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- data/files/A007Y/records.jsonl +3 -0
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data/files/A007Z/project.json
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|
| 1 |
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{
|
| 2 |
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"accession": "A007Z",
|
| 3 |
+
"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4MRT",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 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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|
| 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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"4MRT"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"O30409",
|
| 31 |
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"P39135"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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| 35 |
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| 36 |
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| 37 |
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| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Tyrocidine synthase 3",
|
| 43 |
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"Carrier 3",
|
| 44 |
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"Domain 3 (tyrosine-activating)",
|
| 45 |
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"4'-phosphopantetheinyl transferase Sfp",
|
| 46 |
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"Peptidyl carrier protein binding"
|
| 47 |
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],
|
| 48 |
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"FRAMESTEP": 0.1,
|
| 49 |
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"TIMESTEP": 2,
|
| 50 |
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"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
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"FF": [
|
| 53 |
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"CHARMM36m"
|
| 54 |
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],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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"BOXTYPE": "Dodecahedron",
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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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| 70 |
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| 71 |
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| 72 |
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"INTERACTIONS": [
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| 73 |
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{
|
| 74 |
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"name": "chain A-chain B interaction",
|
| 75 |
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"agent_1": "chain A",
|
| 76 |
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"agent_2": "chain B",
|
| 77 |
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"selection_1": "chain A",
|
| 78 |
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"selection_2": "chain B",
|
| 79 |
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"type": "protein-protein"
|
| 80 |
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}
|
| 81 |
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],
|
| 82 |
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|
| 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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"COLLECTIONS": "dynarepo",
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| 90 |
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"WARNINGS": [],
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| 93 |
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},
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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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| 143 |
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"clusters_01_screenshot_02.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_19.jpg",
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"clusters_01_screenshot_20.jpg",
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"clusters_01_screenshot_21.jpg",
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"clusters_01_screenshot_22.jpg",
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"clusters_01_screenshot_23.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
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| 169 |
+
"pocket_05.pdb",
|
| 170 |
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"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb",
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| 173 |
+
"pocket_09.pdb",
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| 174 |
+
"pocket_10.pdb"
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| 175 |
+
],
|
| 176 |
+
"analyses": [
|
| 177 |
+
"clusters",
|
| 178 |
+
"clusters-00",
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| 179 |
+
"clusters-01",
|
| 180 |
+
"dist-perres",
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| 181 |
+
"energies",
|
| 182 |
+
"fluctuation",
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| 183 |
+
"hbonds",
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| 184 |
+
"interactions",
|
| 185 |
+
"pca",
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| 186 |
+
"pockets",
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| 187 |
+
"rgyr",
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| 188 |
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"rmsd-pairwise",
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| 189 |
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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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| 196 |
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"refframe": 0,
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| 197 |
+
"internalId": "684231cece6d4b51c040151e",
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| 198 |
+
"creationDate": "2025-06-06T00:09:50.000Z",
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+
"identifier": "A007Z"
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}
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data/files/A007Z/records.jsonl
ADDED
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| 3 |
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data/files/A0080/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0080",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4N7V",
|
| 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 |
+
"4N7V"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O00444",
|
| 31 |
+
"O94986"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TLRSITSPLVAHRLKPIRQKTKKAVVSILDSEEVCVELVKEYASQEYVKEVLQISSDGNTITIYYPNGGRGFPLADRPPSPTDNISRYSFDNLPEKYWRKYQYASRFVQLVRSKSPKITYFTRYAKCILMENSPGADFEVWFYDGVKIHKTEDFIQVIEKTGKSYTLKSESEVNSLKEEIKMYMDHANEGHRICLALESIISEEERKTRSAPFFPIIIGRKP",
|
| 38 |
+
"EDEEYDEEDYEREKELQQLLTDLPHDMLDDDLS"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Serine/threonine-protein kinase PLK4",
|
| 43 |
+
"Cryptic POLO box 1 (CPB1)",
|
| 44 |
+
"Cryptic POLO box 2 (CPB2)",
|
| 45 |
+
"Centrosomal protein of 152 kDa",
|
| 46 |
+
"Interaction with PLK4",
|
| 47 |
+
"Disordered"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 7798,
|
| 59 |
+
"SYSTRES": 477,
|
| 60 |
+
"PROTATS": 7798,
|
| 61 |
+
"PROTRES": 477,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
+
"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
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"SOLVRES": 0,
|
| 70 |
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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [
|
| 74 |
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{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
+
{
|
| 83 |
+
"name": "chain A-chain C interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain C",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "chain B-chain C interaction",
|
| 92 |
+
"agent_1": "chain B",
|
| 93 |
+
"agent_2": "chain C",
|
| 94 |
+
"selection_1": "chain B",
|
| 95 |
+
"selection_2": "chain C",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
}
|
| 98 |
+
],
|
| 99 |
+
"PBC_SELECTION": null,
|
| 100 |
+
"CHAINNAMES": null,
|
| 101 |
+
"MEMBRANES": null,
|
| 102 |
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"CUSTOMS": null,
|
| 103 |
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"ORIENTATION": null,
|
| 104 |
+
"PTM": [],
|
| 105 |
+
"MULTIMERIC": null,
|
| 106 |
+
"COLLECTIONS": "dynarepo",
|
| 107 |
+
"WARNINGS": [],
|
| 108 |
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"BOXSIZEX": 12.2792,
|
| 109 |
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"BOXSIZEY": 12.2792,
|
| 110 |
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"BOXSIZEZ": 8.69499,
|
| 111 |
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"mdName": "replica 1",
|
| 112 |
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"mdAtoms": 7798,
|
| 113 |
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"mdFrames": 5001
|
| 114 |
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},
|
| 115 |
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"mds": [
|
| 116 |
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"replica 1",
|
| 117 |
+
"replica 2",
|
| 118 |
+
"replica 3"
|
| 119 |
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],
|
| 120 |
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"mdref": 0,
|
| 121 |
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"files": [
|
| 122 |
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"topology.tpr",
|
| 123 |
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"screenshot.jpg",
|
| 124 |
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"trajectory.bin",
|
| 125 |
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"pca_trajectory_01.bin",
|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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| 131 |
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| 132 |
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| 133 |
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| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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"pca_trajectory_13.bin",
|
| 138 |
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"structure.pdb",
|
| 139 |
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"trajectory.xtc",
|
| 140 |
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|
| 141 |
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|
| 142 |
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| 154 |
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| 160 |
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"clusters_03_screenshot_25.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb",
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"pocket_08.pdb",
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"pocket_09.pdb",
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"pocket_10.pdb"
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],
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"analyses": [
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"clusters",
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"clusters-00",
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"clusters-01",
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"clusters-02",
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"clusters-03",
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| 242 |
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"dist-perres",
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"energies",
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"fluctuation",
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| 245 |
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"hbonds",
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"interactions",
|
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"pca",
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| 248 |
+
"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": "68423367c045cdbd2afab4cb",
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"creationDate": "2025-06-06T00:16:39.000Z",
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"identifier": "A0080"
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}
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data/files/A0080/records.jsonl
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data/files/A0081/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0081",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4NG2",
|
| 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 |
+
"4NG2"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P25084",
|
| 31 |
+
"Q9I494"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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|
| 37 |
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"KTHVDAIIERYKDLMVEIPPADRQPGLSLLWPVPAQPAIDKGVRQAENWLADQIEGQLWTAFAFGRDSLPTPMQKTAFEVAFLTRLQQRLVAAR",
|
| 38 |
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"DLMVEIPPADRQPGLSLLWPVPAQPAIDKGVRQAENWLADQIEGQLWTAFAFGRDSLPTPMQKTAFEVAFLTRLQQRLVAAR",
|
| 39 |
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"ALVDGFLELERSSGKLEWSAILQKMASDLGFSKILFGLLPKDSQDYENAFIVGNYPAAWREHYDRAGYARVDPTVSHCTQSVLPIFWEPSIYQTRKQHEFFEEASAAGLVYGLTMPLHGARGELGALSLSVEAENRAEANRFMESVLPTLWMLKDYALQSGAGLAF"
|
| 40 |
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],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Transcriptional activator protein LasR",
|
| 44 |
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"LasR-specific antiactivator QslA"
|
| 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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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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{
|
| 72 |
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"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
},
|
| 79 |
+
{
|
| 80 |
+
"name": "chain A-chain C interaction",
|
| 81 |
+
"agent_1": "chain A",
|
| 82 |
+
"agent_2": "chain C",
|
| 83 |
+
"selection_1": "chain A",
|
| 84 |
+
"selection_2": "chain C",
|
| 85 |
+
"type": "protein-protein"
|
| 86 |
+
},
|
| 87 |
+
{
|
| 88 |
+
"name": "chain B-chain C interaction",
|
| 89 |
+
"agent_1": "chain B",
|
| 90 |
+
"agent_2": "chain C",
|
| 91 |
+
"selection_1": "chain B",
|
| 92 |
+
"selection_2": "chain C",
|
| 93 |
+
"type": "protein-protein"
|
| 94 |
+
}
|
| 95 |
+
],
|
| 96 |
+
"PBC_SELECTION": null,
|
| 97 |
+
"CHAINNAMES": null,
|
| 98 |
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"MEMBRANES": null,
|
| 99 |
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"CUSTOMS": null,
|
| 100 |
+
"ORIENTATION": null,
|
| 101 |
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"PTM": [],
|
| 102 |
+
"MULTIMERIC": null,
|
| 103 |
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"COLLECTIONS": "dynarepo",
|
| 104 |
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"WARNINGS": [],
|
| 105 |
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"BOXSIZEX": 9.32987,
|
| 106 |
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"BOXSIZEY": 9.32987,
|
| 107 |
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|
| 108 |
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"mdName": "replica 1",
|
| 109 |
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"mdAtoms": 5389,
|
| 110 |
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"mdFrames": 5001
|
| 111 |
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},
|
| 112 |
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"mds": [
|
| 113 |
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"replica 1",
|
| 114 |
+
"replica 2",
|
| 115 |
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"replica 3"
|
| 116 |
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],
|
| 117 |
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"mdref": 0,
|
| 118 |
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"files": [
|
| 119 |
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|
| 120 |
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| 121 |
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"trajectory.bin",
|
| 122 |
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"pca_trajectory_01.bin",
|
| 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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"pca_trajectory_07.bin",
|
| 129 |
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"pca_trajectory_08.bin",
|
| 130 |
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"pca_trajectory_09.bin",
|
| 131 |
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"structure.pdb",
|
| 132 |
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"trajectory.xtc",
|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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|
| 138 |
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"clusters_00_screenshot_05.jpg",
|
| 139 |
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"clusters_00_screenshot_06.jpg",
|
| 140 |
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|
| 141 |
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"clusters_00_screenshot_08.jpg",
|
| 142 |
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"clusters_00_screenshot_09.jpg",
|
| 143 |
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|
| 144 |
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|
| 145 |
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"clusters_00_screenshot_12.jpg",
|
| 146 |
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"clusters_00_screenshot_13.jpg",
|
| 147 |
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"clusters_00_screenshot_14.jpg",
|
| 148 |
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"clusters_00_screenshot_15.jpg",
|
| 149 |
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"clusters_00_screenshot_16.jpg",
|
| 150 |
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"clusters_00_screenshot_17.jpg",
|
| 151 |
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"clusters_00_screenshot_18.jpg",
|
| 152 |
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"clusters_00_screenshot_19.jpg",
|
| 153 |
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"clusters_00_screenshot_20.jpg",
|
| 154 |
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"clusters_00_screenshot_21.jpg",
|
| 155 |
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"clusters_01_screenshot_00.jpg",
|
| 156 |
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"clusters_01_screenshot_01.jpg",
|
| 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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"clusters_01_screenshot_09.jpg",
|
| 165 |
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"clusters_01_screenshot_10.jpg",
|
| 166 |
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"clusters_01_screenshot_11.jpg",
|
| 167 |
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"clusters_01_screenshot_12.jpg",
|
| 168 |
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"clusters_01_screenshot_13.jpg",
|
| 169 |
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"clusters_01_screenshot_14.jpg",
|
| 170 |
+
"clusters_01_screenshot_15.jpg",
|
| 171 |
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"clusters_01_screenshot_16.jpg",
|
| 172 |
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"clusters_01_screenshot_17.jpg",
|
| 173 |
+
"clusters_01_screenshot_18.jpg",
|
| 174 |
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"clusters_01_screenshot_19.jpg",
|
| 175 |
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"clusters_02_screenshot_00.jpg",
|
| 176 |
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"clusters_02_screenshot_01.jpg",
