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- data/files/A0056/project.json +345 -0
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data/files/A0056/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A0056",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3HG0",
|
| 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 |
+
"3HG0"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9G096",
|
| 31 |
+
"Q00420"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"NVVHKTGDETIAGKKTFTGNVEVNGSLTLPTKSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID",
|
| 38 |
+
"SDLGKKLLEAARAGQDDEVRILMANGADVNAEDKVGLTPLHLAAMNDHLEIVEVLLKNGADVNAIDAIGETPLHLVAMYGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKL",
|
| 39 |
+
"GGNVVHKTGDETIAGKKTFTGNVEVNGSLTLPTKSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPID",
|
| 40 |
+
"GNVVHKTGDETIAGKKTFTGNVEVNGSLTLPTKSWSGELGGGIILSLRKKGTTVEYSIGGEISSSILANSNLVNRSVPNEFCPRNRCSLVGHMVGGWNAFHIDIPSSGVCQWFGPTASSGTPRGTGTYPIDHHHHHH"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Lower baseplate protein N-terminal",
|
| 45 |
+
"Receptor-binding protein of phage tail base-plate Siphoviridae head",
|
| 46 |
+
"GA-binding protein subunit beta-1"
|
| 47 |
+
],
|
| 48 |
+
"FRAMESTEP": 0.1,
|
| 49 |
+
"TIMESTEP": 2,
|
| 50 |
+
"TEMP": 310,
|
| 51 |
+
"ENSEMBLE": "NPT",
|
| 52 |
+
"FF": [
|
| 53 |
+
"CHARMM36m"
|
| 54 |
+
],
|
| 55 |
+
"WAT": "TIP3P",
|
| 56 |
+
"BOXTYPE": "Dodecahedron",
|
| 57 |
+
"SYSTATS": 7710,
|
| 58 |
+
"SYSTRES": 523,
|
| 59 |
+
"PROTATS": 7710,
|
| 60 |
+
"PROTRES": 523,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
},
|
| 81 |
+
{
|
| 82 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain A-chain D interaction",
|
| 91 |
+
"agent_1": "chain A",
|
| 92 |
+
"agent_2": "chain D",
|
| 93 |
+
"selection_1": "chain A",
|
| 94 |
+
"selection_2": "chain D",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
},
|
| 97 |
+
{
|
| 98 |
+
"name": "chain B-chain C interaction",
|
| 99 |
+
"agent_1": "chain B",
|
| 100 |
+
"agent_2": "chain C",
|
| 101 |
+
"selection_1": "chain B",
|
| 102 |
+
"selection_2": "chain C",
|
| 103 |
+
"type": "protein-protein"
|
| 104 |
+
},
|
| 105 |
+
{
|
| 106 |
+
"name": "chain B-chain D interaction",
|
| 107 |
+
"agent_1": "chain B",
|
| 108 |
+
"agent_2": "chain D",
|
| 109 |
+
"selection_1": "chain B",
|
| 110 |
+
"selection_2": "chain D",
|
| 111 |
+
"type": "protein-protein"
|
| 112 |
+
},
|
| 113 |
+
{
|
| 114 |
+
"name": "chain C-chain D interaction",
|
| 115 |
+
"agent_1": "chain C",
|
| 116 |
+
"agent_2": "chain D",
|
| 117 |
+
"selection_1": "chain C",
|
| 118 |
+
"selection_2": "chain D",
|
| 119 |
+
"type": "protein-protein"
|
| 120 |
+
}
|
| 121 |
+
],
|
| 122 |
+
"PBC_SELECTION": null,
|
| 123 |
+
"CHAINNAMES": null,
|
| 124 |
+
"MEMBRANES": null,
|
| 125 |
+
"CUSTOMS": null,
|
| 126 |
+
"ORIENTATION": null,
|
| 127 |
+
"PTM": [],
|
| 128 |
+
"MULTIMERIC": null,
|
| 129 |
+
"COLLECTIONS": "dynarepo",
|
| 130 |
+
"WARNINGS": [],
|
| 131 |
+
"BOXSIZEX": 11.9719,
|
| 132 |
+
"BOXSIZEY": 11.9719,
|
| 133 |
+
"BOXSIZEZ": 8.445,
|
| 134 |
+
"mdName": "replica 1",
|
| 135 |
+
"mdAtoms": 7710,
|
| 136 |
+
"mdFrames": 5001
|
| 137 |
+
},
|
| 138 |
+
"mds": [
|
| 139 |
+
"replica 1",
|
| 140 |
+
"replica 2",
|
| 141 |
+
"replica 3"
|
| 142 |
+
],
|
| 143 |
+
"mdref": 0,
|
| 144 |
+
"files": [
|
| 145 |
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"topology.tpr",
|
| 146 |
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"screenshot.jpg",
|
| 147 |
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"trajectory.bin",
|
| 148 |
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"pca_trajectory_01.bin",
|
| 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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"structure.pdb",
|
| 158 |
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"trajectory.xtc",
|
| 159 |
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"clusters_00_screenshot_00.jpg",
|
| 160 |
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| 161 |
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| 162 |
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data/files/A0056/records.jsonl
ADDED
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data/files/A0057/project.json
ADDED
|
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|
| 1 |
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{
