |
+
"2Fe-2S ferredoxin-type"
|
| 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": 8790,
|
| 56 |
+
"SYSTRES": 570,
|
| 57 |
+
"PROTATS": 8790,
|
| 58 |
+
"PROTRES": 570,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "protein-protein interaction B-A",
|
| 73 |
+
"agent_1": "protein B",
|
| 74 |
+
"agent_2": "protein A",
|
| 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 |
+
"BOXSIZEX": 10.3587,
|
| 90 |
+
"BOXSIZEY": 10.3587,
|
| 91 |
+
"BOXSIZEZ": 7.32842,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 8790,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"structure.pdb",
|
| 119 |
+
"trajectory.xtc",
|
| 120 |
+
"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_00_screenshot_20.jpg",
|
| 141 |
+
"clusters_00_screenshot_21.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 |
+
"clusters_01_screenshot_20.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 |
+
"mdNumber": 1,
|
| 194 |
+
"refframe": 0,
|
| 195 |
+
"internalId": "683f210b91aa48f81e5756a4",
|
| 196 |
+
"creationDate": "2025-06-03T16:21:31.000Z",
|
| 197 |
+
"identifier": "A000K"
|
| 198 |
+
}
|
data/files/A000K/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000K", "accession": "A000K", "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 1E6E", "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": ["1E6E"], "FORCED_REFERENCES": null, "REFERENCES": ["P08165", "P00257"], 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data/files/A000L/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000L",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1E96",
|
| 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 |
+
"1E96"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P63000",
|
| 31 |
+
"P19878"
|
| 32 |
+
],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"PQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGLEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLC",
|
| 38 |
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"SLVEAISLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPRHSKIDKAMECVWKQKLYEPVVIPVGKLFRPN"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Ras-related C3 botulinum toxin substrate 1",
|
| 43 |
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"Effector region",
|
| 44 |
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"Neutrophil cytosol factor 2"
|
| 45 |
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],
|
| 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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|
| 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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|
| 69 |
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|
| 70 |
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|
| 71 |
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{
|
| 72 |
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"name": "protein-protein interaction A-B",
|
| 73 |
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"agent_1": "protein A",
|
| 74 |
+
"agent_2": "protein 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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| 95 |
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},
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| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
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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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"structure.pdb",
|
| 111 |
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"trajectory.xtc",
|
| 112 |
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"clusters_00_screenshot_00.jpg",
|
| 113 |
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"clusters_00_screenshot_01.jpg",
|
| 114 |
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"clusters_00_screenshot_02.jpg",
|
| 115 |
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"clusters_00_screenshot_03.jpg",
|
| 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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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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"clusters_00_screenshot_18.jpg",
|
| 131 |
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"clusters_00_screenshot_19.jpg",
|
| 132 |
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"clusters_00_screenshot_20.jpg",
|
| 133 |
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"clusters_01_screenshot_00.jpg",
|
| 134 |
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"clusters_01_screenshot_01.jpg",
|
| 135 |
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"clusters_01_screenshot_02.jpg",
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| 136 |
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"clusters_01_screenshot_03.jpg",
|
| 137 |
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"clusters_01_screenshot_04.jpg",
|
| 138 |
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"clusters_01_screenshot_05.jpg",
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| 139 |
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"clusters_01_screenshot_06.jpg",
|
| 140 |
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"clusters_01_screenshot_07.jpg",
|
| 141 |
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"clusters_01_screenshot_08.jpg",
|
| 142 |
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"clusters_01_screenshot_09.jpg",
|
| 143 |
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"clusters_01_screenshot_10.jpg",
|
| 144 |
+
"clusters_01_screenshot_11.jpg",
|
| 145 |
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"clusters_01_screenshot_12.jpg",
|
| 146 |
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"clusters_01_screenshot_13.jpg",
|
| 147 |
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"clusters_01_screenshot_14.jpg",
|
| 148 |
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"clusters_01_screenshot_15.jpg",
|
| 149 |
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"clusters_01_screenshot_16.jpg",
|
| 150 |
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"clusters_01_screenshot_17.jpg",
|
| 151 |
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"clusters_01_screenshot_18.jpg",
|
| 152 |
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"clusters_01_screenshot_19.jpg",
|
| 153 |
+
"clusters_01_screenshot_20.jpg",
|
| 154 |
+
"clusters_01_screenshot_21.jpg",
|
| 155 |
+
"pocket_01.pdb",
|
| 156 |
+
"pocket_02.pdb",
|
| 157 |
+
"pocket_03.pdb"
|
| 158 |
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],
|
| 159 |
+
"analyses": [
|
| 160 |
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"clusters",
|
| 161 |
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"clusters-00",
|
| 162 |
+
"clusters-01",
|
| 163 |
+
"dist-perres",
|
| 164 |
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"energies",
|
| 165 |
+
"fluctuation",
|
| 166 |
+
"hbonds",
|
| 167 |
+
"interactions",
|
| 168 |
+
"pca",
|
| 169 |
+
"pockets",
|
| 170 |
+
"rgyr",
|
| 171 |
+
"rmsd-pairwise",
|
| 172 |
+
"rmsd-perres",
|
| 173 |
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"rmsds",
|
| 174 |
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"sasa",
|
| 175 |
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"tmscores"
|
| 176 |
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],
|
| 177 |
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|
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"mdNumber": 1,
|
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"creationDate": "2025-06-03T16:27:26.000Z",
|
| 182 |
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"identifier": "A000L"
|
| 183 |
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}
|
data/files/A000L/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000L", "accession": "A000L", "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 1E96", "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": ["1E96"], "FORCED_REFERENCES": null, "REFERENCES": ["P63000", "P19878"], 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data/files/A000M/project.json
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+
{
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| 2 |
+
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|
| 3 |
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|
| 4 |
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"metadata": {
|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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|
| 11 |
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|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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|
| 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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| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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| 33 |
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|
| 34 |
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| 35 |
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|
| 36 |
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|
| 37 |
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|
| 38 |
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"APPRLICDSRVLERYLLEAKEAEKITTGCAEHCSLNEKITVPDTKVNFYAWKRMEVGQQAVEVWQGLALLSEAVLRGQALLVKSSQPWEPLQLHVDKAVSGLRSLTTLLRALGAQKEAISNSDAASAAPLRTITADTFRKLFRVYSNFLRGKLKLYTGEACRTGDR"
|
| 39 |
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],
|
| 40 |
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|
| 41 |
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|
| 42 |
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"Erythropoietin",
|
| 43 |
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"Erythropoietin receptor",
|
| 44 |
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"Fibronectin type-III",
|
| 45 |
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"WSXWS motif",
|
| 46 |
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"Required for ligand binding"
|
| 47 |
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| 48 |
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| 51 |
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|
| 52 |
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|
| 53 |
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"CHARMM36m"
|
| 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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|
| 71 |
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|
| 72 |
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|
| 73 |
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{
|
| 74 |
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"name": "protein-protein interaction B-A",
|
| 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": "protein-protein interaction B-C",
|
| 83 |
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"agent_1": "protein B",
|
| 84 |
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|
| 85 |
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"selection_1": "chain A",
|
| 86 |