|
| 177 |
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"clusters_02_screenshot_02.jpg",
|
| 178 |
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"clusters_02_screenshot_03.jpg",
|
| 179 |
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"clusters_02_screenshot_04.jpg",
|
| 180 |
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|
| 181 |
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|
| 182 |
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"clusters_02_screenshot_07.jpg",
|
| 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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"clusters_02_screenshot_18.jpg",
|
| 194 |
+
"clusters_02_screenshot_19.jpg",
|
| 195 |
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"clusters_02_screenshot_20.jpg",
|
| 196 |
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"clusters_03_screenshot_00.jpg",
|
| 197 |
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"clusters_03_screenshot_01.jpg",
|
| 198 |
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"clusters_03_screenshot_02.jpg",
|
| 199 |
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"clusters_03_screenshot_03.jpg",
|
| 200 |
+
"clusters_03_screenshot_04.jpg",
|
| 201 |
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"clusters_03_screenshot_05.jpg",
|
| 202 |
+
"clusters_03_screenshot_06.jpg",
|
| 203 |
+
"clusters_03_screenshot_07.jpg",
|
| 204 |
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"clusters_03_screenshot_08.jpg",
|
| 205 |
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"clusters_03_screenshot_09.jpg",
|
| 206 |
+
"clusters_03_screenshot_10.jpg",
|
| 207 |
+
"clusters_03_screenshot_11.jpg",
|
| 208 |
+
"clusters_03_screenshot_12.jpg",
|
| 209 |
+
"clusters_03_screenshot_13.jpg",
|
| 210 |
+
"clusters_03_screenshot_14.jpg",
|
| 211 |
+
"clusters_03_screenshot_15.jpg",
|
| 212 |
+
"clusters_03_screenshot_16.jpg",
|
| 213 |
+
"clusters_03_screenshot_17.jpg",
|
| 214 |
+
"clusters_03_screenshot_18.jpg",
|
| 215 |
+
"clusters_03_screenshot_19.jpg",
|
| 216 |
+
"pocket_01.pdb",
|
| 217 |
+
"pocket_02.pdb",
|
| 218 |
+
"pocket_03.pdb",
|
| 219 |
+
"pocket_04.pdb",
|
| 220 |
+
"pocket_05.pdb",
|
| 221 |
+
"pocket_06.pdb",
|
| 222 |
+
"pocket_07.pdb",
|
| 223 |
+
"pocket_08.pdb"
|
| 224 |
+
],
|
| 225 |
+
"analyses": [
|
| 226 |
+
"clusters",
|
| 227 |
+
"clusters-00",
|
| 228 |
+
"clusters-01",
|
| 229 |
+
"clusters-02",
|
| 230 |
+
"clusters-03",
|
| 231 |
+
"dist-perres",
|
| 232 |
+
"energies",
|
| 233 |
+
"fluctuation",
|
| 234 |
+
"hbonds",
|
| 235 |
+
"interactions",
|
| 236 |
+
"pca",
|
| 237 |
+
"pockets",
|
| 238 |
+
"rgyr",
|
| 239 |
+
"rmsd-pairwise",
|
| 240 |
+
"rmsd-perres",
|
| 241 |
+
"rmsds",
|
| 242 |
+
"sasa",
|
| 243 |
+
"tmscores"
|
| 244 |
+
],
|
| 245 |
+
"mdIndex": 0,
|
| 246 |
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"mdNumber": 1,
|
| 247 |
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"refframe": 0,
|
| 248 |
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"internalId": "6842350598db7cd5f808b9f3",
|
| 249 |
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"creationDate": "2025-06-06T00:23:33.000Z",
|
| 250 |
+
"identifier": "A0081"
|
| 251 |
+
}
|
data/files/A0081/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0081", "accession": "A0081", "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 4NG2", "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": ["4NG2"], "FORCED_REFERENCES": null, "REFERENCES": 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| 1 |
+
{
|
| 2 |
+
"accession": "A0082",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4NIQ",
|
| 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 |
+
"4NIQ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P52917",
|
| 31 |
+
"P40080"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MSTGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLMLALKYEKNPKSKDLIRAKFTEYLNRAEQLKKHLESEEANAA",
|
| 38 |
+
"ENYSNTDPEELLRKHVFPSVPK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Vacuolar protein sorting-associated protein 4",
|
| 43 |
+
"MIT",
|
| 44 |
+
"Disordered",
|
| 45 |
+
"VPS4-associated protein 1",
|
| 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": 1685,
|
| 58 |
+
"SYSTRES": 104,
|
| 59 |
+
"PROTATS": 1685,
|
| 60 |
+
"PROTRES": 104,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"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 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 8.01694,
|
| 92 |
+
"BOXSIZEY": 8.01694,
|
| 93 |
+
"BOXSIZEZ": 5.68215,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 1685,
|
| 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 |
+
"structure.pdb",
|
| 118 |
+
"trajectory.xtc",
|
| 119 |
+
"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
+
"clusters_00_screenshot_02.jpg",
|
| 122 |
+
"clusters_00_screenshot_03.jpg",
|
| 123 |
+
"clusters_00_screenshot_04.jpg",
|
| 124 |
+
"clusters_00_screenshot_05.jpg",
|
| 125 |
+
"clusters_00_screenshot_06.jpg",
|
| 126 |
+
"clusters_00_screenshot_07.jpg",
|
| 127 |
+
"clusters_00_screenshot_08.jpg",
|
| 128 |
+
"clusters_00_screenshot_09.jpg",
|
| 129 |
+
"clusters_00_screenshot_10.jpg",
|
| 130 |
+
"clusters_00_screenshot_11.jpg",
|
| 131 |
+
"clusters_00_screenshot_12.jpg",
|
| 132 |
+
"clusters_00_screenshot_13.jpg",
|
| 133 |
+
"clusters_00_screenshot_14.jpg",
|
| 134 |
+
"clusters_00_screenshot_15.jpg",
|
| 135 |
+
"clusters_00_screenshot_16.jpg",
|
| 136 |
+
"clusters_00_screenshot_17.jpg",
|
| 137 |
+
"clusters_00_screenshot_18.jpg",
|
| 138 |
+
"clusters_00_screenshot_19.jpg",
|
| 139 |
+
"clusters_00_screenshot_20.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 |
+
],
|
| 160 |
+
"analyses": [
|
| 161 |
+
"clusters",
|
| 162 |
+
"clusters-00",
|
| 163 |
+
"clusters-01",
|
| 164 |
+
"dist-perres",
|
| 165 |
+
"energies",
|
| 166 |
+
"fluctuation",
|
| 167 |
+
"hbonds",
|
| 168 |
+
"interactions",
|
| 169 |
+
"pca",
|
| 170 |
+
"rgyr",
|
| 171 |
+
"rmsd-pairwise",
|
| 172 |
+
"rmsd-perres",
|
| 173 |
+
"rmsds",
|
| 174 |
+
"sasa",
|
| 175 |
+
"tmscores"
|
| 176 |
+
],
|
| 177 |
+
"mdIndex": 0,
|
| 178 |
+
"mdNumber": 1,
|
| 179 |
+
"refframe": 0,
|
| 180 |
+
"internalId": "6842361a0b5655e9106a82f2",
|
| 181 |
+
"creationDate": "2025-06-06T00:28:10.000Z",
|
| 182 |
+
"identifier": "A0082"
|
| 183 |
+
}
|
data/files/A0082/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
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|
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|
| 1 |
+
{"project_identifier": "A0082", "accession": "A0082", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 4NIQ", "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": ["4NIQ"], "FORCED_REFERENCES": null, "REFERENCES": ["P52917", "P40080"], "INPUT_LIGANDS": null, 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| 1 |
+
{
|
| 2 |
+
"accession": "A0083",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4NL9",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"4NL9"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q6ZW76",
|
| 31 |
+
"Q68DC2"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"APYSGPQDLAALLEQIGCLKYLQVFEEQDVDLREFLTLTESDLKEIGITLFGPKRKMTSAIARW",
|
| 38 |
+
"ELTGILKKLSLEKYQPIFEEQEVDMEAFLTLTDGDLKELGIKTDGSRQQILAAISELNAG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Ankyrin repeat and SAM domain-containing protein 3",
|
| 43 |
+
"SAM",
|
| 44 |
+
"Interaction with NEK7",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Ankyrin repeat and SAM domain-containing protein 6",
|
| 47 |
+
"SAM",
|
| 48 |
+
"Essential for ANKS3 interaction"
|
| 49 |
+
],
|
| 50 |
+
"FRAMESTEP": 0.1,
|
| 51 |
+
"TIMESTEP": 2,
|
| 52 |
+
"TEMP": 310,
|
| 53 |
+
"ENSEMBLE": "NPT",
|
| 54 |
+
"FF": [
|
| 55 |
+
"CHARMM36m"
|
| 56 |
+
],
|
| 57 |
+
"WAT": "TIP3P",
|
| 58 |
+
"BOXTYPE": "Dodecahedron",
|
| 59 |
+
"SYSTATS": 1974,
|
| 60 |
+
"SYSTRES": 124,
|
| 61 |
+
"PROTATS": 1974,
|
| 62 |
+
"PROTRES": 124,
|
| 63 |
+
"NUCLATS": 0,
|
| 64 |
+
"NUCLRES": 0,
|
| 65 |
+
"LIPIATS": 0,
|
| 66 |
+
"LIPIRES": 0,
|
| 67 |
+
"CARBATS": 0,
|
| 68 |
+
"CARBRES": 0,
|
| 69 |
+
"SOLVATS": 0,
|
| 70 |
+
"SOLVRES": 0,
|
| 71 |
+
"COUNCAT": 0,
|
| 72 |
+
"COUNANI": 0,
|
| 73 |
+
"COUNION": 0,
|
| 74 |
+
"INTERACTIONS": [
|
| 75 |
+
{
|
| 76 |
+
"name": "chain A-chain B interaction",
|
| 77 |
+
"agent_1": "chain A",
|
| 78 |
+
"agent_2": "chain B",
|
| 79 |
+
"selection_1": "chain A",
|
| 80 |
+
"selection_2": "chain B",
|
| 81 |
+
"type": "protein-protein"
|
| 82 |
+
}
|
| 83 |
+
],
|
| 84 |
+
"PBC_SELECTION": null,
|
| 85 |
+
"CHAINNAMES": null,
|
| 86 |
+
"MEMBRANES": null,
|
| 87 |
+
"CUSTOMS": null,
|
| 88 |
+
"ORIENTATION": null,
|
| 89 |
+
"PTM": [],
|
| 90 |
+
"MULTIMERIC": null,
|
| 91 |
+
"COLLECTIONS": "dynarepo",
|
| 92 |
+
"WARNINGS": [],
|
| 93 |
+
"BOXSIZEX": 7.47311,
|
| 94 |
+
"BOXSIZEY": 7.47311,
|
| 95 |
+
"BOXSIZEZ": 5.27624,
|
| 96 |
+
"mdName": "replica 1",
|
| 97 |
+
"mdAtoms": 1974,
|
| 98 |
+
"mdFrames": 5001
|
| 99 |
+
},
|
| 100 |
+
"mds": [
|
| 101 |
+
"replica 1",
|
| 102 |
+
"replica 2",
|
| 103 |
+
"replica 3"
|
| 104 |
+
],
|
| 105 |
+
"mdref": 0,
|
| 106 |
+
"files": [
|
| 107 |
+
"topology.tpr",
|
| 108 |
+
"screenshot.jpg",
|
| 109 |
+
"trajectory.bin",
|
| 110 |
+
"pca_trajectory_01.bin",
|
| 111 |
+
"pca_trajectory_02.bin",
|
| 112 |
+
"pca_trajectory_03.bin",
|
| 113 |
+
"pca_trajectory_04.bin",
|
| 114 |
+
"pca_trajectory_05.bin",
|
| 115 |
+
"pca_trajectory_06.bin",
|
| 116 |
+
"pca_trajectory_07.bin",
|
| 117 |
+
"pca_trajectory_08.bin",
|
| 118 |
+
"pca_trajectory_09.bin",
|
| 119 |
+
"pca_trajectory_10.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
+
"clusters_00_screenshot_02.jpg",
|
| 125 |
+
"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
+
"clusters_00_screenshot_05.jpg",
|
| 128 |
+
"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_00_screenshot_20.jpg",
|
| 143 |
+
"clusters_00_screenshot_21.jpg",
|
| 144 |
+
"clusters_01_screenshot_00.jpg",
|
| 145 |
+
"clusters_01_screenshot_01.jpg",
|
| 146 |
+
"clusters_01_screenshot_02.jpg",
|
| 147 |
+
"clusters_01_screenshot_03.jpg",
|
| 148 |
+
"clusters_01_screenshot_04.jpg",
|
| 149 |
+
"clusters_01_screenshot_05.jpg",
|
| 150 |
+
"clusters_01_screenshot_06.jpg",
|
| 151 |
+
"clusters_01_screenshot_07.jpg",
|
| 152 |
+
"clusters_01_screenshot_08.jpg",
|
| 153 |
+
"clusters_01_screenshot_09.jpg",
|
| 154 |
+
"clusters_01_screenshot_10.jpg",
|
| 155 |
+
"clusters_01_screenshot_11.jpg",
|
| 156 |
+
"clusters_01_screenshot_12.jpg",
|
| 157 |
+
"clusters_01_screenshot_13.jpg",
|
| 158 |
+
"clusters_01_screenshot_14.jpg",
|
| 159 |
+
"clusters_01_screenshot_15.jpg",
|
| 160 |
+
"clusters_01_screenshot_16.jpg",
|
| 161 |
+
"clusters_01_screenshot_17.jpg",
|
| 162 |
+
"clusters_01_screenshot_18.jpg",
|
| 163 |
+
"clusters_01_screenshot_19.jpg",
|
| 164 |
+
"pocket_01.pdb"
|
| 165 |
+
],
|
| 166 |
+
"analyses": [
|
| 167 |
+
"clusters",
|
| 168 |
+
"clusters-00",
|
| 169 |
+
"clusters-01",
|
| 170 |
+
"dist-perres",
|
| 171 |
+
"energies",
|
| 172 |
+
"fluctuation",
|
| 173 |
+
"hbonds",
|
| 174 |
+
"interactions",
|
| 175 |
+
"pca",
|
| 176 |
+
"pockets",
|
| 177 |
+
"rgyr",
|
| 178 |
+
"rmsd-pairwise",
|
| 179 |
+
"rmsd-perres",
|
| 180 |
+
"rmsds",
|
| 181 |
+
"sasa",
|
| 182 |
+
"tmscores"
|
| 183 |
+
],
|
| 184 |
+
"mdIndex": 0,
|
| 185 |
+
"mdNumber": 1,
|
| 186 |
+
"refframe": 1,
|
| 187 |
+
"internalId": "684236caea1775be7ff1a7a2",
|
| 188 |
+
"creationDate": "2025-06-06T00:31:06.000Z",
|
| 189 |
+
"identifier": "A0083"
|
| 190 |
+
}
|
data/files/A0083/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0083", "accession": "A0083", "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 4NL9", "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": ["4NL9"], "FORCED_REFERENCES": null, "REFERENCES": ["Q6ZW76", "Q68DC2"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["APYSGPQDLAALLEQIGCLKYLQVFEEQDVDLREFLTLTESDLKEIGITLFGPKRKMTSAIARW", "ELTGILKKLSLEKYQPIFEEQEVDMEAFLTLTDGDLKELGIKTDGSRQQILAAISELNAG"], "NUCLSEQ": [], "DOMAINS": ["Ankyrin repeat and SAM domain-containing protein 3", "SAM", "Interaction with NEK7", "Disordered", "Ankyrin repeat and SAM domain-containing protein 6", "SAM", "Essential for ANKS3 interaction"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 1974, "SYSTRES": 124, "PROTATS": 1974, "PROTRES": 124, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 7.47311, "BOXSIZEY": 7.47311, "BOXSIZEZ": 5.27624, "mdName": "replica 1", "mdAtoms": 1974, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0083/files/topology.tpr", "length": 816068, "contentType": "application/octet-stream", "metadata": {"project": "684236caea1775be7ff1a7a2", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0083/files/screenshot.jpg", "length": 18527, "contentType": "application/octet-stream", "metadata": {"project": "684236caea1775be7ff1a7a2", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0083/files/trajectory.bin", "length": 118463688, "contentType": "application/octet-stream", "metadata": {"project": "684236caea1775be7ff1a7a2", "md": 0, "frames": 5001, "atoms": 1974}}, {"name": "pca_trajectory_01.bin", "downloadUrl": 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data/files/A0084/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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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
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|
| 14 |
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|
| 16 |
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|
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| 18 |
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| 19 |
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"4NSO"
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|
| 29 |
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|
| 30 |
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| 31 |
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|
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| 43 |
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| 44 |
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| 49 |
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| 50 |
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|
| 51 |
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| 52 |
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| 54 |
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| 70 |
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{
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| 71 |
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"name": "chain A-chain B interaction",
|
| 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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],
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|
| 166 |
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],
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"analyses": [
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data/files/A0084/records.jsonl
ADDED
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data/files/A0085/project.json
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| 1 |
+
{
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| 2 |
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"accession": "A0085",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4PJ2",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 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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"4PJ2"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"A0KHJ5",
|
| 31 |
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"P86383"
|
| 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,
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| 36 |
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"PROTSEQ": [
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| 37 |
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| 38 |
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| 39 |
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],
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| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
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| 42 |
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"",
|
| 43 |
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"Lysozyme",
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| 44 |
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"I-type lysozyme"
|
| 45 |
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],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
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| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
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| 55 |
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"SYSTATS": 3622,
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| 56 |
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"SYSTRES": 243,
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| 57 |
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"PROTATS": 3622,
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| 58 |
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"PROTRES": 243,
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| 59 |
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"NUCLATS": 0,
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| 60 |
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"NUCLRES": 0,
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| 61 |
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"LIPIATS": 0,
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| 64 |
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| 65 |
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"SOLVATS": 0,
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| 66 |
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| 67 |
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"COUNCAT": 0,
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| 68 |
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| 69 |
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|
| 70 |
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|
| 71 |
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{
|
| 72 |
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"name": "chain A-chain B interaction",
|
| 73 |
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"agent_1": "chain A",
|
| 74 |
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"agent_2": "chain B",
|
| 75 |
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"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
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"type": "protein-protein"
|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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|
| 82 |
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|
| 83 |
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|
| 84 |
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|
| 85 |
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|
| 86 |
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| 88 |
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| 95 |
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|
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|
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|
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| 100 |
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|
| 101 |
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|
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| 106 |
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"pca_trajectory_01.bin",
|
| 107 |
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|
| 108 |
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|
| 109 |
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"pca_trajectory_04.bin",