|
| 2 |
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"accession": "A0057",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 3HPW",
|
| 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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|
| 25 |
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"PDBIDS": [
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| 26 |
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"3HPW"
|
| 27 |
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],
|
| 28 |
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|
| 29 |
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"REFERENCES": [
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| 30 |
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|
| 31 |
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|
| 32 |
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],
|
| 33 |
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| 34 |
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| 35 |
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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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"Toxin CcdB",
|
| 43 |
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"Antitoxin CcdA",
|
| 44 |
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|
| 45 |
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"Interaction with CcdB"
|
| 46 |
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],
|
| 47 |
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| 48 |
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| 49 |
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| 50 |
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|
| 51 |
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"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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"WAT": "TIP3P",
|
| 55 |
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"BOXTYPE": "Dodecahedron",
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| 56 |
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| 58 |
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| 71 |
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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 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"name": "chain A-chain C interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain C",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain C",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "chain B-chain C interaction",
|
| 90 |
+
"agent_1": "chain B",
|
| 91 |
+
"agent_2": "chain C",
|
| 92 |
+
"selection_1": "chain B",
|
| 93 |
+
"selection_2": "chain C",
|
| 94 |
+
"type": "protein-protein"
|
| 95 |
+
}
|
| 96 |
+
],
|
| 97 |
+
"PBC_SELECTION": null,
|
| 98 |
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"CHAINNAMES": null,
|
| 99 |
+
"MEMBRANES": null,
|
| 100 |
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"CUSTOMS": null,
|
| 101 |
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|
| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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|
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|
| 110 |
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|
| 111 |
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|
| 112 |
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},
|
| 113 |
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"mds": [
|
| 114 |
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"replica 1",
|
| 115 |
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"replica 2",
|
| 116 |
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"replica 3"
|
| 117 |
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],
|
| 118 |
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"mdref": 0,
|
| 119 |
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|
| 120 |
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|
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| 123 |
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|
| 124 |
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|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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|
| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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"pca_trajectory_15.bin",