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|
| 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 A-C",
|
| 91 |
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"agent_1": "protein A",
|
| 92 |
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|
| 93 |
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"selection_1": "chain B",
|
| 94 |
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"selection_2": "chain C",
|
| 95 |
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"type": "protein-protein"
|
| 96 |
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|
| 97 |
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|
| 98 |
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|
| 99 |
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|
| 100 |
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| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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| 105 |
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|
| 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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|
| 113 |
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},
|
| 114 |
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"mds": [
|
| 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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"mdref": 0,
|
| 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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| 136 |
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|
| 137 |
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|
| 138 |
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| 139 |
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|
| 140 |
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| 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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| 155 |
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| 156 |
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| 157 |
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| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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| 163 |
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| 164 |
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| 165 |
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| 166 |
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| 167 |
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| 168 |
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| 169 |
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|
| 170 |
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|
| 171 |
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| 172 |
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| 173 |
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|
| 174 |
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|
| 175 |
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| 176 |
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|
| 177 |
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|
| 178 |
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|
| 179 |
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| 180 |
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|
| 181 |
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| 182 |
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| 183 |
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| 184 |
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| 185 |
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| 186 |
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| 187 |
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| 188 |
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| 189 |
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| 190 |
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| 191 |
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| 192 |
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| 193 |
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| 194 |
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| 195 |
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| 196 |
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| 197 |
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| 198 |
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| 199 |
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| 200 |
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| 201 |
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|
| 202 |
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|
| 203 |
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"clusters_03_screenshot_00.jpg",
|
| 204 |
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|
| 205 |
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|
| 206 |
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|
| 207 |
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|
| 208 |
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|
| 209 |
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| 210 |
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|
| 211 |
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|
| 212 |
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| 213 |
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| 214 |
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|
| 215 |
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|
| 216 |
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"clusters_03_screenshot_13.jpg",
|
| 217 |
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|
| 218 |
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|
| 219 |
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|
| 220 |
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|
| 221 |
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"clusters_03_screenshot_18.jpg",
|
| 222 |
+
"clusters_03_screenshot_19.jpg",
|
| 223 |
+
"pocket_01.pdb",
|
| 224 |
+
"pocket_02.pdb",
|
| 225 |
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"pocket_03.pdb",
|
| 226 |
+
"pocket_04.pdb",
|
| 227 |
+
"pocket_05.pdb",
|
| 228 |
+
"pocket_06.pdb",
|
| 229 |
+
"pocket_07.pdb",
|
| 230 |
+
"pocket_08.pdb",
|
| 231 |
+
"pocket_09.pdb",
|
| 232 |
+
"pocket_10.pdb"
|
| 233 |
+
],
|
| 234 |
+
"analyses": [
|
| 235 |
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"clusters",
|
| 236 |
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"clusters-00",
|
| 237 |
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"clusters-01",
|
| 238 |
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"clusters-02",
|
| 239 |
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"clusters-03",
|
| 240 |
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"dist-perres",
|
| 241 |
+
"energies",
|
| 242 |
+
"fluctuation",
|
| 243 |
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"hbonds",
|
| 244 |
+
"interactions",
|
| 245 |
+
"pca",
|
| 246 |
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"pockets",
|
| 247 |
+
"rgyr",
|
| 248 |
+
"rmsd-pairwise",
|
| 249 |
+
"rmsd-perres",
|
| 250 |
+
"rmsds",
|
| 251 |
+
"sasa",
|
| 252 |
+
"tmscores"
|
| 253 |
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],
|
| 254 |
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"mdIndex": 0,
|
| 255 |
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"mdNumber": 1,
|
| 256 |
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"refframe": 0,
|
| 257 |
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"internalId": "683f236691a8dd7b0e6e3f13",
|
| 258 |
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"creationDate": "2025-06-03T16:31:34.000Z",
|
| 259 |
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"identifier": "A000M"
|
| 260 |
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}
|
data/files/A000M/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000M", "accession": "A000M", "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 1EER", "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": ["1EER"], "FORCED_REFERENCES": null, "REFERENCES": 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data/files/A000N/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000N",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1EMV",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"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 |
+
"1EMV"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"P13479",
|
| 31 |
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"P09883"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
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| 37 |
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"LKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGDDDSPSGIVNTVKQWRAANGKSGFKQ",
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| 38 |
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"MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIH"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Colicin-E9 immunity protein",
|
| 43 |
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"Colicin-E9",
|
| 44 |
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"Disordered"
|
| 45 |
+
],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 3340,
|
| 56 |
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"SYSTRES": 214,
|
| 57 |
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"PROTATS": 3340,
|
| 58 |
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"PROTRES": 214,
|
| 59 |
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"NUCLATS": 0,
|
| 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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|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
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| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
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"name": "protein-protein interaction A-B",
|
| 73 |
+
"agent_1": "protein A",
|
| 74 |
+
"agent_2": "protein 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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"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 8.77429,
|
| 90 |
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"BOXSIZEY": 8.77429,
|
| 91 |
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"BOXSIZEZ": 6.18647,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 3340,
|
| 94 |
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"mdFrames": 5001
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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,
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| 102 |
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"files": [
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| 103 |
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| 104 |
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| 106 |
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| 107 |
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| 108 |
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| 109 |
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| 110 |