|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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"pca_trajectory_08.bin",
|
| 114 |
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|
| 115 |
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|
| 116 |
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"pca_trajectory_11.bin",
|
| 117 |
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"pca_trajectory_12.bin",
|
| 118 |
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"pca_trajectory_13.bin",
|
| 119 |
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"pca_trajectory_14.bin",
|
| 120 |
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"structure.pdb",
|
| 121 |
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|
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|
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|
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|
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| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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| 133 |
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| 134 |
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|
| 135 |
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| 136 |
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|
| 137 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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|
| 143 |
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|
| 144 |
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|
| 145 |
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|
| 146 |
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|
| 147 |
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|
| 148 |
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"clusters_01_screenshot_08.jpg",
|
| 149 |
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"clusters_01_screenshot_09.jpg",
|
| 150 |
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|
| 151 |
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|
| 152 |
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"clusters_01_screenshot_12.jpg",
|
| 153 |
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|
| 154 |
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|
| 155 |
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"clusters_01_screenshot_15.jpg",
|
| 156 |
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"clusters_01_screenshot_16.jpg",
|
| 157 |
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"clusters_01_screenshot_17.jpg",
|
| 158 |
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"clusters_01_screenshot_18.jpg",
|
| 159 |
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"clusters_01_screenshot_19.jpg",
|
| 160 |
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"pocket_01.pdb",
|
| 161 |
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"pocket_02.pdb",
|
| 162 |
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"pocket_03.pdb",
|
| 163 |
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"pocket_04.pdb"
|
| 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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"dist-perres",
|
| 170 |
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"energies",
|
| 171 |
+
"fluctuation",
|
| 172 |
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"hbonds",
|
| 173 |
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"interactions",
|
| 174 |
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"pca",
|
| 175 |
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"pockets",
|
| 176 |
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"rgyr",
|
| 177 |
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"rmsd-pairwise",
|
| 178 |
+
"rmsd-perres",
|
| 179 |
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"rmsds",
|
| 180 |
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"sasa",
|
| 181 |
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"tmscores"
|
| 182 |
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|
| 183 |
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|
| 188 |
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"identifier": "A0085"
|
| 189 |
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}
|
data/files/A0085/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A0086",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4PW9",
|
| 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 |
+
"4PW9"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q92M24",
|
| 31 |
+
"Q92M25"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"LPDYVAWKDADALIVHSDKTLETKRSEFGTSIITPEEKLYIRNNVNTPPESILADRDGWKVEISGVKEPRTLTVAELKTLGLVTAATVLQCSGNGRKYFKDQLTGDQKMSGTPWTVGAAGCVIWSGVPLKAVVDALGGPAEGARFITGTGGEELPAGLDPKLLVVERSVPISNLDNVILAWEMNGRPLSLAHGGPLRMVVPGYSGVNNIKYVKAVAMTEVETDAKIQKTSYRVHALGEKGSPDQPSVWEQPVKSWITTPHEAAKAGQVQIAGVAFGGMNACKSVEVSVDGGQTWQEAEFIGPDLGRFAWRVFALSADLARGTYTLVSRATDTEGNVQPEETEMNGAGYGHNGWRAPAVKLTVA",
|
| 38 |
+
"EDKLALGREIFLERSEPQCALCHTLADAEAVGEVGPNLDELKPDAERVNTAVTNGIGPMPANEILTDEEIEAVALYVSTVAGK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Oxidoreductase molybdopterin-binding",
|
| 43 |
+
"Moybdenum cofactor oxidoreductase dimerisation",
|
| 44 |
+
"Cytochrome c"
|
| 45 |
+
],
|
| 46 |
+
"FRAMESTEP": 0.1,
|
| 47 |
+
"TIMESTEP": 2,
|
| 48 |
+
"TEMP": 310,
|
| 49 |
+
"ENSEMBLE": "NPT",
|
| 50 |
+
"FF": [
|
| 51 |
+
"CHARMM36m"
|
| 52 |
+
],
|
| 53 |
+
"WAT": "TIP3P",
|
| 54 |
+
"BOXTYPE": "Dodecahedron",
|
| 55 |
+
"SYSTATS": 6683,
|
| 56 |
+
"SYSTRES": 446,
|
| 57 |
+
"PROTATS": 6683,
|
| 58 |
+
"PROTRES": 446,
|
| 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": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 9.74978,
|
| 90 |
+
"BOXSIZEY": 9.74978,
|
| 91 |
+
"BOXSIZEZ": 6.93403,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 6683,
|
| 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 |
+
"structure.pdb",
|
| 114 |
+
"trajectory.xtc",
|
| 115 |
+
"clusters_00_screenshot_00.jpg",
|
| 116 |
+
"clusters_00_screenshot_01.jpg",
|
| 117 |
+
"clusters_00_screenshot_02.jpg",
|
| 118 |
+
"clusters_00_screenshot_03.jpg",
|
| 119 |
+
"clusters_00_screenshot_04.jpg",
|
| 120 |
+
"clusters_00_screenshot_05.jpg",
|
| 121 |
+
"clusters_00_screenshot_06.jpg",
|
| 122 |
+
"clusters_00_screenshot_07.jpg",
|
| 123 |
+
"clusters_00_screenshot_08.jpg",
|
| 124 |
+
"clusters_00_screenshot_09.jpg",
|
| 125 |
+
"clusters_00_screenshot_10.jpg",
|
| 126 |
+
"clusters_00_screenshot_11.jpg",
|
| 127 |
+
"clusters_00_screenshot_12.jpg",
|
| 128 |
+
"clusters_00_screenshot_13.jpg",
|
| 129 |
+
"clusters_00_screenshot_14.jpg",
|
| 130 |
+
"clusters_00_screenshot_15.jpg",
|
| 131 |
+
"clusters_00_screenshot_16.jpg",
|
| 132 |
+
"clusters_00_screenshot_17.jpg",
|
| 133 |
+
"clusters_00_screenshot_18.jpg",
|
| 134 |
+
"clusters_00_screenshot_19.jpg",
|
| 135 |
+
"clusters_01_screenshot_00.jpg",
|
| 136 |
+
"clusters_01_screenshot_01.jpg",
|
| 137 |
+
"clusters_01_screenshot_02.jpg",
|
| 138 |
+
"clusters_01_screenshot_03.jpg",
|
| 139 |
+
"clusters_01_screenshot_04.jpg",
|
| 140 |
+
"clusters_01_screenshot_05.jpg",
|
| 141 |
+
"clusters_01_screenshot_06.jpg",
|
| 142 |
+
"clusters_01_screenshot_07.jpg",
|
| 143 |
+
"clusters_01_screenshot_08.jpg",
|
| 144 |
+
"clusters_01_screenshot_09.jpg",
|
| 145 |
+
"clusters_01_screenshot_10.jpg",
|
| 146 |
+
"clusters_01_screenshot_11.jpg",
|
| 147 |
+
"clusters_01_screenshot_12.jpg",
|
| 148 |
+
"clusters_01_screenshot_13.jpg",
|
| 149 |
+
"clusters_01_screenshot_14.jpg",
|
| 150 |
+
"clusters_01_screenshot_15.jpg",
|
| 151 |
+
"clusters_01_screenshot_16.jpg",
|
| 152 |
+
"clusters_01_screenshot_17.jpg",
|
| 153 |
+
"clusters_01_screenshot_18.jpg",
|
| 154 |
+
"clusters_01_screenshot_19.jpg",
|
| 155 |
+
"clusters_01_screenshot_20.jpg",
|
| 156 |
+
"pocket_01.pdb",
|
| 157 |
+
"pocket_02.pdb",
|
| 158 |
+
"pocket_03.pdb",
|
| 159 |
+
"pocket_04.pdb",
|
| 160 |
+
"pocket_05.pdb",
|
| 161 |
+
"pocket_06.pdb",
|
| 162 |
+
"pocket_07.pdb"
|
| 163 |
+
],
|
| 164 |
+
"analyses": [
|
| 165 |
+
"clusters",
|
| 166 |
+
"clusters-00",
|
| 167 |
+
"clusters-01",
|
| 168 |
+
"dist-perres",
|
| 169 |
+
"energies",
|
| 170 |
+
"fluctuation",
|
| 171 |
+
"hbonds",
|
| 172 |
+
"interactions",
|
| 173 |
+
"pca",
|
| 174 |
+
"pockets",
|
| 175 |
+
"rgyr",
|
| 176 |
+
"rmsd-pairwise",
|
| 177 |
+
"rmsd-perres",
|
| 178 |
+
"rmsds",
|
| 179 |
+
"sasa",
|
| 180 |
+
"tmscores"
|
| 181 |
+
],
|
| 182 |
+
"mdIndex": 0,
|
| 183 |
+
"mdNumber": 1,
|
| 184 |
+
"refframe": 1,
|
| 185 |
+
"internalId": "68423a49945502654d43f839",
|
| 186 |
+
"creationDate": "2025-06-06T00:46:01.000Z",
|
| 187 |
+
"identifier": "A0086"
|
| 188 |
+
}
|
data/files/A0086/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0086", "accession": "A0086", "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 4PW9", "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": ["4PW9"], "FORCED_REFERENCES": null, "REFERENCES": ["Q92M24", "Q92M25"], 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"COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.74978, "BOXSIZEY": 9.74978, "BOXSIZEZ": 6.93403, "mdName": "replica 1", "mdAtoms": 6683, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0086/files/topology.tpr", "length": 2093376, "contentType": "application/octet-stream", "metadata": {"project": "68423a49945502654d43f839", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0086/files/screenshot.jpg", "length": 26243, "contentType": "application/octet-stream", "metadata": {"project": "68423a49945502654d43f839", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0086/files/trajectory.bin", 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data/files/A0087/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0087",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4Q5E",
|
| 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 |
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"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"4Q5E"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"Q3YTH2",
|
| 31 |
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"P0CG63",
|
| 32 |
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"P68036"
|
| 33 |
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],
|
| 34 |
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"INPUT_LIGANDS": null,
|
| 35 |
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"LIGANDS": [],
|
| 36 |
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"LIGANDNAMES": null,
|
| 37 |
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"PROTSEQ": [
|
| 38 |
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"HMAASRRLMKELEEIRKSGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAEYPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHPLRADLAEEYSKDRKKFSKNAEEFTKKYGEKRPVD",
|
| 39 |
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"MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGRQLEDGRTLSDYNIQKESTLHLVLRLRGC",
|
| 40 |
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"EPILGKLIGQGSTAEIFEDVNDSSALYKKYDLIGNQYNEILEMAWQESELFNAFYGDEASVVIQYGGDVYLRMLRVPGTPLSDIDTADIPDNIESLYLQLICKLNELSIIHYDLNTGNMLYDKESESLFPIDFRNIYAEYYAATKKDKEIIDRRLQMRTNDFYSLLNR"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Protein kinase OspG",
|
| 45 |
+
"Ubiquitin",
|
| 46 |
+
"Ubiquitin-like 1",
|
| 47 |
+
"Ubiquitin-conjugating enzyme E2 L3",
|
| 48 |
+
"UBC core"
|
| 49 |
+
],
|
| 50 |
+
"FRAMESTEP": 0.1,
|
| 51 |
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"TIMESTEP": 2,
|
| 52 |
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"TEMP": 310,
|
| 53 |
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"ENSEMBLE": "NPT",
|
| 54 |
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"FF": [
|
| 55 |
+
"CHARMM36m"
|
| 56 |
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],
|
| 57 |
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"WAT": "TIP3P",
|
| 58 |
+
"BOXTYPE": "Dodecahedron",
|
| 59 |
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"SYSTATS": 6475,
|
| 60 |
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"SYSTRES": 399,
|
| 61 |
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"PROTATS": 6475,
|
| 62 |
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"PROTRES": 399,
|
| 63 |
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"NUCLATS": 0,
|
| 64 |
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"NUCLRES": 0,
|
| 65 |
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"LIPIATS": 0,
|
| 66 |
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"LIPIRES": 0,
|
| 67 |
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"CARBATS": 0,
|
| 68 |
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"CARBRES": 0,
|
| 69 |
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"SOLVATS": 0,
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| 70 |
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"SOLVRES": 0,
|
| 71 |
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"COUNCAT": 0,
|
| 72 |
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"COUNANI": 0,
|
| 73 |
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"COUNION": 0,
|
| 74 |
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"INTERACTIONS": [
|
| 75 |
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{
|
| 76 |
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"name": "chain A-chain B interaction",
|
| 77 |
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"agent_1": "chain A",
|
| 78 |
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"agent_2": "chain B",
|
| 79 |
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"selection_1": "chain A",
|
| 80 |
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"selection_2": "chain B",
|
| 81 |
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"type": "protein-protein"
|
| 82 |
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},
|
| 83 |
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{
|
| 84 |
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"name": "chain A-chain C interaction",
|
| 85 |
+
"agent_1": "chain A",
|
| 86 |
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"agent_2": "chain C",
|
| 87 |
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"selection_1": "chain A",
|
| 88 |
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"selection_2": "chain C",
|
| 89 |
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"type": "protein-protein"
|
| 90 |
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},
|
| 91 |
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{
|
| 92 |
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"name": "chain B-chain C interaction",
|
| 93 |
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"agent_1": "chain B",
|
| 94 |
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"agent_2": "chain C",
|
| 95 |
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"selection_1": "chain B",
|
| 96 |
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"selection_2": "chain C",
|
| 97 |
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"type": "protein-protein"
|
| 98 |
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}
|
| 99 |
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],
|
| 100 |
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"PBC_SELECTION": null,
|
| 101 |
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"CHAINNAMES": null,
|
| 102 |
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"MEMBRANES": null,
|
| 103 |
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"CUSTOMS": null,
|
| 104 |
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"ORIENTATION": null,
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| 105 |
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"PTM": [],
|
| 106 |
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"MULTIMERIC": null,
|
| 107 |
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"COLLECTIONS": "dynarepo",
|
| 108 |
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"WARNINGS": [],
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| 109 |
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"BOXSIZEX": 10.2362,
|
| 110 |
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"BOXSIZEY": 10.2362,
|
| 111 |
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"BOXSIZEZ": 7.3084,
|
| 112 |
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"mdName": "replica 1",
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| 113 |
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"mdAtoms": 6475,
|
| 114 |
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"mdFrames": 5001
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| 115 |
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},
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| 116 |
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"mds": [
|
| 117 |
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"replica 1",
|
| 118 |
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"replica 2",
|
| 119 |
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"replica 3"
|
| 120 |
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],
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| 121 |
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"mdref": 0,
|
| 122 |
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"files": [
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| 123 |
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| 124 |
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| 125 |
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| 126 |
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| 127 |
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|
| 128 |
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| 129 |
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| 130 |
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| 131 |
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| 132 |
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| 136 |
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"clusters_03_screenshot_22.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb"
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],
|
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"analyses": [
|
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+
"clusters",
|
| 228 |
+
"clusters-00",
|
| 229 |
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"clusters-01",
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| 230 |
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"clusters-02",
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"clusters-03",
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"dist-perres",
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+
"energies",
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| 234 |
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"fluctuation",
|
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+
"hbonds",
|
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+
"interactions",
|
| 237 |
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"pca",
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| 238 |
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"pockets",
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"rgyr",
|
| 240 |
+
"rmsd-pairwise",
|
| 241 |
+
"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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"internalId": "68423bf4ef98220ec7e22e64",
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"creationDate": "2025-06-06T00:53:08.000Z",
|
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"identifier": "A0087"
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}
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data/files/A0087/records.jsonl
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data/files/A0088/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0088",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4Q96",
|
| 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 |
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"PDBIDS": [