|
| 138 |
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"pca_trajectory_16.bin",
|
| 139 |
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"structure.pdb",
|
| 140 |
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"trajectory.xtc",
|
| 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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|
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|
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|
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|
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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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|
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"clusters_00_screenshot_15.jpg",
|
| 157 |
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"clusters_00_screenshot_16.jpg",
|
| 158 |
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"clusters_00_screenshot_17.jpg",
|
| 159 |
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"clusters_01_screenshot_00.jpg",
|
| 160 |
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"clusters_01_screenshot_01.jpg",
|
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|
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|
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"clusters_01_screenshot_04.jpg",
|
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|
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|
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"clusters_01_screenshot_07.jpg",
|
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|
| 168 |
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|
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|
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|
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|
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|
| 173 |
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"clusters_01_screenshot_14.jpg",
|
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"clusters_01_screenshot_15.jpg",
|
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|
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"clusters_01_screenshot_17.jpg",
|
| 177 |
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"clusters_01_screenshot_18.jpg",
|
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"clusters_01_screenshot_19.jpg",
|
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"clusters_01_screenshot_20.jpg",
|
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"clusters_01_screenshot_21.jpg",
|
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"clusters_01_screenshot_22.jpg",
|
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"clusters_01_screenshot_23.jpg",
|
| 183 |
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"clusters_02_screenshot_00.jpg",
|
| 184 |
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"clusters_02_screenshot_01.jpg",
|
| 185 |
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"clusters_02_screenshot_02.jpg",
|
| 186 |
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"clusters_02_screenshot_03.jpg",
|
| 187 |
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|
| 188 |
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|
| 189 |
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|
| 190 |
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"clusters_02_screenshot_07.jpg",
|
| 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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"clusters_02_screenshot_16.jpg",
|
| 200 |
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"clusters_02_screenshot_17.jpg",
|
| 201 |
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"clusters_02_screenshot_18.jpg",
|
| 202 |
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"clusters_02_screenshot_19.jpg",
|
| 203 |
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"clusters_03_screenshot_00.jpg",
|
| 204 |
+
"clusters_03_screenshot_01.jpg",
|
| 205 |
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"clusters_03_screenshot_02.jpg",
|
| 206 |
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"clusters_03_screenshot_03.jpg",
|
| 207 |
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"clusters_03_screenshot_04.jpg",
|
| 208 |
+
"clusters_03_screenshot_05.jpg",
|