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| 111 |
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| 119 |
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| 133 |
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"clusters_01_screenshot_17.jpg",
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"clusters_01_screenshot_18.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb"
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| 165 |
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],
|
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"analyses": [
|
| 167 |
+
"clusters",
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| 168 |
+
"clusters-00",
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"clusters-01",
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| 170 |
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"dist-perres",
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| 171 |
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"energies",
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| 172 |
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "683f24dd40706c8bc89c46ff",
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"creationDate": "2025-06-03T16:37:49.000Z",
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"identifier": "A000N"
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}
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data/files/A000N/records.jsonl
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data/files/A000O/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000O",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1EWY",
|
| 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 |
+
"1EWY"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P21890",
|
| 31 |
+
"P0A3C8"
|
| 32 |
+
],
|
| 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": [
|
| 37 |
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"ATFKVTLINEAEGTKHEIEVPDDEYILDAAEEQGYDLPFSCRAGACSTCAGKLVSGTVDQSDQSFLDDDQIEAGYVLTCVAYPTSDVVIQTHKEEDLY",
|
| 38 |
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"TQAKAKHADVPVNLYRPNAPFIGKVISNEPLVKEGGIGIVQHIKFDLTGGNLKYIEGQSIGIIPPGVDKNGKPEKLRLYSIASTRHGDDVDDKTISLCVRQLEYKHPESGETVYGVCSTYLTHIEPGSEVKITGPVGKEMLLPDDPEANVIMLATGTGIAPMRTYLWRMFKDAERAANPEYQFKGFSWLVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISREQKNPQGGRMYIQDRVAEHADELWQLIKNQKTHTYICGLRGMEEGIDAALSAAAAKEGVTWSDYQKDLKKAGRWHVETY"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ferredoxin--NADP reductase",
|
| 43 |
+
"FAD-binding FR-type",
|
| 44 |
+
"Disordered",
|
| 45 |
+
"Ferredoxin-1",
|
| 46 |
+
"2Fe-2S ferredoxin-type"
|
| 47 |
+
],
|
| 48 |
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|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
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|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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|
| 57 |
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|
| 58 |
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|
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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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|
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|
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|
| 70 |
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|
| 71 |
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|
| 72 |
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|
| 73 |
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{
|
| 74 |
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"name": "protein-protein interaction B-A",
|
| 75 |
+
"agent_1": "protein B",
|
| 76 |
+
"agent_2": "protein A",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
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|
| 83 |
+
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|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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|
| 97 |
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},
|
| 98 |
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"mds": [
|
| 99 |
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"replica 1",
|
| 100 |
+
"replica 2",
|
| 101 |
+
"replica 3"
|
| 102 |
+
],
|
| 103 |
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"mdref": 0,
|
| 104 |
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"files": [
|
| 105 |
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|
| 106 |
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"screenshot.jpg",
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"trajectory.bin",
|
| 108 |
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"pca_trajectory_01.bin",
|
| 109 |
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"pca_trajectory_02.bin",
|
| 110 |
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"pca_trajectory_03.bin",
|
| 111 |
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|
| 112 |
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"pca_trajectory_05.bin",
|
| 113 |
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"pca_trajectory_06.bin",
|
| 114 |
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"pca_trajectory_07.bin",
|
| 115 |
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"pca_trajectory_08.bin",
|
| 116 |
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"pca_trajectory_09.bin",
|
| 117 |
+
"pca_trajectory_10.bin",
|
| 118 |
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"structure.pdb",
|
| 119 |
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"trajectory.xtc",
|
| 120 |
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"clusters_00_screenshot_00.jpg",
|
| 121 |
+
"clusters_00_screenshot_01.jpg",
|
| 122 |
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|
| 123 |
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"clusters_00_screenshot_03.jpg",
|
| 124 |
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|
| 125 |
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"clusters_00_screenshot_05.jpg",
|
| 126 |
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"clusters_00_screenshot_06.jpg",
|
| 127 |
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"clusters_00_screenshot_07.jpg",
|
| 128 |
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|
| 129 |
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"clusters_00_screenshot_09.jpg",
|
| 130 |
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"clusters_00_screenshot_10.jpg",
|
| 131 |
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|
| 132 |
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|
| 133 |
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"clusters_00_screenshot_13.jpg",
|
| 134 |
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|
| 135 |
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|
| 136 |
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"clusters_00_screenshot_16.jpg",
|
| 137 |
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"clusters_00_screenshot_17.jpg",
|
| 138 |
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"clusters_00_screenshot_18.jpg",
|
| 139 |
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"clusters_00_screenshot_19.jpg",
|
| 140 |
+
"clusters_00_screenshot_20.jpg",
|
| 141 |
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"clusters_00_screenshot_21.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 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"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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|
| 152 |
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"clusters_01_screenshot_10.jpg",
|
| 153 |
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"clusters_01_screenshot_11.jpg",
|
| 154 |
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|
| 155 |
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"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
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"clusters_01_screenshot_15.jpg",
|
| 158 |
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"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 |
+
"clusters_01_screenshot_20.jpg",
|
| 163 |
+
"clusters_01_screenshot_21.jpg",
|
| 164 |
+
"clusters_01_screenshot_22.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb",
|
| 173 |
+
"pocket_09.pdb",
|
| 174 |
+
"pocket_10.pdb"
|
| 175 |
+
],
|
| 176 |
+
"analyses": [
|
| 177 |
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"clusters",
|
| 178 |
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"clusters-00",
|
| 179 |
+
"clusters-01",
|
| 180 |
+
"dist-perres",
|
| 181 |
+
"energies",
|
| 182 |
+
"fluctuation",
|
| 183 |
+
"hbonds",
|
| 184 |
+
"interactions",
|
| 185 |
+
"pca",
|
| 186 |
+
"pockets",
|
| 187 |
+
"rgyr",
|
| 188 |
+
"rmsd-pairwise",
|
| 189 |
+
"rmsd-perres",
|
| 190 |
+
"rmsds",
|
| 191 |
+
"sasa",
|
| 192 |
+
"tmscores"
|
| 193 |
+
],
|
| 194 |
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"mdIndex": 0,
|
| 195 |
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"mdNumber": 1,
|
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|
| 197 |
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"internalId": "683f256f3a48bd57c720f955",
|
| 198 |
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"creationDate": "2025-06-03T16:40:15.000Z",
|
| 199 |
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"identifier": "A000O"
|
| 200 |
+
}
|
data/files/A000O/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000O", "accession": "A000O", "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 1EWY", "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": ["1EWY"], "FORCED_REFERENCES": null, "REFERENCES": ["P21890", "P0A3C8"], 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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000P",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1F3V",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
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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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"1F3V"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q15628",
|
| 31 |
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"Q12933"
|
| 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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"HEEWVGSAYLFVESSLDKVVLSDAYAHPQQKVAVYRALQAALAESGGSPDVLQMLKIHRSDPQLIVQLRFCGRQPCGRFLRAYREGALRAALQRSLAAALAQHSVPLQLELRAGAERLDALLADEERCLSCILAQQPDRLRDEELAELEDALRNLKCG",
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| 38 |
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"KDLAMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Tumor necrosis factor receptor type 1-associated DEATH domain protein",
|
| 43 |
+
"Nuclear export signal",
|
| 44 |
+
"TNF receptor-associated factor 2",
|
| 45 |
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"MATH"
|
| 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": 5196,
|
| 57 |
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"SYSTRES": 329,
|
| 58 |
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"PROTATS": 5196,