|
| 26 |
+
"4Q96"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9NQG5"
|
| 31 |
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],
|
| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
|
| 36 |
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"FSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMED",
|
| 37 |
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"SFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSME"
|
| 38 |
+
],
|
| 39 |
+
"NUCLSEQ": [],
|
| 40 |
+
"DOMAINS": [
|
| 41 |
+
"Regulation of nuclear pre-mRNA domain-containing protein 1B",
|
| 42 |
+
"CID",
|
| 43 |
+
"Disordered"
|
| 44 |
+
],
|
| 45 |
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"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": 4219,
|
| 55 |
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"SYSTRES": 256,
|
| 56 |
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"PROTATS": 4219,
|
| 57 |
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"PROTRES": 256,
|
| 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 |
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"SOLVRES": 0,
|
| 66 |
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"COUNCAT": 0,
|
| 67 |
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"COUNANI": 0,
|
| 68 |
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"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
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"MEMBRANES": null,
|
| 82 |
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"CUSTOMS": null,
|
| 83 |
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"ORIENTATION": null,
|
| 84 |
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"PTM": [],
|
| 85 |
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"MULTIMERIC": null,
|
| 86 |
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"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
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"BOXSIZEX": 10.2467,
|
| 89 |
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"BOXSIZEY": 10.2467,
|
| 90 |
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"BOXSIZEZ": 7.2176,
|
| 91 |
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"mdName": "replica 1",
|
| 92 |
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"mdAtoms": 4219,
|
| 93 |
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"mdFrames": 5001
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| 94 |
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},
|
| 95 |
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"mds": [
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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"
|
| 154 |
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|
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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"dist-perres",
|
| 160 |
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|
| 161 |
+
"fluctuation",
|
| 162 |
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"hbonds",
|
| 163 |
+
"interactions",
|
| 164 |
+
"pca",
|
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+
"pockets",
|
| 166 |
+
"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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"identifier": "A0088"
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data/files/A0088/records.jsonl
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data/files/A0089/project.json
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| 1 |
+
{
|
| 2 |
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"accession": "A0089",
|
| 3 |
+
"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4QLP",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"4QLP"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"O05443",
|
| 31 |
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"O05442"
|
| 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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| 38 |
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| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Immunity factor for TNT",
|
| 43 |
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"Outer membrane channel protein CpnT",
|
| 44 |
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"TNT"
|
| 45 |
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],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 5861,
|
| 56 |
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"SYSTRES": 374,
|
| 57 |
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"PROTATS": 5861,
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| 58 |
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"PROTRES": 374,
|
| 59 |
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"NUCLATS": 0,
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| 60 |
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"NUCLRES": 0,
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| 61 |
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"LIPIATS": 0,
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| 62 |
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"LIPIRES": 0,
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| 63 |
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"CARBATS": 0,
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| 64 |
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| 65 |
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| 66 |
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"SOLVRES": 0,
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| 67 |
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"COUNCAT": 0,
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| 68 |
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"COUNANI": 0,
|
| 69 |
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"COUNION": 0,
|
| 70 |
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"INTERACTIONS": [
|
| 71 |
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{
|
| 72 |
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"name": "chain A-chain B interaction",
|
| 73 |
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"agent_1": "chain A",
|
| 74 |
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"agent_2": "chain B",
|
| 75 |
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"selection_1": "chain A",
|
| 76 |
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"selection_2": "chain B",
|
| 77 |
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"type": "protein-protein"
|
| 78 |
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}
|
| 79 |
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],
|
| 80 |
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"PBC_SELECTION": null,
|
| 81 |
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"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
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| 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": 9.23588,
|
| 90 |
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"BOXSIZEY": 9.23588,
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| 91 |
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"BOXSIZEZ": 6.51745,
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| 92 |
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"mdName": "replica 1",
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| 93 |
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"mdAtoms": 5861,
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| 94 |
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"mdFrames": 5001
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| 95 |
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},
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| 96 |
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"mds": [
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| 97 |
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"replica 1",
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| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
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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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| 106 |
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| 107 |
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|
| 113 |
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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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+
],
|
| 164 |
+
"analyses": [
|
| 165 |
+
"mem-map",
|
| 166 |
+
"clusters",
|
| 167 |
+
"clusters-00",
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| 168 |
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"clusters-01",
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| 169 |
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"dist-perres",
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| 170 |
+
"energies",
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| 171 |
+
"fluctuation",
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| 172 |
+
"hbonds",
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| 173 |
+
"interactions",
|
| 174 |
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"pca",
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| 175 |
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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,
|
| 185 |
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"refframe": 0,
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| 186 |
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"internalId": "68423ed0cbf5f0c8e544ba5b",
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| 187 |
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"creationDate": "2025-06-06T01:05:20.000Z",
|
| 188 |
+
"identifier": "A0089"
|
| 189 |
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}
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data/files/A0089/records.jsonl
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+
{
|
| 2 |
+
"accession": "A008A",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4REY",
|
| 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 |
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],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"4REY"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9BQQ3",
|
| 31 |
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"Q08379"
|
| 32 |
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],
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| 33 |
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|
| 34 |
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"LIGANDS": [],
|
| 35 |
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|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"SNPCIPFFYRADENDEVKITVI",
|
| 38 |
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"GGAEGFHLHGVQENSPAQQAGLEPYFDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASVRFCSFRRASEQVWHVLDVEPSSPAALAGLRPYTDYVVGSDQILQESEDFFTLIESHEGKPLKLMVYNSKSDSCREVTVTPNAAWGGEGSLGCGIGYGYLHRIPTQPP"
|
| 39 |
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],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
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"Golgi reassembly-stacking protein 1",
|
| 43 |
+
"PDZ GRASP-type 1",
|
| 44 |
+
"PDZ GRASP-type 2",
|
| 45 |
+
"GRASP",
|
| 46 |
+
"Essential for interaction with GOLGA2/GM130",
|
| 47 |
+
"Disordered",
|
| 48 |
+
"Golgin subfamily A member 2",
|
| 49 |
+
"Interaction with GORASP1/GRASP65"
|
| 50 |
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],
|
| 51 |
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"FRAMESTEP": 0.1,
|
| 52 |
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"TIMESTEP": 2,
|
| 53 |
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"TEMP": 310,
|
| 54 |
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"ENSEMBLE": "NPT",
|
| 55 |
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"FF": [
|
| 56 |
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"CHARMM36m"
|
| 57 |
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],
|
| 58 |
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"WAT": "TIP3P",
|
| 59 |
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"BOXTYPE": "Dodecahedron",
|
| 60 |
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"SYSTATS": 3357,
|
| 61 |
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"SYSTRES": 218,
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| 62 |
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"PROTATS": 3357,
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| 63 |
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"PROTRES": 218,
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"NUCLATS": 0,
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"LIPIATS": 0,
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"LIPIRES": 0,
|
| 68 |
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"CARBATS": 0,
|
| 69 |
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"CARBRES": 0,
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| 70 |
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"SOLVATS": 0,
|
| 71 |
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"SOLVRES": 0,
|
| 72 |
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"COUNCAT": 0,
|
| 73 |
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"COUNANI": 0,
|
| 74 |
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"COUNION": 0,
|
| 75 |
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"INTERACTIONS": [
|
| 76 |
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{
|
| 77 |
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"name": "chain A-chain B interaction",
|
| 78 |
+
"agent_1": "chain A",
|
| 79 |
+
"agent_2": "chain B",
|
| 80 |
+
"selection_1": "chain A",
|
| 81 |
+
"selection_2": "chain B",
|
| 82 |
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"type": "protein-protein"
|
| 83 |
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}
|
| 84 |
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],
|
| 85 |
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"PBC_SELECTION": null,
|
| 86 |
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|
| 87 |
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"MEMBRANES": null,
|
| 88 |
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|
| 89 |
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"ORIENTATION": null,
|
| 90 |
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"PTM": [],
|
| 91 |
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"MULTIMERIC": null,
|
| 92 |
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"COLLECTIONS": "dynarepo",
|
| 93 |
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"WARNINGS": [],
|
| 94 |
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"BOXSIZEX": 8.99586,
|
| 95 |
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"BOXSIZEY": 8.99586,
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| 96 |
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"BOXSIZEZ": 6.35554,
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| 97 |
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"mdName": "replica 1",
|
| 98 |
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"mdAtoms": 3357,
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| 99 |
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"mdFrames": 5001
|
| 100 |
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},
|
| 101 |
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"mds": [
|
| 102 |
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"replica 1",
|
| 103 |
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"replica 2",
|
| 104 |
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"replica 3"
|
| 105 |
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],
|
| 106 |
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"mdref": 0,
|
| 107 |
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"files": [
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"topology.tpr",
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"screenshot.jpg",
|
| 110 |
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"trajectory.bin",
|
| 111 |
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"pca_trajectory_01.bin",
|
| 112 |
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"pca_trajectory_02.bin",
|
| 113 |
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"pca_trajectory_03.bin",
|
| 114 |
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"pca_trajectory_04.bin",
|
| 115 |
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"pca_trajectory_05.bin",
|
| 116 |
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"pca_trajectory_06.bin",
|
| 117 |
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"pca_trajectory_07.bin",
|
| 118 |
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"pca_trajectory_08.bin",
|
| 119 |
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"pca_trajectory_09.bin",
|
| 120 |
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"pca_trajectory_10.bin",
|
| 121 |
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"pca_trajectory_11.bin",
|
| 122 |
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|
| 123 |
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"pca_trajectory_13.bin",
|
| 124 |
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"pca_trajectory_14.bin",
|
| 125 |
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"pca_trajectory_15.bin",
|
| 126 |
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"pca_trajectory_16.bin",
|
| 127 |
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"pca_trajectory_17.bin",
|
| 128 |
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"structure.pdb",
|
| 129 |
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"trajectory.xtc",
|
| 130 |
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|
| 131 |
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"clusters_00_screenshot_01.jpg",
|
| 132 |
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|
| 133 |
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|
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|
| 135 |
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"clusters_00_screenshot_05.jpg",
|
| 136 |
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"clusters_00_screenshot_06.jpg",
|
| 137 |
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"clusters_00_screenshot_07.jpg",
|
| 138 |
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"clusters_00_screenshot_08.jpg",
|
| 139 |
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"clusters_00_screenshot_09.jpg",
|
| 140 |
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"clusters_00_screenshot_10.jpg",
|
| 141 |
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"clusters_00_screenshot_11.jpg",
|
| 142 |
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"clusters_00_screenshot_12.jpg",
|
| 143 |
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"clusters_00_screenshot_13.jpg",
|
| 144 |
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"clusters_00_screenshot_14.jpg",
|
| 145 |
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"clusters_00_screenshot_15.jpg",
|
| 146 |
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"clusters_00_screenshot_16.jpg",
|
| 147 |
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"clusters_00_screenshot_17.jpg",
|
| 148 |
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"clusters_00_screenshot_18.jpg",
|
| 149 |
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"clusters_01_screenshot_00.jpg",
|
| 150 |
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"clusters_01_screenshot_01.jpg",
|
| 151 |
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"clusters_01_screenshot_02.jpg",
|
| 152 |
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"clusters_01_screenshot_03.jpg",
|
| 153 |
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"clusters_01_screenshot_04.jpg",
|
| 154 |