| 209 |
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"clusters_03_screenshot_06.jpg",
|
| 210 |
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"clusters_03_screenshot_07.jpg",
|
| 211 |
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"clusters_03_screenshot_08.jpg",
|
| 212 |
+
"clusters_03_screenshot_09.jpg",
|
| 213 |
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"clusters_03_screenshot_10.jpg",
|
| 214 |
+
"clusters_03_screenshot_11.jpg",
|
| 215 |
+
"clusters_03_screenshot_12.jpg",
|
| 216 |
+
"clusters_03_screenshot_13.jpg",
|
| 217 |
+
"clusters_03_screenshot_14.jpg",
|
| 218 |
+
"clusters_03_screenshot_15.jpg",
|
| 219 |
+
"clusters_03_screenshot_16.jpg",
|
| 220 |
+
"clusters_03_screenshot_17.jpg",
|
| 221 |
+
"clusters_03_screenshot_18.jpg",
|
| 222 |
+
"pocket_01.pdb",
|
| 223 |
+
"pocket_02.pdb",
|
| 224 |
+
"pocket_03.pdb",
|
| 225 |
+
"pocket_04.pdb",
|
| 226 |
+
"pocket_05.pdb",
|
| 227 |
+
"pocket_06.pdb",
|
| 228 |
+
"pocket_07.pdb",
|
| 229 |
+
"pocket_08.pdb",
|
| 230 |
+
"pocket_09.pdb"
|
| 231 |
+
],
|
| 232 |
+
"analyses": [
|
| 233 |
+
"clusters",
|
| 234 |
+
"clusters-00",
|
| 235 |
+
"clusters-01",
|
| 236 |
+
"clusters-02",
|
| 237 |
+
"clusters-03",
|
| 238 |
+
"dist-perres",
|
| 239 |
+
"energies",
|
| 240 |
+
"fluctuation",
|
| 241 |
+
"hbonds",
|
| 242 |
+
"interactions",
|
| 243 |
+
"pca",
|
| 244 |
+
"pockets",
|
| 245 |
+
"rgyr",
|
| 246 |
+
"rmsd-pairwise",
|
| 247 |
+
"rmsd-perres",
|
| 248 |
+
"rmsds",
|
| 249 |
+
"sasa",
|
| 250 |
+
"tmscores"
|
| 251 |
+
],
|
| 252 |
+
"mdIndex": 0,
|
| 253 |
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"mdNumber": 1,
|
| 254 |
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"refframe": 0,
|
| 255 |
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"internalId": "6840fe1b2416c29d74991a8f",
|
| 256 |
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"creationDate": "2025-06-05T02:16:59.000Z",
|
| 257 |
+
"identifier": "A0057"
|
| 258 |
+
}
|
data/files/A0057/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
|
|
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|
|
|
|
| 1 |
+
{"project_identifier": "A0057", "accession": "A0057", "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 3HPW", "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": ["3HPW"], "FORCED_REFERENCES": null, "REFERENCES": 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| 1 |
+
{
|
| 2 |
+
"accession": "A0058",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3HTU",
|
| 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 |
+
"3HTU"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9BRG1",
|
| 31 |
+
"Q96FZ7"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GSRVTEQDKAILQLKQQRDKLRQYQKRIAQQLERE",
|
| 38 |
+
"RRPEEWGKLIYQWVSRSGQNNSVFTLYELTNGEDTEDEEFHGLDEATLLRALQALQQEHKAEIITVSDGRGVKFF"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Vacuolar protein-sorting-associated protein 25",
|
| 43 |
+
"Charged multivesicular body protein 6"
|
| 44 |
+
],
|
| 45 |
+
"FRAMESTEP": 0.1,
|
| 46 |
+
"TIMESTEP": 2,
|
| 47 |
+
"TEMP": 310,
|
| 48 |
+
"ENSEMBLE": "NPT",
|
| 49 |
+
"FF": [
|
| 50 |
+
"CHARMM36m"
|
| 51 |
+
],
|
| 52 |
+
"WAT": "TIP3P",
|
| 53 |
+
"BOXTYPE": "Dodecahedron",
|
| 54 |
+
"SYSTATS": 1820,
|
| 55 |
+
"SYSTRES": 110,
|
| 56 |
+
"PROTATS": 1820,
|
| 57 |
+
"PROTRES": 110,
|
| 58 |
+
"NUCLATS": 0,
|
| 59 |
+
"NUCLRES": 0,
|
| 60 |
+
"LIPIATS": 0,
|
| 61 |
+
"LIPIRES": 0,
|
| 62 |
+
"CARBATS": 0,
|
| 63 |
+
"CARBRES": 0,
|
| 64 |
+
"SOLVATS": 0,
|
| 65 |
+
"SOLVRES": 0,
|
| 66 |
+
"COUNCAT": 0,
|
| 67 |
+
"COUNANI": 0,
|
| 68 |
+
"COUNION": 0,
|
| 69 |
+
"INTERACTIONS": [
|
| 70 |
+
{
|
| 71 |
+
"name": "chain A-chain B interaction",
|
| 72 |
+
"agent_1": "chain A",
|
| 73 |
+
"agent_2": "chain B",
|
| 74 |
+
"selection_1": "chain A",
|
| 75 |
+
"selection_2": "chain B",
|
| 76 |
+
"type": "protein-protein"
|
| 77 |
+
}
|
| 78 |
+
],
|
| 79 |
+
"PBC_SELECTION": null,
|
| 80 |
+
"CHAINNAMES": null,
|
| 81 |
+
"MEMBRANES": null,
|
| 82 |
+
"CUSTOMS": null,
|
| 83 |
+
"ORIENTATION": null,
|
| 84 |
+
"PTM": [],
|
| 85 |
+
"MULTIMERIC": null,
|
| 86 |
+
"COLLECTIONS": "dynarepo",
|
| 87 |
+
"WARNINGS": [],
|
| 88 |
+
"BOXSIZEX": 8.03379,
|
| 89 |
+
"BOXSIZEY": 8.03379,
|
| 90 |
+
"BOXSIZEZ": 5.65359,
|
| 91 |
+
"mdName": "replica 1",
|
| 92 |
+
"mdAtoms": 1820,
|
| 93 |
+
"mdFrames": 5001
|
| 94 |