|
| 59 |
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"PROTRES": 329,
|
| 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,
|
| 63 |
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"LIPIRES": 0,
|
| 64 |
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"CARBATS": 0,
|
| 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,
|
| 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": "protein-protein interaction B-A",
|
| 74 |
+
"agent_1": "protein B",
|
| 75 |
+
"agent_2": "protein A",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
|
| 79 |
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}
|
| 80 |
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],
|
| 81 |
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"PBC_SELECTION": null,
|
| 82 |
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"CHAINNAMES": null,
|
| 83 |
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"MEMBRANES": null,
|
| 84 |
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"CUSTOMS": null,
|
| 85 |
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"ORIENTATION": null,
|
| 86 |
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"PTM": [],
|
| 87 |
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"MULTIMERIC": null,
|
| 88 |
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"COLLECTIONS": "dynarepo",
|
| 89 |
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"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 10.4253,
|
| 91 |
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"BOXSIZEY": 10.4253,
|
| 92 |
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"BOXSIZEZ": 7.32503,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 5196,
|
| 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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| 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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| 114 |
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| 115 |
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| 127 |
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"clusters_01_screenshot_17.jpg",
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"clusters_01_screenshot_18.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb"
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| 163 |
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],
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"analyses": [
|
| 165 |
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"clusters",
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| 166 |
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"clusters-00",
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"clusters-01",
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| 168 |
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"dist-perres",
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"energies",
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| 170 |
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"fluctuation",
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"hbonds",
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"interactions",
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| 173 |
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 1,
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"internalId": "683f267399f4c482e6d05bf0",
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"creationDate": "2025-06-03T16:44:35.000Z",
|
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+
"identifier": "A000P"
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}
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data/files/A000P/records.jsonl
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data/files/A000Q/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A000Q",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1FC2",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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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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"1FC2"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P38507",
|
| 31 |
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"P01857"
|
| 32 |
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],
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| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
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| 35 |
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| 36 |
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"PROTSEQ": [
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| 37 |
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| 38 |
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| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
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| 41 |
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"DOMAINS": [
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| 42 |
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"Immunoglobulin G-binding protein A",
|
| 43 |
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"Immunoglobulin heavy constant gamma 1",
|
| 44 |
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"Ig-like 2",
|
| 45 |
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"Ig-like 3",
|
| 46 |
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"CH2",
|
| 47 |
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"CH3"
|
| 48 |
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],
|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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"WAT": "TIP3P",
|
| 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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|
| 64 |
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|
| 65 |
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| 66 |
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| 67 |
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|
| 68 |
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| 69 |
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|
| 70 |
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| 71 |
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|
| 72 |
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|
| 73 |
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|
| 74 |
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{
|
| 75 |
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"name": "protein-protein interaction A-B",
|
| 76 |
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"agent_1": "protein A",
|
| 77 |
+
"agent_2": "protein B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
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"selection_2": "chain B",
|
| 80 |
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"type": "protein-protein"
|
| 81 |
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}
|
| 82 |
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],
|
| 83 |
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|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
| 91 |
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| 92 |
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| 93 |
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"replica 2",
|
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"replica 3"
|
| 103 |
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],
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| 104 |
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"mdref": 0,
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| 105 |
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"files": [
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| 106 |
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"screenshot.jpg",
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| 108 |
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"trajectory.bin",
|
| 109 |
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"pca_trajectory_01.bin",
|
| 110 |
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"pca_trajectory_02.bin",
|
| 111 |
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"pca_trajectory_03.bin",
|
| 112 |
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"pca_trajectory_04.bin",
|
| 113 |
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"pca_trajectory_05.bin",
|
| 114 |
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"pca_trajectory_06.bin",
|
| 115 |
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"pca_trajectory_07.bin",
|
| 116 |
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"pca_trajectory_08.bin",
|
| 117 |
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"pca_trajectory_09.bin",
|
| 118 |
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"structure.pdb",
|
| 119 |
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"trajectory.xtc",
|
| 120 |
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"clusters_00_screenshot_00.jpg",
|
| 121 |
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"clusters_00_screenshot_01.jpg",
|
| 122 |
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|
| 123 |
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| 125 |
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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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"clusters_00_screenshot_14.jpg",
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| 135 |
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"clusters_00_screenshot_15.jpg",
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| 136 |
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"clusters_00_screenshot_16.jpg",
|
| 137 |
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"clusters_00_screenshot_17.jpg",
|
| 138 |
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"clusters_00_screenshot_18.jpg",
|
| 139 |
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"clusters_00_screenshot_19.jpg",
|
| 140 |
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"clusters_00_screenshot_20.jpg",
|
| 141 |
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"clusters_00_screenshot_21.jpg",
|
| 142 |
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"clusters_01_screenshot_00.jpg",
|
| 143 |
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"clusters_01_screenshot_01.jpg",
|
| 144 |
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|
| 145 |
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| 146 |
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|
| 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",
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| 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",
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| 156 |
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"clusters_01_screenshot_14.jpg",
|
| 157 |
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"clusters_01_screenshot_15.jpg",
|
| 158 |
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"clusters_01_screenshot_16.jpg",
|
| 159 |