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"clusters_01_screenshot_05.jpg",
|
| 155 |
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"clusters_01_screenshot_06.jpg",
|
| 156 |
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|
| 157 |
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"clusters_01_screenshot_08.jpg",
|
| 158 |
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"clusters_01_screenshot_09.jpg",
|
| 159 |
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"clusters_01_screenshot_10.jpg",
|
| 160 |
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|
| 161 |
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|
| 162 |
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|
| 163 |
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"clusters_01_screenshot_14.jpg",
|
| 164 |
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"clusters_01_screenshot_15.jpg",
|
| 165 |
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"clusters_01_screenshot_16.jpg",
|
| 166 |
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"clusters_01_screenshot_17.jpg",
|
| 167 |
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"clusters_01_screenshot_18.jpg",
|
| 168 |
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"clusters_01_screenshot_19.jpg",
|
| 169 |
+
"pocket_01.pdb",
|
| 170 |
+
"pocket_02.pdb",
|
| 171 |
+
"pocket_03.pdb",
|
| 172 |
+
"pocket_04.pdb",
|
| 173 |
+
"pocket_05.pdb",
|
| 174 |
+
"pocket_06.pdb",
|
| 175 |
+
"pocket_07.pdb",
|
| 176 |
+
"pocket_08.pdb"
|
| 177 |
+
],
|
| 178 |
+
"analyses": [
|
| 179 |
+
"clusters",
|
| 180 |
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"clusters-00",
|
| 181 |
+
"clusters-01",
|
| 182 |
+
"dist-perres",
|
| 183 |
+
"energies",
|
| 184 |
+
"fluctuation",
|
| 185 |
+
"hbonds",
|
| 186 |
+
"interactions",
|
| 187 |
+
"pca",
|
| 188 |
+
"pockets",
|
| 189 |
+
"rgyr",
|
| 190 |
+
"rmsd-pairwise",
|
| 191 |
+
"rmsd-perres",
|
| 192 |
+
"rmsds",
|
| 193 |
+
"sasa",
|
| 194 |
+
"tmscores"
|
| 195 |
+
],
|
| 196 |
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"mdIndex": 0,
|
| 197 |
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"mdNumber": 1,
|
| 198 |
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"refframe": 0,
|
| 199 |
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"internalId": "684240173e4214067b352630",
|
| 200 |
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"creationDate": "2025-06-06T01:10:47.000Z",
|
| 201 |
+
"identifier": "A008A"
|
| 202 |
+
}
|
data/files/A008A/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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{"project_identifier": "A008A", "accession": "A008A", "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 4REY", "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": ["4REY"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9BQQ3", "Q08379"], 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data/files/A008B/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A008B",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4U2X",
|
| 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 |
+
"4U2X"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q05322",
|
| 31 |
+
"O15131"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
+
"DLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLHRLKTNDFAPAWSMTRNLFPHLFQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALGLISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKFINKLDALHVVNYNGLLSSIEIGTQNHTIIITRTNMGFLVELQEPDKSAMNRMKPGPAKFSLLHESTLKAFT",
|
| 38 |
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"ILNCSALPCLLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFRTRKEAAWAITNATSGGTPEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLENILRLGEQESKQNGIGINPYCALIEEAYGLDKIEFLQSHENQEIYQKAFDLIEHYFG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Membrane-associated protein VP24",
|
| 43 |
+
"Importin subunit alpha-6",
|
| 44 |
+
"NLS binding site (minor)"
|
| 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": 6188,
|
| 56 |
+
"SYSTRES": 388,
|
| 57 |
+
"PROTATS": 6188,
|
| 58 |
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"PROTRES": 388,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
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"NUCLRES": 0,
|
| 61 |
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"LIPIATS": 0,
|
| 62 |
+
"LIPIRES": 0,
|
| 63 |
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"CARBATS": 0,
|
| 64 |
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"CARBRES": 0,
|
| 65 |
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"SOLVATS": 0,
|
| 66 |
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"SOLVRES": 0,
|
| 67 |
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"COUNCAT": 0,
|
| 68 |
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"COUNANI": 0,
|
| 69 |
+
"COUNION": 0,
|
| 70 |
+
"INTERACTIONS": [
|
| 71 |
+
{
|
| 72 |
+
"name": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
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"MEMBRANES": null,
|
| 83 |
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"CUSTOMS": null,
|
| 84 |
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"ORIENTATION": null,
|
| 85 |
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"PTM": [],
|
| 86 |
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"MULTIMERIC": null,
|
| 87 |
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"COLLECTIONS": "dynarepo",
|
| 88 |
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"WARNINGS": [],
|
| 89 |
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"BOXSIZEX": 10.0744,
|
| 90 |
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"BOXSIZEY": 10.0744,
|
| 91 |
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"BOXSIZEZ": 7.08951,
|
| 92 |
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"mdName": "replica 1",
|
| 93 |
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"mdAtoms": 6188,
|
| 94 |
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"mdFrames": 5001
|
| 95 |
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},
|
| 96 |
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"mds": [
|
| 97 |
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"replica 1",
|
| 98 |
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"replica 2",
|
| 99 |
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"replica 3"
|
| 100 |
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],
|
| 101 |
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"mdref": 0,
|
| 102 |
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"files": [
|
| 103 |
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"topology.tpr",
|
| 104 |
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"screenshot.jpg",
|
| 105 |
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"trajectory.bin",
|
| 106 |
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"pca_trajectory_01.bin",
|
| 107 |
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|
| 108 |
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|
| 109 |
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"pca_trajectory_04.bin",
|
| 110 |
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|
| 111 |
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|
| 112 |
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"pca_trajectory_07.bin",
|
| 113 |
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|
| 114 |
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"pca_trajectory_09.bin",
|
| 115 |
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|
| 116 |
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"pca_trajectory_11.bin",
|
| 117 |
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|
| 118 |
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"pca_trajectory_13.bin",
|
| 119 |
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"pca_trajectory_14.bin",
|
| 120 |
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"pca_trajectory_15.bin",
|
| 121 |
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"pca_trajectory_16.bin",
|
| 122 |
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"pca_trajectory_17.bin",
|
| 123 |
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"structure.pdb",
|
| 124 |
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"trajectory.xtc",
|
| 125 |
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|
| 126 |
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|
| 127 |
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb",
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"pocket_05.pdb",
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"pocket_06.pdb",
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"pocket_07.pdb",
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"pocket_08.pdb",
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"pocket_09.pdb",
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"pocket_10.pdb"
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],
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"analyses": [
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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": 0,
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"internalId": "6842415cb04df8c80609b181",
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"creationDate": "2025-06-06T01:16:12.000Z",
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+
"identifier": "A008B"
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}
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data/files/A008B/records.jsonl
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A008C",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4UDM",
|
| 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 |
+
"4UDM"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P02984",
|
| 31 |
+
"P00646"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIAEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL",
|
| 38 |
+
"GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Colicin E3 immunity protein",
|
| 43 |
+
"Colicin E3",
|
| 44 |
+
"Disordered",
|
| 45 |
+
"Linker",
|
| 46 |
+
"Ribosome inactivating activity",
|
| 47 |
+
"Cytotoxic RNase (C) domain",
|
| 48 |
+
"Binding of immunity protein",
|
| 49 |
+
"Stabilizes positive charge on His-513"
|
| 50 |
+
],
|
| 51 |
+
"FRAMESTEP": 0.1,
|
| 52 |
+
"TIMESTEP": 2,
|
| 53 |
+
"TEMP": 310,
|
| 54 |
+
"ENSEMBLE": "NPT",
|
| 55 |
+
"FF": [
|
| 56 |
+
"CHARMM36m"
|
| 57 |
+
],
|
| 58 |
+
"WAT": "TIP3P",
|
| 59 |
+
"BOXTYPE": "Dodecahedron",
|
| 60 |
+
"SYSTATS": 2816,
|
| 61 |
+
"SYSTRES": 180,
|
| 62 |
+
"PROTATS": 2816,
|
| 63 |
+
"PROTRES": 180,
|
| 64 |
+
"NUCLATS": 0,
|
| 65 |
+
"NUCLRES": 0,
|
| 66 |
+
"LIPIATS": 0,
|
| 67 |
+
"LIPIRES": 0,
|
| 68 |
+
"CARBATS": 0,
|
| 69 |
+
"CARBRES": 0,
|
| 70 |
+
"SOLVATS": 0,
|
| 71 |
+
"SOLVRES": 0,
|
| 72 |
+
"COUNCAT": 0,
|
| 73 |
+
"COUNANI": 0,
|
| 74 |
+
"COUNION": 0,
|
| 75 |
+
"INTERACTIONS": [
|
| 76 |
+
{
|
| 77 |
+
"name": "chain A-chain B interaction",
|
| 78 |
+
"agent_1": "chain A",
|
| 79 |
+
"agent_2": "chain B",
|
| 80 |
+
"selection_1": "chain A",
|
| 81 |
+
"selection_2": "chain B",
|
| 82 |
+
"type": "protein-protein"
|
| 83 |
+
}
|
| 84 |
+
],
|
| 85 |
+
"PBC_SELECTION": null,
|
| 86 |
+
"CHAINNAMES": null,
|
| 87 |
+
"MEMBRANES": null,
|
| 88 |
+
"CUSTOMS": null,
|
| 89 |
+
"ORIENTATION": null,
|
| 90 |
+
"PTM": [],
|
| 91 |
+
"MULTIMERIC": null,
|
| 92 |
+
"COLLECTIONS": "dynarepo",
|
| 93 |
+
"WARNINGS": [],
|
| 94 |
+
"BOXSIZEX": 7.3251,
|
| 95 |
+
"BOXSIZEY": 7.3251,
|
| 96 |
+
"BOXSIZEZ": 5.25622,
|
| 97 |
+
"mdName": "replica 1",
|
| 98 |
+
"mdAtoms": 2816,
|
| 99 |
+
"mdFrames": 5001
|
| 100 |
+
},
|
| 101 |
+
"mds": [
|
| 102 |
+
"replica 1",
|
| 103 |
+
"replica 2",
|
| 104 |
+
"replica 3"
|
| 105 |
+
],
|
| 106 |
+
"mdref": 0,
|
| 107 |
+
"files": [
|
| 108 |
+
"topology.tpr",
|
| 109 |
+
"screenshot.jpg",
|
| 110 |
+
"trajectory.bin",
|
| 111 |
+
"pca_trajectory_01.bin",
|
| 112 |
+
"pca_trajectory_02.bin",
|
| 113 |
+
"pca_trajectory_03.bin",
|
| 114 |
+
"pca_trajectory_04.bin",
|
| 115 |
+
"pca_trajectory_05.bin",
|
| 116 |
+
"pca_trajectory_06.bin",
|
| 117 |
+
"pca_trajectory_07.bin",
|
| 118 |
+
"pca_trajectory_08.bin",
|
| 119 |
+
"pca_trajectory_09.bin",
|
| 120 |
+
"pca_trajectory_10.bin",
|
| 121 |
+
"pca_trajectory_11.bin",
|
| 122 |
+
"pca_trajectory_12.bin",
|
| 123 |
+
"pca_trajectory_13.bin",
|
| 124 |
+
"pca_trajectory_14.bin",
|
| 125 |
+
"pca_trajectory_15.bin",
|
| 126 |
+
"structure.pdb",
|
| 127 |
+
"trajectory.xtc",
|
| 128 |
+
"clusters_00_screenshot_00.jpg",
|
| 129 |
+
"clusters_00_screenshot_01.jpg",
|
| 130 |
+
"clusters_00_screenshot_02.jpg",
|
| 131 |
+
"clusters_00_screenshot_03.jpg",
|
| 132 |
+
"clusters_00_screenshot_04.jpg",
|
| 133 |
+
"clusters_00_screenshot_05.jpg",
|
| 134 |
+
"clusters_00_screenshot_06.jpg",
|
| 135 |
+
"clusters_00_screenshot_07.jpg",
|
| 136 |
+
"clusters_00_screenshot_08.jpg",
|
| 137 |
+
"clusters_00_screenshot_09.jpg",
|
| 138 |
+
"clusters_00_screenshot_10.jpg",
|
| 139 |
+
"clusters_00_screenshot_11.jpg",
|
| 140 |
+
"clusters_00_screenshot_12.jpg",
|
| 141 |
+
"clusters_00_screenshot_13.jpg",
|
| 142 |
+
"clusters_00_screenshot_14.jpg",
|
| 143 |
+
"clusters_00_screenshot_15.jpg",
|
| 144 |
+
"clusters_00_screenshot_16.jpg",
|
| 145 |
+
"clusters_00_screenshot_17.jpg",
|
| 146 |
+
"clusters_00_screenshot_18.jpg",
|
| 147 |
+
"clusters_00_screenshot_19.jpg",
|
| 148 |
+
"clusters_00_screenshot_20.jpg",
|
| 149 |
+
"clusters_00_screenshot_21.jpg",
|
| 150 |
+
"clusters_00_screenshot_22.jpg",
|
| 151 |
+
"clusters_01_screenshot_00.jpg",
|
| 152 |
+
"clusters_01_screenshot_01.jpg",
|
| 153 |
+
"clusters_01_screenshot_02.jpg",
|
| 154 |
+
"clusters_01_screenshot_03.jpg",
|
| 155 |
+
"clusters_01_screenshot_04.jpg",
|
| 156 |
+
"clusters_01_screenshot_05.jpg",
|
| 157 |
+
"clusters_01_screenshot_06.jpg",
|
| 158 |
+
"clusters_01_screenshot_07.jpg",
|
| 159 |
+
"clusters_01_screenshot_08.jpg",
|
| 160 |
+
"clusters_01_screenshot_09.jpg",
|
| 161 |
+
"clusters_01_screenshot_10.jpg",
|
| 162 |
+
"clusters_01_screenshot_11.jpg",
|
| 163 |
+
"clusters_01_screenshot_12.jpg",
|
| 164 |
+
"clusters_01_screenshot_13.jpg",
|
| 165 |
+
"clusters_01_screenshot_14.jpg",
|
| 166 |
+
"clusters_01_screenshot_15.jpg",
|
| 167 |
+
"clusters_01_screenshot_16.jpg",
|
| 168 |
+
"clusters_01_screenshot_17.jpg",
|
| 169 |
+
"clusters_01_screenshot_18.jpg",
|
| 170 |
+
"pocket_01.pdb",
|
| 171 |
+
"pocket_02.pdb",
|
| 172 |
+
"pocket_03.pdb",
|
| 173 |
+
"pocket_04.pdb"
|
| 174 |
+
],
|
| 175 |
+
"analyses": [
|
| 176 |
+
"clusters",
|
| 177 |
+
"clusters-00",
|
| 178 |
+
"clusters-01",
|
| 179 |
+
"dist-perres",
|
| 180 |
+
"energies",
|
| 181 |
+
"fluctuation",
|
| 182 |
+
"hbonds",
|
| 183 |
+
"interactions",
|
| 184 |
+
"pca",
|
| 185 |
+
"pockets",
|
| 186 |
+
"rgyr",
|
| 187 |
+
"rmsd-pairwise",
|
| 188 |
+
"rmsd-perres",
|
| 189 |
+
"rmsds",
|
| 190 |
+
"sasa",
|
| 191 |
+
"tmscores"
|
| 192 |
+
],
|
| 193 |
+
"mdIndex": 0,
|
| 194 |
+
"mdNumber": 1,
|
| 195 |
+
"refframe": 2,
|
| 196 |
+
"internalId": "684242a130085057f4cf24d1",
|
| 197 |
+
"creationDate": "2025-06-06T01:21:37.000Z",
|
| 198 |
+
"identifier": "A008C"
|
| 199 |
+
}
|
data/files/A008C/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A008C", "accession": "A008C", "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 4UDM", "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": ["4UDM"], "FORCED_REFERENCES": null, "REFERENCES": ["P02984", "P00646"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["GFKDYGHDYHPAPKTENIKGLGDLKPGIPKTPKQNGGGKRKRWTGDKGRKIAEWDSQHGELEGYRASDGQHLGSFDPKTGNQLKGPDPKRNIKKYL", "GLKLDLTWFDKSTEDFKGEEYSKDFGDDGSVMESLGVPFKDNVNNGCFDVIAEWVPLLQPYFNHQIDISDNEYFVSFDYRDGDW"], "NUCLSEQ": [], "DOMAINS": ["Colicin E3 immunity protein", "Colicin E3", "Disordered", "Linker", "Ribosome inactivating activity", "Cytotoxic RNase (C) domain", "Binding of immunity protein", "Stabilizes positive charge on His-513"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 180, "PROTATS": 2816, "PROTRES": 180, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", 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data/files/A008D/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A008D",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4UU9",
|
| 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 |
+
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|
| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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|
| 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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"EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDDDYEEWPWYYGMDVWGQGTMVTVS",
|
| 39 |
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"ALTQPASVSGSPGQSITISCTGTSSDIGGSKYVSWYQQHPGKAPKLIIFDVNRRPSGLSNRFSASKSGNTASLTISGLQAEDEADYYCTSYHPTKTILFGGGTKLTVLA",
|
| 40 |
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"STLQKKIEEIAAKYKHSVVKKCCYDGACVNNDETCEQRAARISLGPRCIKAFTECCVVASQLRAN"
|
| 41 |
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|
| 42 |
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"NUCLSEQ": [],
|
| 43 |
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"DOMAINS": [
|
| 44 |
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"Immunoglobulin heavy variable 3-23",
|
| 45 |
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"Ig-like",
|
| 46 |
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|
| 47 |
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"Complementarity-determining-1",
|
| 48 |
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|
| 49 |
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"Complementarity-determining-2",
|
| 50 |
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|
| 51 |
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"Complementarity-determining-3",
|
| 52 |
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"Immunoglobulin lambda-1 light chain",
|
| 53 |
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"Ig-like 1",
|
| 54 |
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"Variable (V) domain, involved in antigen recognition",
|
| 55 |
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"Complement C5 alpha chain",
|
| 56 |
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"C5a anaphylatoxin",
|
| 57 |
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"Anaphylatoxin-like",
|
| 58 |
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"Involved in C5AR1 binding"
|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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| 72 |
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|
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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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"name": "chain A-chain B interaction",
|
| 87 |
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|
| 88 |
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|
| 89 |
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"selection_1": "chain A",
|
| 90 |
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"selection_2": "chain B",
|
| 91 |
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"type": "protein-protein"
|
| 92 |
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},
|
| 93 |
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{
|
| 94 |
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"name": "chain A-chain C interaction",
|
| 95 |
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"agent_1": "chain A",
|
| 96 |
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|
| 97 |
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"selection_1": "chain A",
|
| 98 |
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"selection_2": "chain C",
|
| 99 |
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"type": "protein-protein"
|
| 100 |
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},
|
| 101 |