+
},
|
| 95 |
+
"mds": [
|
| 96 |
+
"replica 1",
|
| 97 |
+
"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
+
"mdref": 0,
|
| 101 |
+
"files": [
|
| 102 |
+
"topology.tpr",
|
| 103 |
+
"screenshot.jpg",
|
| 104 |
+
"trajectory.bin",
|
| 105 |
+
"pca_trajectory_01.bin",
|
| 106 |
+
"pca_trajectory_02.bin",
|
| 107 |
+
"pca_trajectory_03.bin",
|
| 108 |
+
"pca_trajectory_04.bin",
|
| 109 |
+
"pca_trajectory_05.bin",
|
| 110 |
+
"pca_trajectory_06.bin",
|
| 111 |
+
"pca_trajectory_07.bin",
|
| 112 |
+
"pca_trajectory_08.bin",
|
| 113 |
+
"pca_trajectory_09.bin",
|
| 114 |
+
"pca_trajectory_10.bin",
|
| 115 |
+
"pca_trajectory_11.bin",
|
| 116 |
+
"pca_trajectory_12.bin",
|
| 117 |
+
"structure.pdb",
|
| 118 |
+
"trajectory.xtc",
|
| 119 |
+
"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
+
"clusters_00_screenshot_02.jpg",
|
| 122 |
+
"clusters_00_screenshot_03.jpg",
|
| 123 |
+
"clusters_00_screenshot_04.jpg",
|
| 124 |
+
"clusters_00_screenshot_05.jpg",
|
| 125 |
+
"clusters_00_screenshot_06.jpg",
|
| 126 |
+
"clusters_00_screenshot_07.jpg",
|
| 127 |
+
"clusters_00_screenshot_08.jpg",
|
| 128 |
+
"clusters_00_screenshot_09.jpg",
|
| 129 |
+
"clusters_00_screenshot_10.jpg",
|
| 130 |
+
"clusters_00_screenshot_11.jpg",
|
| 131 |
+
"clusters_00_screenshot_12.jpg",
|
| 132 |
+
"clusters_00_screenshot_13.jpg",
|
| 133 |
+
"clusters_00_screenshot_14.jpg",
|
| 134 |
+
"clusters_00_screenshot_15.jpg",
|
| 135 |
+
"clusters_00_screenshot_16.jpg",
|
| 136 |
+
"clusters_00_screenshot_17.jpg",
|
| 137 |
+
"clusters_00_screenshot_18.jpg",
|
| 138 |
+
"clusters_00_screenshot_19.jpg",
|
| 139 |
+
"clusters_01_screenshot_00.jpg",
|
| 140 |
+
"clusters_01_screenshot_01.jpg",
|
| 141 |
+
"clusters_01_screenshot_02.jpg",
|
| 142 |
+
"clusters_01_screenshot_03.jpg",
|
| 143 |
+
"clusters_01_screenshot_04.jpg",
|
| 144 |
+
"clusters_01_screenshot_05.jpg",
|
| 145 |
+
"clusters_01_screenshot_06.jpg",
|
| 146 |
+
"clusters_01_screenshot_07.jpg",
|
| 147 |
+
"clusters_01_screenshot_08.jpg",
|
| 148 |
+
"clusters_01_screenshot_09.jpg",
|
| 149 |
+
"clusters_01_screenshot_10.jpg",
|
| 150 |
+
"clusters_01_screenshot_11.jpg",
|
| 151 |
+
"clusters_01_screenshot_12.jpg",
|
| 152 |
+
"clusters_01_screenshot_13.jpg",
|
| 153 |
+
"clusters_01_screenshot_14.jpg",
|
| 154 |
+
"clusters_01_screenshot_15.jpg",
|
| 155 |
+
"clusters_01_screenshot_16.jpg",
|
| 156 |
+
"clusters_01_screenshot_17.jpg",
|
| 157 |
+
"clusters_01_screenshot_18.jpg",
|
| 158 |
+
"clusters_01_screenshot_19.jpg",
|
| 159 |
+
"clusters_01_screenshot_20.jpg",
|
| 160 |
+
"clusters_01_screenshot_21.jpg",
|
| 161 |
+
"pocket_01.pdb",
|
| 162 |
+
"pocket_02.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": 0,
|
| 185 |
+
"internalId": "6840ff689c3871d470993255",
|
| 186 |
+
"creationDate": "2025-06-05T02:22:32.000Z",
|
| 187 |
+
"identifier": "A0058"
|
| 188 |
+
}
|
data/files/A0058/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A0058", "accession": "A0058", "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 3HTU", "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": ["3HTU"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9BRG1", "Q96FZ7"], 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data/files/A0059/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A0059",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3HUG",
|
| 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 |
+
"3HUG"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P9WGH5",
|
| 31 |
+
"P9WJ67"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"HHYAMWDAAYVLGALSAADRREFEAHLAGXPEXRGAVTELCGVPALLSQLDRDEVAAISESA",
|
| 38 |
+
"DHHYAMWDAAYVLGALSAADRREFEAHLAGXPEXRGAVTELCGVPALLSQLDRDEVAAISES",
|
| 39 |
+
"DPEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR",
|
| 40 |
+
"QSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"ECF RNA polymerase sigma factor SigL",
|
| 45 |
+
"Sigma-70 factor domain-4",
|
| 46 |
+
"Anti-sigma-L factor RslA"
|
| 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": 4263,
|
| 58 |
+
"SYSTRES": 281,
|
| 59 |
+
"PROTATS": 4263,
|
| 60 |
+
"PROTRES": 281,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
+
"NUCLRES": 0,
|
| 63 |
+
"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
+
"CARBATS": 0,
|
| 66 |
+
"CARBRES": 0,
|
| 67 |
+
"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
},
|
| 81 |
+
{
|
| 82 |
+