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"clusters_01_screenshot_17.jpg",
|
| 160 |
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"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.jpg",
|
| 162 |
+
"clusters_01_screenshot_20.jpg",
|
| 163 |
+
"pocket_01.pdb",
|
| 164 |
+
"pocket_02.pdb"
|
| 165 |
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],
|
| 166 |
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|
| 167 |
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"clusters",
|
| 168 |
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"clusters-00",
|
| 169 |
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"clusters-01",
|
| 170 |
+
"dist-perres",
|
| 171 |
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"energies",
|
| 172 |
+
"fluctuation",
|
| 173 |
+
"hbonds",
|
| 174 |
+
"interactions",
|
| 175 |
+
"pca",
|
| 176 |
+
"pockets",
|
| 177 |
+
"rgyr",
|
| 178 |
+
"rmsd-pairwise",
|
| 179 |
+
"rmsd-perres",
|
| 180 |
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"rmsds",
|
| 181 |
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"sasa",
|
| 182 |
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"tmscores"
|
| 183 |
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],
|
| 184 |
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| 188 |
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|
| 189 |
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"identifier": "A000Q"
|
| 190 |
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}
|
data/files/A000Q/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
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|
|
|
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|
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| 1 |
+
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| 3 |
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| 1 |
+
{
|
| 2 |
+
"accession": "A000R",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1FFW",
|
| 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 |
+
"1FFW"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0AE67",
|
| 31 |
+
"P07363"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ARRIILSRLKAGEVDLLEEELGHLTTLTDVVKGADSLSAILPGDIAEDDITAVLCFVIEADQITFETV",
|
| 38 |
+
"ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKLGM"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Chemotaxis protein CheY",
|
| 43 |
+
"Response regulatory",
|
| 44 |
+
"Chemotaxis protein CheA"
|
| 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": 3022,
|
| 56 |
+
"SYSTRES": 196,
|
| 57 |
+
"PROTATS": 3022,
|
| 58 |
+
"PROTRES": 196,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
+
"NUCLRES": 0,
|
| 61 |
+
"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
+
"CARBATS": 0,
|
| 64 |
+
"CARBRES": 0,
|
| 65 |
+
"SOLVATS": 0,
|
| 66 |
+
"SOLVRES": 0,
|
| 67 |
+
"COUNCAT": 0,
|
| 68 |
+
"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 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 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 8.33268,
|
| 90 |
+
"BOXSIZEY": 8.33268,
|
| 91 |
+
"BOXSIZEZ": 5.87696,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 3022,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"pca_trajectory_13.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_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 |
+
],
|
| 166 |
+
"analyses": [
|
| 167 |
+
"clusters",
|
| 168 |
+
"clusters-00",
|
| 169 |
+
"clusters-01",
|
| 170 |
+
"dist-perres",
|
| 171 |
+
"energies",
|
| 172 |
+
"fluctuation",
|
| 173 |
+
"hbonds",
|
| 174 |
+
"interactions",
|
| 175 |
+
"pca",
|
| 176 |
+
"pockets",
|
| 177 |
+
"rgyr",
|
| 178 |
+
"rmsd-pairwise",
|
| 179 |
+
"rmsd-perres",
|
| 180 |
+
"rmsds",
|
| 181 |
+
"sasa",
|
| 182 |
+
"tmscores"
|
| 183 |
+
],
|
| 184 |
+
"mdIndex": 0,
|
| 185 |
+
"mdNumber": 1,
|
| 186 |
+
"refframe": 0,
|
| 187 |
+
"internalId": "683f2813ec13df7674eecaac",
|
| 188 |
+
"creationDate": "2025-06-03T16:51:31.000Z",
|
| 189 |
+
"identifier": "A000R"
|
| 190 |
+
}
|
data/files/A000R/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000R", "accession": "A000R", "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 1FFW", "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": ["1FFW"], "FORCED_REFERENCES": null, "REFERENCES": ["P0AE67", "P07363"], 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data/files/A000S/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000S",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1FLT",
|
| 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 |
+
"1FLT"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P15692",
|
| 31 |
+
"P17948"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQ",
|
| 38 |
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"EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPK",
|
| 39 |
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"GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT",
|
| 40 |
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"HEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Vascular endothelial growth factor A, long form",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Vascular endothelial growth factor receptor 1",
|
| 47 |
+
"Ig-like C2-type 2"
|
| 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": 6155,
|
| 59 |
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"SYSTRES": 382,
|
| 60 |
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"PROTATS": 6155,
|
| 61 |
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"PROTRES": 382,
|
| 62 |
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"NUCLATS": 0,
|
| 63 |
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"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
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"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
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"SOLVRES": 0,
|
| 70 |
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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
+
"name": "protein-protein interaction A-D",
|
| 76 |
+
"agent_1": "protein A",
|
| 77 |
+
"agent_2": "protein D",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"name": "protein-protein interaction A-B",
|
| 84 |
+
"agent_1": "protein A",
|
| 85 |
+
"agent_2": "protein B",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "protein-protein interaction A-C",
|
| 92 |
+
"agent_1": "protein A",
|
| 93 |
+
"agent_2": "protein C",
|
| 94 |
+
"selection_1": "chain A",
|
| 95 |
+
"selection_2": "chain D",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
},
|
| 98 |
+
{
|
| 99 |
+
"name": "protein-protein interaction D-B",
|
| 100 |
+
"agent_1": "protein D",
|
| 101 |
+
"agent_2": "protein B",
|
| 102 |
+
"selection_1": "chain B",
|
| 103 |
+
"selection_2": "chain C",
|
| 104 |
+
"type": "protein-protein"
|
| 105 |
+
},
|
| 106 |
+
{
|
| 107 |
+
"name": "protein-protein interaction B-C",
|
| 108 |
+
"agent_1": "protein B",
|
| 109 |
+
"agent_2": "protein C",
|
| 110 |
+
"selection_1": "chain B",
|
| 111 |
+
"selection_2": "chain D",
|
| 112 |
+
"type": "protein-protein"
|
| 113 |
+
}
|
| 114 |
+
],
|
| 115 |
+
"PBC_SELECTION": null,
|
| 116 |
+
"CHAINNAMES": null,
|
| 117 |
+
"MEMBRANES": null,
|
| 118 |
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"CUSTOMS": null,
|
| 119 |
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"ORIENTATION": null,
|
| 120 |
+
"PTM": [],
|
| 121 |
+
"MULTIMERIC": null,
|
| 122 |
+
"COLLECTIONS": "dynarepo",
|
| 123 |
+
"WARNINGS": [],
|
| 124 |
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"BOXSIZEX": 12.2762,
|
| 125 |
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"BOXSIZEY": 12.2762,
|
| 126 |
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"BOXSIZEZ": 8.68755,
|
| 127 |
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"mdName": "replica 1",
|
| 128 |
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"mdAtoms": 6155,
|
| 129 |
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"mdFrames": 5001
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| 130 |
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},
|
| 131 |
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"mds": [
|
| 132 |
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"replica 1",
|
| 133 |
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"replica 2",
|
| 134 |
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"replica 3"
|
| 135 |
+
],
|
| 136 |
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"mdref": 0,
|
| 137 |
+
"files": [
|
| 138 |
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"topology.tpr",
|
| 139 |
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"screenshot.jpg",
|
| 140 |
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"trajectory.bin",
|
| 141 |
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"pca_trajectory_01.bin",
|
| 142 |
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|
| 143 |
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|
| 144 |
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|
| 145 |
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| 146 |
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|
| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 259 |
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|
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|
| 265 |
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|
| 266 |
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|
| 267 |
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"pocket_01.pdb",
|
| 268 |
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|
| 269 |
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|
| 270 |
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"pocket_04.pdb",
|
| 271 |
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|
| 272 |
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"pocket_06.pdb",
|
| 273 |
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"pocket_07.pdb",
|
| 274 |
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"pocket_08.pdb"
|
| 275 |
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|
| 276 |
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|
| 277 |
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"clusters",
|
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|
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|
| 280 |
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|
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|
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|
| 283 |
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|
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|
| 285 |
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|
| 286 |
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|
| 287 |
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|
| 288 |
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|
| 289 |
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|
| 290 |
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|
| 291 |
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|
| 292 |
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|