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{
|
| 102 |
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"name": "chain B-chain C interaction",
|
| 103 |
+
"agent_1": "chain B",
|
| 104 |
+
"agent_2": "chain C",
|
| 105 |
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"selection_1": "chain B",
|
| 106 |
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"selection_2": "chain C",
|
| 107 |
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"type": "protein-protein"
|
| 108 |
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}
|
| 109 |
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],
|
| 110 |
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|
| 111 |
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|
| 112 |
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|
| 113 |
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|
| 114 |
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|
| 115 |
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|
| 116 |
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|
| 117 |
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|
| 118 |
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|
| 119 |
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|
| 120 |
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|
| 121 |
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|
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|
| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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"mds": [
|
| 127 |
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"replica 1",
|
| 128 |
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"replica 2",
|
| 129 |
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"replica 3"
|
| 130 |
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|
| 131 |
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"mdref": 0,
|
| 132 |
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|
| 133 |
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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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| 143 |
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| 144 |
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| 147 |
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| 150 |
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| 151 |
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|
| 152 |
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|
| 153 |
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"structure.pdb",
|
| 154 |
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"trajectory.xtc",
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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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| 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_05.jpg",
|
| 217 |
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|
| 218 |
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|
| 219 |
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|
| 220 |
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"clusters_03_screenshot_09.jpg",
|
| 221 |
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"clusters_03_screenshot_10.jpg",
|
| 222 |
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"clusters_03_screenshot_11.jpg",
|
| 223 |
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"clusters_03_screenshot_12.jpg",
|
| 224 |
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"clusters_03_screenshot_13.jpg",
|
| 225 |
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"clusters_03_screenshot_14.jpg",
|
| 226 |
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"clusters_03_screenshot_15.jpg",
|
| 227 |
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"clusters_03_screenshot_16.jpg",
|
| 228 |
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"clusters_03_screenshot_17.jpg",
|
| 229 |
+
"clusters_03_screenshot_18.jpg",
|
| 230 |
+
"clusters_03_screenshot_19.jpg",
|
| 231 |
+
"clusters_03_screenshot_20.jpg",
|
| 232 |
+
"clusters_03_screenshot_21.jpg",
|
| 233 |
+
"pocket_01.pdb",
|
| 234 |
+
"pocket_02.pdb",
|
| 235 |
+
"pocket_03.pdb",
|
| 236 |
+
"pocket_04.pdb",
|
| 237 |
+
"pocket_05.pdb",
|
| 238 |
+
"pocket_06.pdb",
|
| 239 |
+
"pocket_07.pdb",
|
| 240 |
+
"pocket_08.pdb",
|
| 241 |
+
"pocket_09.pdb",
|
| 242 |
+
"pocket_10.pdb"
|
| 243 |
+
],
|
| 244 |
+
"analyses": [
|
| 245 |
+
"clusters",
|
| 246 |
+
"clusters-00",
|
| 247 |
+
"clusters-01",
|
| 248 |
+
"clusters-02",
|
| 249 |
+
"clusters-03",
|
| 250 |
+
"dist-perres",
|
| 251 |
+
"energies",
|
| 252 |
+
"fluctuation",
|
| 253 |
+
"hbonds",
|
| 254 |
+
"interactions",
|
| 255 |
+
"pca",
|
| 256 |
+
"pockets",
|
| 257 |
+
"rgyr",
|
| 258 |
+
"rmsd-pairwise",
|
| 259 |
+
"rmsd-perres",
|
| 260 |
+
"rmsds",
|
| 261 |
+
"sasa",
|
| 262 |
+
"tmscores"
|
| 263 |
+
],
|
| 264 |
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"mdIndex": 0,
|
| 265 |
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"mdNumber": 1,
|
| 266 |
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"refframe": 0,
|
| 267 |
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"internalId": "6842440b1697821589bbc2e6",
|
| 268 |
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"creationDate": "2025-06-06T01:27:39.000Z",
|
| 269 |
+
"identifier": "A008D"
|
| 270 |
+
}
|
data/files/A008D/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A008D", "accession": "A008D", "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 4UU9", "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": ["4UU9"], "FORCED_REFERENCES": null, "REFERENCES": 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data/files/A008E/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A008E",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4W4L",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"4W4L"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"A0A0H3LBR3",
|
| 31 |
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"A0A0H3LBN6",
|
| 32 |
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"A0A0H3LAM1"
|
| 33 |
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],
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| 34 |
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"INPUT_LIGANDS": null,
|
| 35 |
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|
| 36 |
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|
| 37 |
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"PROTSEQ": [
|
| 38 |
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"TRTDITVNVDGFWMLQALLDIRHVAPELRCRPYVSTDSNDWLNEHPGMAVMREQGIVVNDAVNEQVAARMKVLAAPDLEVVALLSRGKLLYGVIDDENQPPGSRDIPDNEFRVVLARRGQHWVSAVRVGNDITVDDVTVSDSASIAALVMDGLESIHHADPAAINAVNVPMEEMLEATKSWQESGFNVFSGGDLRRMGISAATVAALGQALSDPAAEVAVYARQYRDDAKGPSASVLSLKDGSGGRIALYQQARTAGSGEAWLAICPATPQLVQVGVKTVLDTLPYGEWKTHSRVSS",
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| 39 |
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"NPEALTVAATEVRRIRDRAIQSDAQVAPMTTAVRPPAADLVSEKAATFLVEYARKYRQTIAAAAVVLEEFAHALTTGADKYATA",
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| 40 |
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|
| 41 |
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],
|
| 42 |
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"NUCLSEQ": [],
|
| 43 |
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"DOMAINS": [
|
| 44 |
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"PE",
|
| 45 |
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"PPE"
|
| 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": 8497,
|
| 57 |
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"SYSTRES": 555,
|
| 58 |
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| 59 |
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"PROTRES": 555,
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| 60 |
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"NUCLATS": 0,
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| 61 |
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"NUCLRES": 0,
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| 62 |
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| 68 |
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| 69 |
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"COUNANI": 0,
|
| 70 |
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"COUNION": 0,
|
| 71 |
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"INTERACTIONS": [
|
| 72 |
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{
|
| 73 |
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"name": "chain A-chain B interaction",
|
| 74 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
|
| 79 |
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},
|
| 80 |
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{
|
| 81 |
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"name": "chain B-chain C interaction",
|
| 82 |
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"agent_1": "chain B",
|
| 83 |
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"agent_2": "chain C",
|
| 84 |
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"selection_1": "chain A",
|
| 85 |
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"selection_2": "chain C",
|
| 86 |
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"type": "protein-protein"
|
| 87 |
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}
|
| 88 |
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],
|
| 89 |
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|
| 90 |
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| 91 |
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| 92 |
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| 95 |
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| 96 |
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"COLLECTIONS": "dynarepo",
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| 97 |
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| 104 |
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},
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| 106 |
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| 107 |
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"replica 2",
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| 108 |
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|
| 109 |
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],
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| 110 |
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"mdref": 0,
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| 111 |
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"files": [
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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| 117 |
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| 118 |
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| 119 |
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| 120 |
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| 121 |
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| 122 |
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| 184 |
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"analyses": [
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| 185 |
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"clusters",
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| 186 |
+
"clusters-00",
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| 187 |
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"clusters-01",
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| 188 |
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"clusters-02",
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| 189 |
+
"dist-perres",
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| 190 |
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"energies",
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| 191 |
+
"fluctuation",
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| 192 |
+
"hbonds",
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| 193 |
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"interactions",
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| 194 |
+
"pca",
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| 195 |
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"rgyr",
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| 196 |
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"rmsd-pairwise",
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| 197 |
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"rmsd-perres",
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| 198 |
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"rmsds",
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| 199 |
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"sasa",
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| 200 |
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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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| 204 |
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"refframe": 0,
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"internalId": "684245ab3ca26c909743c5eb",
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"creationDate": "2025-06-06T01:34:35.000Z",
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"identifier": "A008E"
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}
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data/files/A008E/records.jsonl
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| 1 |
+
{
|
| 2 |
+
"accession": "A008F",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4WNN",
|
| 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 |
+
"4WNN"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P04911",
|
| 31 |
+
"P02293"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MKKRSKARKETYSSYIYKVLKQTHPDTGISQKSMSILNSFVNDIFERIATEASKLAAYNKKSTISAREIQTAVRLILPGELAKHAVSEGTRAVTKYSS",
|
| 38 |
+
"QSRSAKAGLTFPVGRVHRLLRRGNYAQRIGSGAPVYLTAVLEYLAAEILELAGNAARDNKKTRIIPRHLQLAIRNDDELNKLLGNV"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Histone H2A.1",
|
| 43 |
+
"Histone H2B.1",
|
| 44 |
+
"Disordered"
|
| 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": 2958,
|
| 56 |
+
"SYSTRES": 184,
|
| 57 |
+
"PROTATS": 2958,
|
| 58 |
+
"PROTRES": 184,
|
| 59 |
+
"NUCLATS": 0,
|
| 60 |
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"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": "chain A-chain B interaction",
|
| 73 |
+
"agent_1": "chain A",
|
| 74 |
+
"agent_2": "chain B",
|
| 75 |
+
"selection_1": "chain A",
|
| 76 |
+
"selection_2": "chain B",
|
| 77 |
+
"type": "protein-protein"
|
| 78 |
+
}
|
| 79 |
+
],
|
| 80 |
+
"PBC_SELECTION": null,
|
| 81 |
+
"CHAINNAMES": null,
|
| 82 |
+
"MEMBRANES": null,
|
| 83 |
+
"CUSTOMS": null,
|
| 84 |
+
"ORIENTATION": null,
|
| 85 |
+
"PTM": [],
|
| 86 |
+
"MULTIMERIC": null,
|
| 87 |
+
"COLLECTIONS": "dynarepo",
|
| 88 |
+
"WARNINGS": [],
|
| 89 |
+
"BOXSIZEX": 8.34631,
|
| 90 |
+
"BOXSIZEY": 8.34631,
|
| 91 |
+
"BOXSIZEZ": 5.89718,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 2958,
|
| 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 |
+
"structure.pdb",
|
| 116 |
+
"trajectory.xtc",
|
| 117 |
+
"clusters_00_screenshot_00.jpg",
|
| 118 |
+
"clusters_00_screenshot_01.jpg",
|
| 119 |
+
"clusters_00_screenshot_02.jpg",
|
| 120 |
+
"clusters_00_screenshot_03.jpg",
|
| 121 |
+
"clusters_00_screenshot_04.jpg",
|
| 122 |
+
"clusters_00_screenshot_05.jpg",
|
| 123 |
+
"clusters_00_screenshot_06.jpg",
|
| 124 |
+
"clusters_00_screenshot_07.jpg",
|
| 125 |
+
"clusters_00_screenshot_08.jpg",
|
| 126 |
+
"clusters_00_screenshot_09.jpg",
|
| 127 |
+
"clusters_00_screenshot_10.jpg",
|
| 128 |
+
"clusters_00_screenshot_11.jpg",
|
| 129 |
+
"clusters_00_screenshot_12.jpg",
|
| 130 |
+
"clusters_00_screenshot_13.jpg",
|
| 131 |
+
"clusters_00_screenshot_14.jpg",
|
| 132 |
+
"clusters_00_screenshot_15.jpg",
|
| 133 |
+
"clusters_00_screenshot_16.jpg",
|
| 134 |
+
"clusters_00_screenshot_17.jpg",
|
| 135 |
+
"clusters_00_screenshot_18.jpg",
|
| 136 |
+
"clusters_00_screenshot_19.jpg",
|
| 137 |
+
"clusters_00_screenshot_20.jpg",
|
| 138 |
+
"clusters_01_screenshot_00.jpg",
|
| 139 |
+
"clusters_01_screenshot_01.jpg",
|
| 140 |
+
"clusters_01_screenshot_02.jpg",
|
| 141 |
+
"clusters_01_screenshot_03.jpg",
|
| 142 |
+
"clusters_01_screenshot_04.jpg",
|
| 143 |
+
"clusters_01_screenshot_05.jpg",
|
| 144 |
+
"clusters_01_screenshot_06.jpg",
|
| 145 |
+
"clusters_01_screenshot_07.jpg",
|
| 146 |
+
"clusters_01_screenshot_08.jpg",
|
| 147 |
+
"clusters_01_screenshot_09.jpg",
|
| 148 |
+
"clusters_01_screenshot_10.jpg",
|
| 149 |
+
"clusters_01_screenshot_11.jpg",
|
| 150 |
+
"clusters_01_screenshot_12.jpg",
|
| 151 |
+
"clusters_01_screenshot_13.jpg",
|
| 152 |
+
"clusters_01_screenshot_14.jpg",
|
| 153 |
+
"clusters_01_screenshot_15.jpg",
|
| 154 |
+
"clusters_01_screenshot_16.jpg",
|
| 155 |
+
"clusters_01_screenshot_17.jpg",
|
| 156 |
+
"clusters_01_screenshot_18.jpg",
|
| 157 |
+
"clusters_01_screenshot_19.jpg",
|
| 158 |
+
"pocket_01.pdb",
|
| 159 |
+
"pocket_02.pdb",
|
| 160 |
+
"pocket_03.pdb",
|
| 161 |
+
"pocket_04.pdb"
|
| 162 |
+
],
|
| 163 |
+
"analyses": [
|
| 164 |
+
"clusters",
|
| 165 |
+
"clusters-00",
|
| 166 |
+
"clusters-01",
|
| 167 |
+
"dist-perres",
|
| 168 |
+
"energies",
|
| 169 |
+
"fluctuation",
|
| 170 |
+
"hbonds",
|
| 171 |
+
"interactions",
|
| 172 |
+
"pca",
|
| 173 |
+
"pockets",
|
| 174 |
+
"rgyr",
|
| 175 |
+
"rmsd-pairwise",
|
| 176 |
+
"rmsd-perres",
|
| 177 |
+
"rmsds",
|
| 178 |
+
"sasa",
|
| 179 |
+
"tmscores"
|
| 180 |
+
],
|
| 181 |
+
"mdIndex": 0,
|
| 182 |
+
"mdNumber": 1,
|
| 183 |
+
"refframe": 0,
|
| 184 |
+
"internalId": "68424730355de95c01f56008",
|
| 185 |
+
"creationDate": "2025-06-06T01:41:04.000Z",
|
| 186 |
+
"identifier": "A008F"
|
| 187 |
+
}
|
data/files/A008F/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A008F", "accession": "A008F", "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 4WNN", "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": ["4WNN"], "FORCED_REFERENCES": null, "REFERENCES": ["P04911", "P02293"], 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data/files/A008G/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A008G",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4XKH",
|
| 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 |
+
"4XKH"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0CH28",
|
| 31 |
+
"Q91X58"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL",
|
| 38 |
+
"NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE",
|
| 39 |
+
"QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRL"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Ubiquitin",
|
| 44 |
+
"Ubiquitin-like 2",
|
| 45 |
+
"AN1-type zinc finger protein 2B",
|
| 46 |
+
"UIM 1",
|
| 47 |
+
"UIM 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": 2995,
|
| 59 |
+
"SYSTRES": 188,
|
| 60 |
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"PROTATS": 2995,
|
| 61 |
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"PROTRES": 188,
|
| 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 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [
|
| 74 |
+
{
|
| 75 |
+
"name": "chain A-chain B interaction",
|
| 76 |
+
"agent_1": "chain A",
|
| 77 |
+
"agent_2": "chain B",
|
| 78 |
+
"selection_1": "chain A",
|
| 79 |
+
"selection_2": "chain B",
|
| 80 |
+
"type": "protein-protein"
|
| 81 |
+
},
|
| 82 |
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{
|
| 83 |
+
"name": "chain A-chain C interaction",
|
| 84 |
+
"agent_1": "chain A",
|
| 85 |
+
"agent_2": "chain C",
|
| 86 |
+
"selection_1": "chain A",
|
| 87 |
+
"selection_2": "chain C",
|
| 88 |
+
"type": "protein-protein"
|
| 89 |
+
},
|
| 90 |
+
{
|
| 91 |
+
"name": "chain B-chain C interaction",
|
| 92 |
+
"agent_1": "chain B",
|
| 93 |
+
"agent_2": "chain C",
|
| 94 |
+
"selection_1": "chain B",
|
| 95 |
+