"name": "chain A-chain C interaction",
|
| 83 |
+
"agent_1": "chain A",
|
| 84 |
+
"agent_2": "chain C",
|
| 85 |
+
"selection_1": "chain A",
|
| 86 |
+
"selection_2": "chain C",
|
| 87 |
+
"type": "protein-protein"
|
| 88 |
+
},
|
| 89 |
+
{
|
| 90 |
+
"name": "chain A-chain D interaction",
|
| 91 |
+
"agent_1": "chain A",
|
| 92 |
+
"agent_2": "chain D",
|
| 93 |
+
"selection_1": "chain A",
|
| 94 |
+
"selection_2": "chain D",
|
| 95 |
+
"type": "protein-protein"
|
| 96 |
+
},
|
| 97 |
+
{
|
| 98 |
+
"name": "chain B-chain C interaction",
|
| 99 |
+
"agent_1": "chain B",
|
| 100 |
+
"agent_2": "chain C",
|
| 101 |
+
"selection_1": "chain B",
|
| 102 |
+
"selection_2": "chain C",
|
| 103 |
+
"type": "protein-protein"
|
| 104 |
+
},
|
| 105 |
+
{
|
| 106 |
+
"name": "chain B-chain D interaction",
|
| 107 |
+
"agent_1": "chain B",
|
| 108 |
+
"agent_2": "chain D",
|
| 109 |
+
"selection_1": "chain B",
|
| 110 |
+
"selection_2": "chain D",
|
| 111 |
+
"type": "protein-protein"
|
| 112 |
+
},
|
| 113 |
+
{
|
| 114 |
+
"name": "chain C-chain D interaction",
|
| 115 |
+
"agent_1": "chain C",
|
| 116 |
+
"agent_2": "chain D",
|
| 117 |
+
"selection_1": "chain C",
|
| 118 |
+
"selection_2": "chain D",
|
| 119 |
+
"type": "protein-protein"
|
| 120 |
+
}
|
| 121 |
+
],
|
| 122 |
+
"PBC_SELECTION": null,
|
| 123 |
+
"CHAINNAMES": null,
|
| 124 |
+
"MEMBRANES": null,
|
| 125 |
+
"CUSTOMS": null,
|
| 126 |
+
"ORIENTATION": null,
|
| 127 |
+
"PTM": [],
|
| 128 |
+
"MULTIMERIC": null,
|
| 129 |
+
"COLLECTIONS": "dynarepo",
|
| 130 |
+
"WARNINGS": [],
|
| 131 |
+
"BOXSIZEX": 8.33443,
|
| 132 |
+
"BOXSIZEY": 8.33443,
|
| 133 |
+
"BOXSIZEZ": 5.91382,
|
| 134 |
+
"mdName": "replica 1",
|
| 135 |
+
"mdAtoms": 4263,
|
| 136 |
+
"mdFrames": 5001
|
| 137 |
+
},
|
| 138 |
+
"mds": [
|
| 139 |
+
"replica 1",
|
| 140 |
+
"replica 2",
|
| 141 |
+
"replica 3"
|
| 142 |
+
],
|
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| 330 |
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| 331 |
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| 332 |
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|
| 336 |
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| 337 |
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|
| 338 |
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"tmscores"
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| 339 |
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],
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"creationDate": "2025-06-05T02:28:31.000Z",
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"identifier": "A0059"
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| 346 |
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}
|
data/files/A0059/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
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|
data/files/A005A/project.json
ADDED
|
@@ -0,0 +1,196 @@
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|
| 1 |
+
{
|
| 2 |
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"accession": "A005A",
|
| 3 |
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"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3IA3",
|
| 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 |
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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 |
+
"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"3IA3"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"Q9NZD4",
|
| 31 |
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"P69905"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL",
|
| 38 |
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"ALLKANKDLISAGLKEFSVLLNQQVFNDPLVSEEDMVTVVEDWMNFYINYYRQQVTGEPQERDKALQELRQELNTLANPFLAKYRDFLKS"
|
| 39 |
+
],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Alpha-hemoglobin-stabilizing protein",
|
| 43 |
+
"Hemoglobin subunit alpha",
|
| 44 |
+
"Globin",
|
| 45 |
+
"(Microbial infection) Cleavage; by N.americanus apr-2",
|
| 46 |
+
"Not glycated"
|
| 47 |
+
],
|
| 48 |
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"FRAMESTEP": 0.1,
|
| 49 |
+
"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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|
| 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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|
| 70 |
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|