| 293 |
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|
| 294 |
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|
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|
| 296 |
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|
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|
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|
| 304 |
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}
|
data/files/A000S/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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|
data/files/A000T/project.json
ADDED
|
@@ -0,0 +1,263 @@
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|
| 1 |
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{
|
| 2 |
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"accession": "A000T",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1FSK",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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|
| 25 |
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| 26 |
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"1FSK"
|
| 27 |
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| 29 |
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| 30 |
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| 31 |
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| 32 |
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|
| 33 |
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| 34 |
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| 35 |
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],
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"DOMAINS": [
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| 45 |
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| 46 |
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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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],
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| 53 |
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|
| 54 |
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|
| 55 |
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| 57 |
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"CHARMM36m"
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| 59 |
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| 60 |
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|
| 77 |
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"INTERACTIONS": [
|
| 78 |
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{
|
| 79 |
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"name": "protein-protein interaction C-B",
|
| 80 |
+
"agent_1": "protein C",
|
| 81 |
+
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|
| 82 |
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"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
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"type": "protein-protein"
|
| 85 |
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},
|
| 86 |
+
{
|
| 87 |
+
"name": "protein-protein interaction C-A",
|
| 88 |
+
"agent_1": "protein C",
|
| 89 |
+
"agent_2": "protein A",
|
| 90 |
+
"selection_1": "chain A",
|
| 91 |
+
"selection_2": "chain C",
|
| 92 |
+
"type": "protein-protein"
|
| 93 |
+
},
|
| 94 |
+
{
|
| 95 |
+
"name": "protein-protein interaction B-A",
|
| 96 |
+
"agent_1": "protein B",
|
| 97 |
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"agent_2": "protein A",
|
| 98 |
+
"selection_1": "chain B",
|
| 99 |
+
"selection_2": "chain C",
|
| 100 |
+
"type": "protein-protein"
|
| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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|
| 111 |
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|
| 112 |
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|
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|
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|
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|
| 116 |
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|
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|
| 118 |
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|
| 119 |
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"mds": [
|
| 120 |
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"replica 1",
|
| 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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|
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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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|
| 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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| 162 |
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|
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|
| 164 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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| 175 |
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|
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|
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| 182 |
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| 183 |
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| 184 |
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| 185 |
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| 188 |
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|
| 189 |
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|
| 190 |
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|
| 191 |
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|
| 192 |
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|
| 193 |
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|
| 194 |
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| 195 |
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|
| 196 |
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|
| 197 |
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| 198 |
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| 199 |
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|
| 200 |
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| 201 |
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| 202 |
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|
| 203 |
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|
| 204 |
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|
| 205 |
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|
| 206 |
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"clusters_03_screenshot_00.jpg",
|
| 207 |
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"clusters_03_screenshot_01.jpg",
|
| 208 |
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|
| 209 |
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"clusters_03_screenshot_03.jpg",
|
| 210 |
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|
| 211 |
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|
| 212 |
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"clusters_03_screenshot_06.jpg",
|
| 213 |
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|
| 214 |
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"clusters_03_screenshot_08.jpg",
|
| 215 |
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"clusters_03_screenshot_09.jpg",
|
| 216 |
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"clusters_03_screenshot_10.jpg",
|
| 217 |
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"clusters_03_screenshot_11.jpg",
|
| 218 |
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"clusters_03_screenshot_12.jpg",
|
| 219 |
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"clusters_03_screenshot_13.jpg",
|
| 220 |
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"clusters_03_screenshot_14.jpg",
|
| 221 |
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"clusters_03_screenshot_15.jpg",
|
| 222 |
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"clusters_03_screenshot_16.jpg",
|
| 223 |
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"clusters_03_screenshot_17.jpg",
|
| 224 |
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"clusters_03_screenshot_18.jpg",
|
| 225 |
+
"clusters_03_screenshot_19.jpg",
|
| 226 |
+
"pocket_01.pdb",
|
| 227 |
+
"pocket_02.pdb",
|
| 228 |
+
"pocket_03.pdb",
|
| 229 |
+
"pocket_04.pdb",
|
| 230 |
+
"pocket_05.pdb",
|
| 231 |
+
"pocket_06.pdb",
|
| 232 |
+
"pocket_07.pdb",
|
| 233 |
+
"pocket_08.pdb",
|
| 234 |
+
"pocket_09.pdb",
|
| 235 |
+
"pocket_10.pdb"
|
| 236 |
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],
|
| 237 |
+
"analyses": [
|
| 238 |
+
"clusters",
|
| 239 |
+
"clusters-00",
|
| 240 |
+
"clusters-01",
|
| 241 |
+
"clusters-02",
|
| 242 |
+
"clusters-03",
|
| 243 |
+
"dist-perres",
|
| 244 |
+
"energies",
|
| 245 |
+
"fluctuation",
|
| 246 |
+
"hbonds",
|
| 247 |
+
"interactions",
|
| 248 |
+
"pca",
|
| 249 |
+
"pockets",
|
| 250 |
+
"rgyr",
|
| 251 |
+
"rmsd-pairwise",
|
| 252 |
+
"rmsd-perres",
|
| 253 |
+
"rmsds",
|
| 254 |
+
"sasa",
|
| 255 |
+
"tmscores"
|
| 256 |
+
],
|
| 257 |
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"mdIndex": 0,
|
| 258 |
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"mdNumber": 1,
|
| 259 |
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"refframe": 1,
|
| 260 |
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"internalId": "683f29c91f5bd3de94eae679",
|
| 261 |
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"creationDate": "2025-06-03T16:58:49.000Z",
|
| 262 |
+
"identifier": "A000T"
|
| 263 |
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}
|
data/files/A000T/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000T", "accession": "A000T", "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 1FSK", "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": ["1FSK"], "FORCED_REFERENCES": null, "REFERENCES": 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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 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"1GCQ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P62993",
|
| 31 |
+
"P27870"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TYVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPVNR",
|
| 38 |
+
"STYVQALFDFDPQEDGELGFRRGDFIHVMDNSDPNWWKGACHGQTGMFPRNYVTPV",
|
| 39 |
+
"GSHMPKMEVFQEYYGIPPPPGAFGPFLRLNPGDIVELTKAEAEHNWWEGRNTATNEVGWFPCNRVHPYV"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Growth factor receptor-bound protein 2",
|
| 44 |
+
"SH3 2",
|
| 45 |
+
"Proto-oncogene vav",
|
| 46 |
+
"SH3 1"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 2832,
|
| 58 |
+
"SYSTRES": 182,
|
| 59 |
+
"PROTATS": 2832,
|
| 60 |
+
"PROTRES": 182,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "protein-protein interaction C-B",
|
| 75 |
+
"agent_1": "protein C",
|
| 76 |
+
"agent_2": "protein B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
},
|
| 81 |
+
{
|
| 82 |
+
"name": "protein-protein interaction C-A",
|
| 83 |
+
"agent_1": "protein C",
|
| 84 |
+
"agent_2": "protein A",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "protein-protein interaction B-A",
|
| 91 |
+
"agent_1": "protein B",
|
| 92 |
+
"agent_2": "protein A",
|
| 93 |
+