"selection_2": "chain C",
|
| 96 |
+
"type": "protein-protein"
|
| 97 |
+
}
|
| 98 |
+
],
|
| 99 |
+
"PBC_SELECTION": null,
|
| 100 |
+
"CHAINNAMES": null,
|
| 101 |
+
"MEMBRANES": null,
|
| 102 |
+
"CUSTOMS": null,
|
| 103 |
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"ORIENTATION": null,
|
| 104 |
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"PTM": [],
|
| 105 |
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"MULTIMERIC": null,
|
| 106 |
+
"COLLECTIONS": "dynarepo",
|
| 107 |
+
"WARNINGS": [
|
| 108 |
+
{
|
| 109 |
+
"tag": "intrajrity",
|
| 110 |
+
"message": "RMSD check has failed: there may be sudden jumps along the trajectory"
|
| 111 |
+
}
|
| 112 |
+
],
|
| 113 |
+
"BOXSIZEX": 9.244,
|
| 114 |
+
"BOXSIZEY": 9.244,
|
| 115 |
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"BOXSIZEZ": 6.57436,
|
| 116 |
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"mdName": "replica 1",
|
| 117 |
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"mdAtoms": 2995,
|
| 118 |
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"mdFrames": 5001
|
| 119 |
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},
|
| 120 |
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"mds": [
|
| 121 |
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"replica 1",
|
| 122 |
+
"replica 2",
|
| 123 |
+
"replica 3"
|
| 124 |
+
],
|
| 125 |
+
"mdref": 0,
|
| 126 |
+
"files": [
|
| 127 |
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"topology.tpr",
|
| 128 |
+
"screenshot.jpg",
|
| 129 |
+
"trajectory.bin",
|
| 130 |
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"pca_trajectory_01.bin",
|
| 131 |
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|
| 132 |
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|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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|
| 138 |
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"structure.pdb",
|
| 139 |
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| 140 |
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|
| 141 |
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|
| 142 |
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"clusters_03_screenshot_19.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb"
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],
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"analyses": [
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"mem-map",
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"clusters",
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"clusters-00",
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"clusters-01",
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"clusters-02",
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"clusters-03",
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"dist-perres",
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"energies",
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"fluctuation",
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"hbonds",
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"interactions",
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"pca",
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"pockets",
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"rgyr",
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"rmsd-pairwise",
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"rmsd-perres",
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"rmsds",
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"sasa",
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"tmscores"
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],
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"mdIndex": 0,
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"mdNumber": 1,
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"refframe": 0,
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"internalId": "6842484d046ce6e10d49165d",
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"creationDate": "2025-06-06T01:45:49.000Z",
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"identifier": "A008G"
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}
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data/files/A008G/records.jsonl
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data/files/A008H/project.json
ADDED
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@@ -0,0 +1,194 @@
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| 1 |
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{
|
| 2 |
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"accession": "A008H",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4XL5",
|
| 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",
|
| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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"4XL5"
|
| 27 |
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],
|
| 28 |
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|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P42212",
|
| 31 |
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"P50037"
|
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],
|
| 33 |
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| 36 |
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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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"Green fluorescent protein",
|
| 43 |
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"Phycocyanobilin lyase subunit alpha"
|
| 44 |
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],
|
| 45 |
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"FRAMESTEP": 0.1,
|
| 46 |
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"TIMESTEP": 2,
|
| 47 |
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"TEMP": 310,
|
| 48 |
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"ENSEMBLE": "NPT",
|
| 49 |
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"FF": [
|
| 50 |
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"CHARMM36m"
|
| 51 |
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],
|
| 52 |
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"WAT": "TIP3P",
|
| 53 |
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"BOXTYPE": "Dodecahedron",
|
| 54 |
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"SYSTATS": 7390,
|
| 55 |
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"SYSTRES": 474,
|
| 56 |
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"PROTATS": 7390,
|
| 57 |
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"PROTRES": 474,
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| 68 |
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"COUNION": 0,
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| 69 |
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"INTERACTIONS": [
|
| 70 |
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{
|
| 71 |
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"name": "chain A-chain B interaction",
|
| 72 |
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"agent_1": "chain A",
|
| 73 |
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"agent_2": "chain B",
|
| 74 |
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"selection_1": "chain A",
|
| 75 |
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"selection_2": "chain B",
|
| 76 |
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"type": "protein-protein"
|
| 77 |
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}
|
| 78 |
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],
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| 79 |
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| 80 |
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| 81 |
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| 83 |
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| 84 |
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| 86 |
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"COLLECTIONS": "dynarepo",
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| 87 |
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"WARNINGS": [],
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| 88 |
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},
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| 99 |
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| 109 |
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| 137 |
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| 139 |
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| 140 |
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| 141 |
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| 142 |
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| 143 |
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| 144 |
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| 145 |
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| 146 |
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| 147 |
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| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
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|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
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|
| 162 |
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|
| 163 |
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|
| 164 |
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|
| 165 |
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|
| 166 |
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"pocket_08.pdb",
|
| 167 |
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"pocket_09.pdb",
|
| 168 |
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"pocket_10.pdb"
|
| 169 |
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],
|
| 170 |
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"analyses": [
|
| 171 |
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"clusters",
|
| 172 |
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"clusters-00",
|
| 173 |
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|
| 174 |
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|
| 175 |
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|
| 176 |
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|
| 177 |
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|
| 178 |
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|
| 179 |
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|
| 180 |
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| 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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],
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"internalId": "68424a8d25fda489d8757231",
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| 192 |
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"creationDate": "2025-06-06T01:55:25.000Z",
|
| 193 |
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"identifier": "A008H"
|
| 194 |
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}
|
data/files/A008H/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
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data/files/A008I/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A008I",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4XVP",
|
| 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 |
+
"4XVP"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P42212",
|
| 31 |
+
"P50037"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"HHTDPEKVEMYIKNLQDDSMRVRYNAATALGKIGDERAVEPLIKALKDEDGYVRLEAAEALGEIGDERAVEPLIKALKDEDPDVRSEAALALGKIGDERAVEPLIKALKDEDRYVRMAAAWALGKIGGERVRAAMEKLAETGTGFARKVAVNYLETHK",
|
| 38 |
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"SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Green fluorescent protein",
|
| 43 |
+
"Phycocyanobilin lyase subunit alpha"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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"COUNANI": 0,
|
| 68 |
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"COUNION": 0,
|
| 69 |
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"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
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|
| 81 |
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"MEMBRANES": null,
|
| 82 |
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"CUSTOMS": null,
|
| 83 |
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|
| 84 |
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|
| 85 |
+
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|
| 86 |
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"COLLECTIONS": "dynarepo",
|
| 87 |
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"WARNINGS": [],
|
| 88 |
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|
| 89 |
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|
| 90 |
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"BOXSIZEZ": 6.51662,
|
| 91 |
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|
| 92 |
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|
| 93 |
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"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
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"mdref": 0,
|
| 101 |
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"files": [
|
| 102 |
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"topology.tpr",
|
| 103 |
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"screenshot.jpg",
|
| 104 |
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"trajectory.bin",
|
| 105 |
+
"pca_trajectory_01.bin",
|
| 106 |
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"pca_trajectory_02.bin",
|
| 107 |
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"pca_trajectory_03.bin",
|
| 108 |
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"pca_trajectory_04.bin",
|
| 109 |
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"pca_trajectory_05.bin",
|
| 110 |
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"pca_trajectory_06.bin",
|
| 111 |
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"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 |
+
"pca_trajectory_15.bin",
|
| 120 |
+
"structure.pdb",
|
| 121 |
+
"trajectory.xtc",
|
| 122 |
+
"clusters_00_screenshot_00.jpg",
|
| 123 |
+
"clusters_00_screenshot_01.jpg",
|
| 124 |
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"clusters_00_screenshot_02.jpg",
|
| 125 |
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"clusters_00_screenshot_03.jpg",
|
| 126 |
+
"clusters_00_screenshot_04.jpg",
|
| 127 |
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"clusters_00_screenshot_05.jpg",
|
| 128 |
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"clusters_00_screenshot_06.jpg",
|
| 129 |
+
"clusters_00_screenshot_07.jpg",
|
| 130 |
+
"clusters_00_screenshot_08.jpg",
|
| 131 |
+
"clusters_00_screenshot_09.jpg",
|
| 132 |
+
"clusters_00_screenshot_10.jpg",
|
| 133 |
+
"clusters_00_screenshot_11.jpg",
|
| 134 |
+
"clusters_00_screenshot_12.jpg",
|
| 135 |
+
"clusters_00_screenshot_13.jpg",
|
| 136 |
+
"clusters_00_screenshot_14.jpg",
|
| 137 |
+
"clusters_00_screenshot_15.jpg",
|
| 138 |
+
"clusters_00_screenshot_16.jpg",
|
| 139 |
+
"clusters_00_screenshot_17.jpg",
|
| 140 |
+
"clusters_00_screenshot_18.jpg",
|
| 141 |
+
"clusters_00_screenshot_19.jpg",
|
| 142 |
+
"clusters_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.pdb",
|
| 163 |
+
"pocket_03.pdb",
|
| 164 |
+
"pocket_04.pdb",
|
| 165 |
+
"pocket_05.pdb",
|
| 166 |
+
"pocket_06.pdb",
|
| 167 |
+
"pocket_07.pdb",
|
| 168 |
+
"pocket_08.pdb",
|
| 169 |
+
"pocket_09.pdb",
|
| 170 |
+
"pocket_10.pdb"
|
| 171 |
+
],
|
| 172 |
+
"analyses": [
|
| 173 |
+
"clusters",
|
| 174 |
+
"clusters-00",
|
| 175 |
+
"clusters-01",
|
| 176 |
+
"dist-perres",
|
| 177 |
+
"energies",
|
| 178 |
+
"fluctuation",
|
| 179 |
+
"hbonds",
|
| 180 |
+
"interactions",
|
| 181 |
+
"pca",
|
| 182 |
+
"pockets",
|
| 183 |
+
"rgyr",
|
| 184 |
+
"rmsd-pairwise",
|
| 185 |
+
"rmsd-perres",
|
| 186 |
+
"rmsds",
|
| 187 |
+
"sasa",
|
| 188 |
+
"tmscores"
|
| 189 |
+
],
|
| 190 |
+
"mdIndex": 0,
|
| 191 |
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"mdNumber": 1,
|
| 192 |
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"refframe": 0,
|
| 193 |
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"internalId": "68424df17e33d191600e369c",
|
| 194 |
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"creationDate": "2025-06-06T02:09:53.000Z",
|
| 195 |
+
"identifier": "A008I"
|
| 196 |
+
}
|
data/files/A008I/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A008I", "accession": "A008I", "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 4XVP", "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": ["4XVP"], "FORCED_REFERENCES": null, "REFERENCES": ["P42212", "P50037"], 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| 3 |
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data/files/A008J/project.json
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| 1 |
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{
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| 2 |
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"accession": "A008J",
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| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4XWJ",
|
| 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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],
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| 12 |
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"GROUPS": [
|
| 13 |
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|
| 14 |
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],
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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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| 18 |
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| 19 |
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| 20 |
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| 21 |
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| 22 |
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| 23 |
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| 24 |
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| 25 |
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| 26 |
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"4XWJ"
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| 27 |
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],
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| 28 |
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| 29 |
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| 30 |
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"P0AFX4",
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| 31 |
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"P0AA04"
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| 32 |
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],
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| 33 |
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| 39 |
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],
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| 40 |
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|
| 41 |
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|
| 42 |
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"Regulator of sigma D",
|
| 43 |
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"Interaction with RpoD",
|
| 44 |
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"Phosphocarrier protein HPr",
|
| 45 |
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"HPr"
|
| 46 |
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],
|
| 47 |
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"FRAMESTEP": 0.1,
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| 48 |
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| 49 |
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"TEMP": 310,