| 71 |
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|
| 72 |
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|
| 73 |
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{
|
| 74 |
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"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"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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|
| 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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|
| 97 |
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},
|
| 98 |
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"mds": [
|
| 99 |
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"replica 1",
|
| 100 |
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"replica 2",
|
| 101 |
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"replica 3"
|
| 102 |
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|
| 103 |
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|
| 104 |
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"files": [
|
| 105 |
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|
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| 108 |
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"pca_trajectory_01.bin",
|
| 109 |
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"pca_trajectory_02.bin",
|
| 110 |
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"pca_trajectory_03.bin",
|
| 111 |
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"pca_trajectory_04.bin",
|
| 112 |
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"pca_trajectory_05.bin",
|
| 113 |
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"pca_trajectory_06.bin",
|
| 114 |
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"pca_trajectory_07.bin",
|
| 115 |
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"pca_trajectory_08.bin",
|
| 116 |
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"pca_trajectory_09.bin",
|
| 117 |
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|
| 118 |
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"pca_trajectory_11.bin",
|
| 119 |
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"pca_trajectory_12.bin",
|
| 120 |
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"pca_trajectory_13.bin",
|
| 121 |
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"pca_trajectory_14.bin",
|
| 122 |
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"pca_trajectory_15.bin",
|
| 123 |
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"structure.pdb",
|
| 124 |
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"trajectory.xtc",
|
| 125 |
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"clusters_00_screenshot_00.jpg",
|
| 126 |
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"clusters_00_screenshot_01.jpg",
|
| 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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"clusters_00_screenshot_09.jpg",
|
| 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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"clusters_00_screenshot_17.jpg",
|
| 143 |
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"clusters_00_screenshot_18.jpg",
|
| 144 |
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|
| 145 |
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"clusters_01_screenshot_00.jpg",
|
| 146 |
+
"clusters_01_screenshot_01.jpg",
|
| 147 |
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"clusters_01_screenshot_02.jpg",
|
| 148 |
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"clusters_01_screenshot_03.jpg",
|
| 149 |
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"clusters_01_screenshot_04.jpg",
|
| 150 |
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|
| 151 |
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|
| 152 |
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"clusters_01_screenshot_07.jpg",
|
| 153 |
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"clusters_01_screenshot_08.jpg",
|
| 154 |
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"clusters_01_screenshot_09.jpg",
|
| 155 |
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"clusters_01_screenshot_10.jpg",
|
| 156 |
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"clusters_01_screenshot_11.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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"clusters_01_screenshot_16.jpg",