"selection_1": "chain B",
|
| 94 |
+
"selection_2": "chain C",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
}
|
| 97 |
+
],
|
| 98 |
+
"PBC_SELECTION": null,
|
| 99 |
+
"CHAINNAMES": null,
|
| 100 |
+
"MEMBRANES": null,
|
| 101 |
+
"CUSTOMS": null,
|
| 102 |
+
"ORIENTATION": null,
|
| 103 |
+
"PTM": [],
|
| 104 |
+
"MULTIMERIC": null,
|
| 105 |
+
"COLLECTIONS": "dynarepo",
|
| 106 |
+
"WARNINGS": [],
|
| 107 |
+
"BOXSIZEX": 8.83195,
|
| 108 |
+
"BOXSIZEY": 8.83195,
|
| 109 |
+
"BOXSIZEZ": 6.20451,
|
| 110 |
+
"mdName": "replica 1",
|
| 111 |
+
"mdAtoms": 2832,
|
| 112 |
+
"mdFrames": 5001
|
| 113 |
+
},
|
| 114 |
+
"mds": [
|
| 115 |
+
"replica 1",
|
| 116 |
+
"replica 2",
|
| 117 |
+
"replica 3"
|
| 118 |
+
],
|
| 119 |
+
"mdref": 0,
|
| 120 |
+
"files": [
|
| 121 |
+
"topology.tpr",
|
| 122 |
+
"screenshot.jpg",
|
| 123 |
+
"trajectory.bin",
|
| 124 |
+
"pca_trajectory_01.bin",
|
| 125 |
+
"pca_trajectory_02.bin",
|
| 126 |
+
"pca_trajectory_03.bin",
|
| 127 |
+
"pca_trajectory_04.bin",
|
| 128 |
+
"pca_trajectory_05.bin",
|
| 129 |
+
"pca_trajectory_06.bin",
|
| 130 |
+
"structure.pdb",
|
| 131 |
+
"trajectory.xtc",
|
| 132 |
+
"clusters_00_screenshot_00.jpg",
|
| 133 |
+
"clusters_00_screenshot_01.jpg",
|
| 134 |
+
"clusters_00_screenshot_02.jpg",
|
| 135 |
+
"clusters_00_screenshot_03.jpg",
|
| 136 |
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"clusters_00_screenshot_04.jpg",
|
| 137 |
+
"clusters_00_screenshot_05.jpg",
|
| 138 |
+
"clusters_00_screenshot_06.jpg",
|
| 139 |
+
"clusters_00_screenshot_07.jpg",
|
| 140 |
+
"clusters_00_screenshot_08.jpg",
|
| 141 |
+
"clusters_00_screenshot_09.jpg",
|
| 142 |
+
"clusters_00_screenshot_10.jpg",
|
| 143 |
+
"clusters_00_screenshot_11.jpg",
|
| 144 |
+
"clusters_00_screenshot_12.jpg",
|
| 145 |
+
"clusters_00_screenshot_13.jpg",
|
| 146 |
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"clusters_00_screenshot_14.jpg",
|
| 147 |
+
"clusters_00_screenshot_15.jpg",
|
| 148 |
+
"clusters_00_screenshot_16.jpg",
|
| 149 |
+
"clusters_00_screenshot_17.jpg",
|
| 150 |
+
"clusters_00_screenshot_18.jpg",
|
| 151 |
+
"clusters_00_screenshot_19.jpg",
|
| 152 |
+
"clusters_00_screenshot_20.jpg",
|
| 153 |
+
"clusters_01_screenshot_00.jpg",
|
| 154 |
+
"clusters_01_screenshot_01.jpg",
|
| 155 |
+
"clusters_01_screenshot_02.jpg",
|
| 156 |
+
"clusters_01_screenshot_03.jpg",
|
| 157 |
+
"clusters_01_screenshot_04.jpg",
|
| 158 |
+
"clusters_01_screenshot_05.jpg",
|
| 159 |
+
"clusters_01_screenshot_06.jpg",
|
| 160 |
+
"clusters_01_screenshot_07.jpg",
|
| 161 |
+
"clusters_01_screenshot_08.jpg",
|
| 162 |
+
"clusters_01_screenshot_09.jpg",
|
| 163 |
+
"clusters_01_screenshot_10.jpg",
|
| 164 |
+
"clusters_01_screenshot_11.jpg",
|
| 165 |
+
"clusters_01_screenshot_12.jpg",
|
| 166 |
+
"clusters_01_screenshot_13.jpg",
|
| 167 |
+
"clusters_01_screenshot_14.jpg",
|
| 168 |
+
"clusters_01_screenshot_15.jpg",
|
| 169 |
+
"clusters_01_screenshot_16.jpg",
|
| 170 |
+
"clusters_01_screenshot_17.jpg",
|
| 171 |
+
"clusters_01_screenshot_18.jpg",
|
| 172 |
+
"clusters_01_screenshot_19.jpg",
|
| 173 |
+
"clusters_02_screenshot_00.jpg",
|
| 174 |
+
"clusters_02_screenshot_01.jpg",
|
| 175 |
+
"clusters_02_screenshot_02.jpg",
|
| 176 |
+
"clusters_02_screenshot_03.jpg",
|
| 177 |
+
"clusters_02_screenshot_04.jpg",
|
| 178 |
+
"clusters_02_screenshot_05.jpg",
|
| 179 |
+
"clusters_02_screenshot_06.jpg",
|
| 180 |
+
"clusters_02_screenshot_07.jpg",
|
| 181 |
+
"clusters_02_screenshot_08.jpg",
|
| 182 |
+
"clusters_02_screenshot_09.jpg",
|
| 183 |
+
"clusters_02_screenshot_10.jpg",
|
| 184 |
+
"clusters_02_screenshot_11.jpg",
|
| 185 |
+
"clusters_02_screenshot_12.jpg",
|
| 186 |
+
"clusters_02_screenshot_13.jpg",
|
| 187 |
+
"clusters_02_screenshot_14.jpg",
|
| 188 |
+
"clusters_02_screenshot_15.jpg",
|
| 189 |
+
"clusters_02_screenshot_16.jpg",
|
| 190 |
+
"clusters_02_screenshot_17.jpg",
|
| 191 |
+
"clusters_02_screenshot_18.jpg",
|
| 192 |
+
"clusters_02_screenshot_19.jpg",
|
| 193 |
+
"clusters_03_screenshot_00.jpg",
|
| 194 |
+
"clusters_03_screenshot_01.jpg",
|
| 195 |
+
"clusters_03_screenshot_02.jpg",
|
| 196 |
+
"clusters_03_screenshot_03.jpg",
|
| 197 |
+
"clusters_03_screenshot_04.jpg",
|
| 198 |
+
"clusters_03_screenshot_05.jpg",
|
| 199 |
+
"clusters_03_screenshot_06.jpg",
|
| 200 |
+
"clusters_03_screenshot_07.jpg",
|
| 201 |
+
"clusters_03_screenshot_08.jpg",
|
| 202 |
+
"clusters_03_screenshot_09.jpg",
|
| 203 |
+
"clusters_03_screenshot_10.jpg",
|
| 204 |
+
"clusters_03_screenshot_11.jpg",
|
| 205 |
+
"clusters_03_screenshot_12.jpg",
|
| 206 |
+
"clusters_03_screenshot_13.jpg",
|
| 207 |
+
"clusters_03_screenshot_14.jpg",
|
| 208 |
+
"clusters_03_screenshot_15.jpg",
|
| 209 |
+
"clusters_03_screenshot_16.jpg",
|
| 210 |
+
"clusters_03_screenshot_17.jpg",
|
| 211 |
+
"clusters_03_screenshot_18.jpg",
|
| 212 |
+
"clusters_03_screenshot_19.jpg"
|
| 213 |
+
],
|
| 214 |
+
"analyses": [
|
| 215 |
+
"clusters",
|
| 216 |
+
"clusters-00",
|
| 217 |
+
"clusters-01",
|
| 218 |
+
"clusters-02",
|
| 219 |
+
"clusters-03",
|
| 220 |
+
"dist-perres",
|
| 221 |
+
"energies",
|
| 222 |
+
"fluctuation",
|
| 223 |
+
"hbonds",
|
| 224 |
+
"interactions",
|
| 225 |
+
"pca",
|
| 226 |
+
"rgyr",
|
| 227 |
+
"rmsd-pairwise",
|
| 228 |
+
"rmsd-perres",
|
| 229 |
+
"rmsds",
|
| 230 |
+
"sasa",
|
| 231 |
+
"tmscores"
|
| 232 |
+
],
|
| 233 |
+
"mdIndex": 0,
|
| 234 |
+
"mdNumber": 1,
|
| 235 |
+
"refframe": 0,
|
| 236 |
+
"internalId": "683f2afac496a23309feadf5",
|
| 237 |
+
"creationDate": "2025-06-03T17:03:54.000Z",
|
| 238 |
+
"identifier": "A000U"
|
| 239 |
+
}
|
data/files/A000U/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000U", "accession": "A000U", "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", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1GCQ", "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": ["1GCQ"], "FORCED_REFERENCES": null, "REFERENCES": ["P62993", 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|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A000V",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1GO4",
|
| 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 |
+
"1GO4"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q13257",
|
| 31 |
+
"Q9Y6D9"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"EQGITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIAQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPV",
|
| 38 |
+
"ITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIAQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPV",
|
| 39 |
+
"AEQSFLFSREEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRGLLRAME",
|
| 40 |
+
"SSAEQSFLFSREEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRGLLRAMERGGTV",
|
| 41 |
+
"FSREEADTLRLKVEELEGERSRLEEEKRMLEAQLERRALQGDYDQSRTKVLHMSLNPTSVARQRLREDHSQLQAECERLRGLLRAME",
|
| 42 |
+
"GITLRGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIAQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVN"
|
| 43 |
+
],
|
| 44 |
+
"NUCLSEQ": [],
|
| 45 |
+
"DOMAINS": [
|
| 46 |
+
"Mitotic spindle assembly checkpoint protein MAD2A",
|
| 47 |
+
"HORMA",
|
| 48 |
+
"Required for assuming the closed conformation and for interaction with CDC20",
|
| 49 |
+
"Mitotic spindle assembly checkpoint protein MAD1",
|
| 50 |
+
"Necessary for interaction with NEK2",
|
| 51 |
+
"Necessary for interaction with MAD2L1"
|
| 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": 18703,
|
| 63 |
+
"SYSTRES": 1146,
|
| 64 |
+
"PROTATS": 18703,
|
| 65 |
+
"PROTRES": 1146,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "protein-protein interaction E-F",
|
| 80 |
+
"agent_1": "protein E",
|
| 81 |
+
"agent_2": "protein F",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
+
"name": "protein-protein interaction E-G",
|
| 88 |
+
"agent_1": "protein E",
|
| 89 |
+
"agent_2": "protein G",
|
| 90 |
+
"selection_1": "chain A",
|
| 91 |
+
"selection_2": "chain C",
|
| 92 |
+
"type": "protein-protein"
|
| 93 |
+
},
|
| 94 |
+
{
|
| 95 |
+
"name": "protein-protein interaction E-C",
|
| 96 |
+
"agent_1": "protein E",
|
| 97 |
+
"agent_2": "protein C",
|
| 98 |
+
"selection_1": "chain A",
|
| 99 |
+
"selection_2": "chain D",
|
| 100 |
+
"type": "protein-protein"
|
| 101 |
+
},
|
| 102 |
+
{
|
| 103 |
+
"name": "protein-protein interaction E-D",
|
| 104 |
+
"agent_1": "protein E",
|
| 105 |
+
"agent_2": "protein D",
|
| 106 |
+
"selection_1": "chain A",
|
| 107 |
+
"selection_2": "chain E",
|
| 108 |
+
"type": "protein-protein"
|
| 109 |
+
},
|
| 110 |
+
{
|
| 111 |
+
"name": "protein-protein interaction E-B",
|
| 112 |
+
"agent_1": "protein E",
|
| 113 |
+
"agent_2": "protein B",
|
| 114 |
+
"selection_1": "chain A",
|
| 115 |
+
"selection_2": "chain F",
|
| 116 |
+
"type": "protein-protein"
|
| 117 |
+
},
|
| 118 |
+
{
|
| 119 |
+
"name": "protein-protein interaction E-A",
|
| 120 |
+
"agent_1": "protein E",
|
| 121 |
+
"agent_2": "protein A",
|
| 122 |
+
"selection_1": "chain A",
|
| 123 |
+
"selection_2": "chain G",
|
| 124 |
+
"type": "protein-protein"
|
| 125 |
+
},
|
| 126 |
+
{
|
| 127 |
+
"name": "protein-protein interaction E-H",
|
| 128 |
+
"agent_1": "protein E",
|
| 129 |
+
"agent_2": "protein H",
|
| 130 |
+
"selection_1": "chain A",
|
| 131 |
+
"selection_2": "chain H",
|
| 132 |
+
"type": "protein-protein"
|
| 133 |
+
},
|
| 134 |
+
{
|
| 135 |
+
"name": "protein-protein interaction F-G",
|
| 136 |
+
"agent_1": "protein F",
|
| 137 |
+
"agent_2": "protein G",
|
| 138 |
+
"selection_1": "chain B",
|
| 139 |
+
"selection_2": "chain C",
|
| 140 |
+
"type": "protein-protein"
|
| 141 |
+
},
|
| 142 |
+
{
|
| 143 |
+
"name": "protein-protein interaction F-C",
|
| 144 |
+
"agent_1": "protein F",
|
| 145 |
+
"agent_2": "protein C",
|
| 146 |
+
"selection_1": "chain B",
|
| 147 |
+
"selection_2": "chain D",
|
| 148 |
+
"type": "protein-protein"
|
| 149 |
+
},
|
| 150 |
+
{
|
| 151 |
+
"name": "protein-protein interaction F-D",
|
| 152 |
+
"agent_1": "protein F",
|
| 153 |
+
"agent_2": "protein D",
|
| 154 |
+
"selection_1": "chain B",
|
| 155 |
+
"selection_2": "chain E",
|
| 156 |
+
"type": "protein-protein"
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|
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|
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|
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| 801 |
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|
| 802 |
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|
| 803 |
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|
| 804 |
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|
| 805 |
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"rgyr",
|
| 806 |
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|
| 807 |
+
"rmsd-perres",
|
| 808 |
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"rmsds",
|
| 809 |
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"sasa",
|
| 810 |
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"tmscores"
|
| 811 |
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|
| 812 |
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|
| 817 |
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|
| 818 |
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|