|
| 50 |
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| 51 |
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"FF": [
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| 52 |
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"CHARMM36m"
|
| 53 |
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],
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| 54 |
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"WAT": "TIP3P",
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| 55 |
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| 56 |
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| 57 |
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| 58 |
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| 65 |
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| 69 |
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"COUNANI": 0,
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| 70 |
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"COUNION": 0,
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| 71 |
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"INTERACTIONS": [
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| 72 |
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{
|
| 73 |
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"name": "chain A-chain B interaction",
|
| 74 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
|
| 79 |
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}
|
| 80 |
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],
|
| 81 |
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| 82 |
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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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| 94 |
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},
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| 98 |
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| 99 |
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| 100 |
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| 101 |
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|
| 148 |
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"clusters_01_screenshot_16.jpg",
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"clusters_01_screenshot_20.jpg",
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"clusters_01_screenshot_21.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb"
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| 163 |
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],
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| 164 |
+
"analyses": [
|
| 165 |
+
"clusters",
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| 166 |
+
"clusters-00",
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| 167 |
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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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"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": "68424f4495013c6e1f96509d",
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"creationDate": "2025-06-06T02:15:32.000Z",
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"identifier": "A008J"
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}
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data/files/A008J/records.jsonl
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|
data/files/A008K/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A008K",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 4Y61",
|
| 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 |
+
"4Y61"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q64487",
|
| 31 |
+
"Q810C0"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGSVLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEESDQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAVGSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVKALPKPPGTPVVTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSVAGLSPYSDYEFRVVAVNNIGRGPASEPVLTQ",
|
| 38 |
+
"CKIRCLCEEKENVLNINCENKGFTTVSLLQPPQYRIYQLFLNGNLLTRLYPNEFVNYSNAVTLHLGNNGLQEIRPGAFSGLKTLKRLHLNNNKLEVLREDTFLGLESLEYLQADYNYISTIEAGAFSKLNKLKVLILNDNLLLSLPSNVFRFVLLTHLDLRGNRLKVMPFAGVLEHIGGIMEIQLEENPWNCTCDLLPLKAWLDTITVFVGEIVCETPFRLHGKDVTQLTRQDLC"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Receptor-type tyrosine-protein phosphatase delta",
|
| 43 |
+
"Ig-like C2-type 1",
|
| 44 |
+
"Ig-like C2-type 2",
|
| 45 |
+
"Ig-like C2-type 3",
|
| 46 |
+
"Fibronectin type-III 1",
|
| 47 |
+
"Mini-exon peptide A9; sufficient for interaction with IL1RAPL1",
|
| 48 |
+
"Mini-exon peptide B; required for interaction with SLITRK2 and in the function in pre-synaptic differentiation; Acts as an adjustable linker to control relative positions and orientations of the PTPRD second and third immunoglobilin domains for their simultaneous interactions with the first immunoglobilin domain of IL1RAPL1 and IL1RAP; Modulates affinity for IL1RAPL1 and IL1RAP",
|
| 49 |
+
"Required for interaction with IL1RAP",
|
| 50 |
+
"SLIT and NTRK-like protein 2",
|
| 51 |
+
"LRRCT 1",
|
| 52 |
+
"Required for interaction with PTPRD",
|
| 53 |
+
"Disordered"
|
| 54 |
+
],
|
| 55 |
+
"FRAMESTEP": 0.1,
|
| 56 |
+
"TIMESTEP": 2,
|
| 57 |
+
"TEMP": 310,
|
| 58 |
+
"ENSEMBLE": "NPT",
|
| 59 |
+
"FF": [
|
| 60 |
+
"CHARMM36m"
|
| 61 |
+
],
|
| 62 |
+
"WAT": "TIP3P",
|
| 63 |
+
"BOXTYPE": "Dodecahedron",
|
| 64 |
+
"SYSTATS": 9789,
|
| 65 |
+
"SYSTRES": 626,
|
| 66 |
+
"PROTATS": 9789,
|
| 67 |
+
"PROTRES": 626,
|
| 68 |
+
"NUCLATS": 0,
|
| 69 |
+
"NUCLRES": 0,
|
| 70 |
+
"LIPIATS": 0,
|
| 71 |
+
"LIPIRES": 0,
|
| 72 |
+
"CARBATS": 0,
|
| 73 |
+
"CARBRES": 0,
|
| 74 |
+
"SOLVATS": 0,
|
| 75 |
+
"SOLVRES": 0,
|
| 76 |
+
"COUNCAT": 0,
|
| 77 |
+
"COUNANI": 0,
|
| 78 |
+
"COUNION": 0,
|
| 79 |
+
"INTERACTIONS": [
|
| 80 |
+
{
|
| 81 |
+
"name": "chain A-chain B interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain B",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain B",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
}
|
| 88 |
+
],
|
| 89 |
+
"PBC_SELECTION": null,
|
| 90 |
+
"CHAINNAMES": null,
|
| 91 |
+
"MEMBRANES": null,
|
| 92 |
+
"CUSTOMS": null,
|
| 93 |
+
"ORIENTATION": null,
|
| 94 |
+
"PTM": [],
|
| 95 |
+
"MULTIMERIC": null,
|
| 96 |
+
"COLLECTIONS": "dynarepo",
|
| 97 |
+
"WARNINGS": [],
|
| 98 |
+
"BOXSIZEX": 17.9621,
|
| 99 |
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"BOXSIZEY": 17.9621,
|
| 100 |
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"BOXSIZEZ": 12.7039,
|
| 101 |
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"mdName": "replica 1",
|
| 102 |
+
"mdAtoms": 9789,
|
| 103 |
+
"mdFrames": 5001
|
| 104 |
+
},
|
| 105 |
+
"mds": [
|
| 106 |
+
"replica 1",
|
| 107 |
+
"replica 2",
|
| 108 |
+
"replica 3"
|
| 109 |
+
],
|
| 110 |
+
"mdref": 0,
|
| 111 |
+
"files": [
|
| 112 |
+
"topology.tpr",
|
| 113 |
+
"screenshot.jpg",
|
| 114 |
+
"trajectory.bin",
|
| 115 |
+
"pca_trajectory_01.bin",
|
| 116 |
+
"pca_trajectory_02.bin",
|
| 117 |
+
"pca_trajectory_03.bin",
|
| 118 |
+
"pca_trajectory_04.bin",
|
| 119 |
+
"pca_trajectory_05.bin",
|
| 120 |
+
"pca_trajectory_06.bin",
|
| 121 |
+
"pca_trajectory_07.bin",
|
| 122 |
+
"pca_trajectory_08.bin",
|
| 123 |
+
"structure.pdb",
|
| 124 |
+
"trajectory.xtc",
|
| 125 |
+
"clusters_00_screenshot_00.jpg",
|
| 126 |
+
"clusters_00_screenshot_01.jpg",
|
| 127 |
+
"clusters_00_screenshot_02.jpg",
|
| 128 |
+
"clusters_00_screenshot_03.jpg",
|
| 129 |
+
"clusters_00_screenshot_04.jpg",
|
| 130 |
+
"clusters_00_screenshot_05.jpg",
|
| 131 |
+
"clusters_00_screenshot_06.jpg",
|
| 132 |
+
"clusters_00_screenshot_07.jpg",
|
| 133 |
+
"clusters_00_screenshot_08.jpg",
|
| 134 |
+
"clusters_00_screenshot_09.jpg",
|
| 135 |
+
"clusters_00_screenshot_10.jpg",
|
| 136 |
+
"clusters_00_screenshot_11.jpg",
|
| 137 |
+
"clusters_00_screenshot_12.jpg",
|
| 138 |
+
"clusters_00_screenshot_13.jpg",
|
| 139 |
+
"clusters_00_screenshot_14.jpg",
|
| 140 |
+
"clusters_00_screenshot_15.jpg",
|
| 141 |
+
"clusters_00_screenshot_16.jpg",
|
| 142 |
+
"clusters_00_screenshot_17.jpg",
|
| 143 |
+
"clusters_00_screenshot_18.jpg",
|
| 144 |
+
"clusters_00_screenshot_19.jpg",
|
| 145 |
+
"clusters_00_screenshot_20.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 |
+
"clusters_01_screenshot_20.jpg",
|
| 167 |
+
"clusters_01_screenshot_21.jpg",
|
| 168 |
+
"clusters_01_screenshot_22.jpg",
|
| 169 |
+
"pocket_01.pdb",
|
| 170 |
+
"pocket_02.pdb",
|
| 171 |
+
"pocket_03.pdb"
|
| 172 |
+
],
|
| 173 |
+
"analyses": [
|
| 174 |
+
"clusters",
|
| 175 |
+
"clusters-00",
|
| 176 |
+
"clusters-01",
|
| 177 |
+
"dist-perres",
|
| 178 |
+
"energies",
|
| 179 |
+
"fluctuation",
|
| 180 |
+
"hbonds",
|
| 181 |
+
"interactions",
|
| 182 |
+
"pca",
|
| 183 |
+
"pockets",
|
| 184 |
+
"rgyr",
|
| 185 |
+
"rmsd-pairwise",
|
| 186 |
+
"rmsd-perres",
|
| 187 |
+
"rmsds",
|
| 188 |
+
"sasa",
|
| 189 |
+
"tmscores"
|
| 190 |
+
],
|
| 191 |
+
"mdIndex": 0,
|
| 192 |
+
"mdNumber": 1,
|
| 193 |
+
"refframe": 0,
|
| 194 |
+
"internalId": "684250ecabc301e71f4f08e2",
|
| 195 |
+
"creationDate": "2025-06-06T02:22:36.000Z",
|
| 196 |
+
"identifier": "A008K"
|
| 197 |
+
}
|
data/files/A008K/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A008K", "accession": "A008K", "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 4Y61", "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": ["4Y61"], "FORCED_REFERENCES": null, "REFERENCES": ["Q64487", "Q810C0"], 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data/files/A008L/project.json
ADDED
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@@ -0,0 +1,179 @@
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| 1 |
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{
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| 2 |
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"accession": "A008L",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4YIQ",
|
| 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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|
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"PROGRAM": "GROMACS",
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"VERSION": "2024.2",
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"TYPE": "trajectory",
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| 19 |
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"METHOD": "Classical MD",
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| 38 |
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|
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"NUCLSEQ": [],
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|
| 42 |
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"Cell adhesion molecule CEACAM8",
|
| 43 |
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"Ig-like V-type",
|
| 44 |
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"Cell adhesion molecule CEACAM6",
|
| 45 |
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"Ig-like V-type"
|
| 46 |
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],
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"FRAMESTEP": 0.1,
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| 48 |
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|
| 50 |
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"ENSEMBLE": "NPT",
|
| 51 |
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"FF": [
|
| 52 |
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"CHARMM36m"
|
| 53 |
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],
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| 54 |
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"WAT": "TIP3P",
|
| 55 |
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"BOXTYPE": "Dodecahedron",
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"SYSTATS": 3342,
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"COUNION": 0,
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"INTERACTIONS": [
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| 72 |
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{
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"name": "chain A-chain B interaction",
|
| 74 |
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"agent_1": "chain A",
|
| 75 |
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"agent_2": "chain B",
|
| 76 |
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"selection_1": "chain A",
|
| 77 |
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"selection_2": "chain B",
|
| 78 |
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"type": "protein-protein"
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| 79 |
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}
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],
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"PBC_SELECTION": null,
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"COLLECTIONS": "dynarepo",
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| 145 |
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|
| 154 |
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|
| 155 |
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],
|
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"analyses": [
|
| 157 |
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"clusters",
|
| 158 |
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"clusters-00",
|
| 159 |
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|
| 160 |
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|
| 161 |
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"energies",
|
| 162 |
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"fluctuation",
|
| 163 |
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"hbonds",
|
| 164 |
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|
| 165 |
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|
| 166 |
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"rgyr",
|
| 167 |
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|
| 168 |
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|
| 169 |
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|
| 170 |
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|
| 171 |
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],
|
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"creationDate": "2025-06-06T02:29:46.000Z",
|
| 178 |
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"identifier": "A008L"
|
| 179 |
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}
|
data/files/A008L/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
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data/files/A008M/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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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 4YN0",
|
| 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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|
| 11 |
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|
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|
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"PROGRAM": "GROMACS",
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"VERSION": "2024.2",
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"TYPE": "trajectory",
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| 19 |
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"METHOD": "Classical MD",
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| 43 |
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| 44 |
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|
| 45 |
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| 46 |
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|
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|
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|
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],
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| 54 |
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|
| 56 |
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],
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| 57 |
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"WAT": "TIP3P",
|
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"BOXTYPE": "Dodecahedron",
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| 59 |
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| 61 |
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|
| 75 |
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{
|
| 76 |
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"name": "chain A-chain B interaction",
|
| 77 |
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"agent_1": "chain A",
|
| 78 |
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"agent_2": "chain B",
|
| 79 |
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"selection_1": "chain A",
|
| 80 |
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"selection_2": "chain B",
|
| 81 |
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"type": "protein-protein"
|
| 82 |
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}
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],
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"COLLECTIONS": "dynarepo",
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| 137 |
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| 140 |
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| 141 |
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| 146 |
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| 147 |
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| 148 |
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| 149 |
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| 150 |
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| 151 |
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| 152 |
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| 153 |
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| 154 |
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| 155 |
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|
| 156 |
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| 157 |
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| 158 |
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| 159 |
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|
| 160 |
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|
| 161 |
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"clusters_01_screenshot_19.jpg",
|
| 162 |
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"pocket_01.pdb",
|
| 163 |
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"pocket_02.pdb"
|
| 164 |
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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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|
| 169 |
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|
| 170 |
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|
| 171 |
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"fluctuation",
|
| 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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"sasa",
|
| 181 |
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"tmscores"
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| 182 |
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],
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| 183 |
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"mdIndex": 0,
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| 185 |
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"internalId": "684253ce86baaa8f38e031b9",
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| 187 |
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"creationDate": "2025-06-06T02:34:54.000Z",
|
| 188 |
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"identifier": "A008M"
|
| 189 |
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}
|
data/files/A008M/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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