data/files/A000V/records.jsonl
ADDED
|
The diff for this file is too large to render.
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data/files/A000W/project.json
ADDED
|
@@ -0,0 +1,198 @@
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| 1 |
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{
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| 2 |
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"accession": "A000W",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 1GPW",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
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"CONTACT": "yasaman.karami@inria.fr",
|
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"PROGRAM": "GROMACS",
|
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
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"LICENSE": "Apache License 2.0",
|
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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|
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"1GPW"
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| 29 |
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|
| 31 |
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| 32 |
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| 33 |
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| 37 |
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| 38 |
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|
| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Imidazole glycerol phosphate synthase subunit HisF",
|
| 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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| 51 |
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| 52 |
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| 53 |
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| 54 |
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{
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"name": "protein-protein interaction A-B",
|
| 73 |
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|
| 74 |
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|
| 75 |
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|
| 76 |
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|
| 77 |
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"type": "protein-protein"
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| 173 |
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],
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"analyses": [
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| 175 |
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| 178 |
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| 182 |
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"creationDate": "2025-06-03T17:18:20.000Z",
|
| 197 |
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"identifier": "A000W"
|
| 198 |
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}
|
data/files/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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| 1 |
+
{
|
| 2 |
+
"accession": "A000X",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1GUA",
|
| 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 |
+
"1GUA"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P62834",
|
| 31 |
+
"P04049"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MREYKLVVLGSGGVGKSALTVQFVQGIFVDEYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINR",
|
| 38 |
+
"NTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ras-related protein Rap-1A",
|
| 43 |
+
"Effector region",
|
| 44 |
+
"RAF proto-oncogene serine/threonine-protein kinase",
|
| 45 |
+
"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": 3884,
|
| 57 |
+
"SYSTRES": 243,
|
| 58 |
+
"PROTATS": 3884,
|
| 59 |
+
"PROTRES": 243,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
+
"CARBATS": 0,
|
| 65 |
+
"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
+
"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "protein-protein interaction B-A",
|
| 74 |
+
"agent_1": "protein B",
|
| 75 |
+
"agent_2": "protein A",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
+
"CHAINNAMES": null,
|
| 83 |
+
"MEMBRANES": null,
|
| 84 |
+
"CUSTOMS": null,
|
| 85 |
+
"ORIENTATION": null,
|
| 86 |
+
"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
+
"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
+
"BOXSIZEX": 8.83532,
|
| 91 |
+
"BOXSIZEY": 8.83532,
|
| 92 |
+
"BOXSIZEZ": 6.26172,
|
| 93 |
+
"mdName": "replica 1",
|
| 94 |
+
"mdAtoms": 3884,
|
| 95 |
+
"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
+
"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
+
"files": [
|
| 104 |
+
"topology.tpr",
|
| 105 |
+
"screenshot.jpg",
|
| 106 |
+
"trajectory.bin",
|
| 107 |
+
"pca_trajectory_01.bin",
|
| 108 |
+
"pca_trajectory_02.bin",
|
| 109 |
+
"pca_trajectory_03.bin",
|
| 110 |
+
"pca_trajectory_04.bin",
|
| 111 |
+
"pca_trajectory_05.bin",
|
| 112 |
+
"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
+
"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"pca_trajectory_13.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
+
"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_01_screenshot_00.jpg",
|
| 141 |
+
"clusters_01_screenshot_01.jpg",
|
| 142 |
+
"clusters_01_screenshot_02.jpg",
|
| 143 |
+
"clusters_01_screenshot_03.jpg",
|
| 144 |
+
"clusters_01_screenshot_04.jpg",
|
| 145 |
+
"clusters_01_screenshot_05.jpg",
|
| 146 |
+
"clusters_01_screenshot_06.jpg",
|
| 147 |
+
"clusters_01_screenshot_07.jpg",
|
| 148 |
+
"clusters_01_screenshot_08.jpg",
|
| 149 |
+
"clusters_01_screenshot_09.jpg",
|
| 150 |
+
"clusters_01_screenshot_10.jpg",
|
| 151 |
+
"clusters_01_screenshot_11.jpg",
|
| 152 |
+
"clusters_01_screenshot_12.jpg",
|
| 153 |
+
"clusters_01_screenshot_13.jpg",
|
| 154 |
+
"clusters_01_screenshot_14.jpg",
|
| 155 |
+
"clusters_01_screenshot_15.jpg",
|
| 156 |
+
"clusters_01_screenshot_16.jpg",
|
| 157 |
+
"clusters_01_screenshot_17.jpg",
|
| 158 |
+
"clusters_01_screenshot_18.jpg",
|
| 159 |
+
"clusters_01_screenshot_19.jpg",
|
| 160 |
+
"pocket_01.pdb",
|
| 161 |
+
"pocket_02.pdb",
|
| 162 |
+
"pocket_03.pdb",
|
| 163 |
+
"pocket_04.pdb"
|
| 164 |
+
],
|
| 165 |
+
"analyses": [
|
| 166 |
+
"clusters",
|
| 167 |
+
"clusters-00",
|
| 168 |
+
"clusters-01",
|
| 169 |
+
"dist-perres",
|
| 170 |
+
"energies",
|
| 171 |
+
"fluctuation",
|
| 172 |
+
"hbonds",
|
| 173 |
+
"interactions",
|
| 174 |
+
"pca",
|
| 175 |
+
"pockets",
|
| 176 |
+
"rgyr",
|
| 177 |
+
"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
+
"rmsds",
|
| 180 |
+
"sasa",
|
| 181 |
+
"tmscores"
|
| 182 |
+
],
|
| 183 |
+
"mdIndex": 0,
|
| 184 |
+
"mdNumber": 1,
|
| 185 |
+
"refframe": 0,
|
| 186 |
+
"internalId": "683f2fcae9bb553720789924",
|
| 187 |
+
"creationDate": "2025-06-03T17:24:26.000Z",
|
| 188 |
+
"identifier": "A000X"
|
| 189 |
+
}
|
data/files/A000X/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A000X", "accession": "A000X", "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 1GUA", "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": ["1GUA"], "FORCED_REFERENCES": null, "REFERENCES": ["P62834", "P04049"], 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"PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.83532, "BOXSIZEY": 8.83532, "BOXSIZEZ": 6.26172, "mdName": "replica 1", "mdAtoms": 3884, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A000X/files/topology.tpr", "length": 1342468, "contentType": "application/octet-stream", "metadata": {"project": "683f2fcae9bb553720789924", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A000X/files/screenshot.jpg", "length": 23215, "contentType": "application/octet-stream", "metadata": {"project": "683f2fcae9bb553720789924", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A000X/files/trajectory.bin", "length": 233086608, "contentType": "application/octet-stream", "metadata": {"project": "683f2fcae9bb553720789924", "md": 0, "frames": 5001, "atoms": 3884}}, {"name": "pca_trajectory_01.bin", 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|
data/files/A000Y/project.json
ADDED
|
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A000Y",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 1I51",
|
| 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 |
+
"1I51"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P55210",
|
| 31 |
+
"P98170"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"THADYLLRTGQVVDISDT",
|
| 38 |
+
"YQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVIVYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGARCKTLLEKPKLFFIQACRGTELDDGIQ",
|
| 39 |
+
"KIPVEADFLFAYSTVPGYYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSDDPHFHEKKQIPCVVSMLTKELYFSQ"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Caspase-7 subunit p20",
|
| 44 |
+
"Caspase-7 subunit p11",
|
| 45 |
+
"Loop L1",
|
| 46 |
+
"Loop L2",
|
| 47 |
+
"Loop L3",
|
| 48 |
+
"Loop L4",
|
| 49 |
+
"Involved in allosteric regulation",
|
| 50 |
+
"E3 ubiquitin-protein ligase XIAP",
|
| 51 |
+
"Interaction with caspase-7"
|
| 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": 7884,
|
| 63 |
+
"SYSTRES": 498,
|
| 64 |
+
"PROTATS": 7884,
|
| 65 |
+
"PROTRES": 498,
|
| 66 |
+
"NUCLATS": 0,
|
| 67 |
+
"NUCLRES": 0,
|
| 68 |
+
"LIPIATS": 0,
|
| 69 |
+
"LIPIRES": 0,
|
| 70 |
+
"CARBATS": 0,
|
| 71 |
+
"CARBRES": 0,
|
| 72 |
+
"SOLVATS": 0,
|
| 73 |
+
"SOLVRES": 0,
|
| 74 |
+
"COUNCAT": 0,
|
| 75 |
+
"COUNANI": 0,
|
| 76 |
+
"COUNION": 0,
|
| 77 |
+
"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "protein-protein interaction C-D",
|
| 80 |
+
"agent_1": "protein C",
|
| 81 |
+
"agent_2": "protein D",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
+
"name": "protein-protein interaction C-B",
|
| 88 |
+
"agent_1": "protein C",
|
| 89 |
+
"agent_2": "protein B",
|
| 90 |
+
"selection_1": "chain A",
|
| 91 |
+
"selection_2": "chain C",
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| 92 |
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| 422 |
+
"pocket_07.pdb",
|
| 423 |
+
"pocket_08.pdb",
|
| 424 |
+
"pocket_09.pdb",
|
| 425 |
+
"pocket_10.pdb"
|
| 426 |
+
],
|
| 427 |
+
"analyses": [
|
| 428 |
+
"clusters",
|
| 429 |
+
"clusters-00",
|
| 430 |
+
"clusters-01",
|
| 431 |
+
"clusters-02",
|
| 432 |
+
"clusters-03",
|
| 433 |
+
"clusters-04",
|
| 434 |
+
"clusters-05",
|
| 435 |
+
"clusters-06",
|
| 436 |
+
"clusters-07",
|
| 437 |
+
"clusters-08",
|
| 438 |
+
"clusters-09",
|
| 439 |
+
"clusters-10",
|
| 440 |
+
"dist-perres",
|
| 441 |
+
"energies",
|
| 442 |
+
"fluctuation",
|
| 443 |
+
"hbonds",
|
| 444 |
+
"interactions",
|
| 445 |
+
"pca",
|
| 446 |
+
"pockets",
|
| 447 |
+
"rgyr",
|
| 448 |
+
"rmsd-pairwise",
|
| 449 |
+
"rmsd-perres",
|
| 450 |
+
"rmsds",
|
| 451 |
+
"sasa",
|
| 452 |
+
"tmscores"
|
| 453 |
+
],
|
| 454 |
+
"mdIndex": 0,
|
| 455 |
+
"mdNumber": 1,
|
| 456 |
+
"refframe": 0,
|
| 457 |
+
"internalId": "683f314f80abfac908a71971",
|
| 458 |
+
"creationDate": "2025-06-03T17:30:55.000Z",
|
| 459 |
+
"identifier": "A000Y"
|
| 460 |
+
}
|
data/files/A000Y/records.jsonl
ADDED
|
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|
|