|
| 162 |
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"clusters_01_screenshot_17.jpg",
|
| 163 |
+
"clusters_01_screenshot_18.jpg",
|
| 164 |
+
"clusters_01_screenshot_19.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb"
|
| 171 |
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],
|
| 172 |
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|
| 173 |
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"clusters",
|
| 174 |
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"clusters-00",
|
| 175 |
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"clusters-01",
|
| 176 |
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"dist-perres",
|
| 177 |
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"energies",
|
| 178 |
+
"fluctuation",
|
| 179 |
+
"hbonds",
|
| 180 |
+
"interactions",
|
| 181 |
+
"pca",
|
| 182 |
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"pockets",
|
| 183 |
+
"rgyr",
|
| 184 |
+
"rmsd-pairwise",
|
| 185 |
+
"rmsd-perres",
|
| 186 |
+
"rmsds",
|
| 187 |
+
"sasa",
|
| 188 |
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"tmscores"
|
| 189 |
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],
|
| 190 |
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"mdIndex": 0,
|
| 191 |
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|
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|
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|
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|
| 195 |
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"identifier": "A005A"
|
| 196 |
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}
|
data/files/A005A/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
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|
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|
| 1 |
+
{"project_identifier": "A005A", "accession": "A005A", "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 3IA3", "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": ["3IA3"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NZD4", "P69905"], 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data/files/A005B/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005B",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3IT8",
|
| 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 |
+
"3IT8"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01375",
|
| 31 |
+
"Q9DHW0"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"ITLKYNYTVTLKDDGLYDGVFYDHYNDQLVTKISYNHETRHGNVNFRADWFNISRSPHTPGNDYNFNFWYSLMKETLEEINKNDSTKTTSLSLITGCYETGLLFGSYGYVETANGPLARYHTGDKRFTKMTHKGFPKVGMLTVKNTLWKDVKAYLGGFEYMGCSLAILDYQKMAKGKIPKDTTPTVKVTGNELEDGNMTLECTVNSFYPPDVITKWIESEHFKGEYKYVNGRYYPEWGRKSNYEPGEPGFPWNIKKDKDANTYSLTDLVRTTSKMSSQPVCVVFHDTLEAQVYTCSEGC",
|
| 38 |
+
"RTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLLFAESGQVYFGIIAL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Tumor necrosis factor, membrane form",
|
| 43 |
+
"Tumor necrosis factor, soluble form",
|
| 44 |
+
"THD",
|
| 45 |
+
"Ig-like"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 21354,
|
| 57 |
+
"SYSTRES": 1353,
|
| 58 |
+
"PROTATS": 21354,
|
| 59 |
+
"PROTRES": 1353,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
+
"CARBATS": 0,
|
| 65 |
+
"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
+
"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"name": "chain A-chain C interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain C",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain C",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "chain A-chain D interaction",
|
| 90 |
+
"agent_1": "chain A",
|
| 91 |
+
"agent_2": "chain D",
|
| 92 |
+
"selection_1": "chain A",
|
| 93 |
+
"selection_2": "chain D",
|
| 94 |
+
"type": "protein-protein"
|
| 95 |
+
},
|
| 96 |
+
{
|
| 97 |
+
"name": "chain A-chain F interaction",
|
| 98 |
+
"agent_1": "chain A",
|
| 99 |
+
"agent_2": "chain F",
|
| 100 |
+
"selection_1": "chain A",
|
| 101 |
+
"selection_2": "chain E",
|
| 102 |
+
"type": "protein-protein"
|
| 103 |
+
},
|
| 104 |
+
{
|
| 105 |
+
"name": "chain B-chain C interaction",
|
| 106 |
+
"agent_1": "chain B",
|
| 107 |
+
"agent_2": "chain C",
|
| 108 |
+
"selection_1": "chain A",
|
| 109 |
+
"selection_2": "chain F",
|
| 110 |
+
"type": "protein-protein"
|
| 111 |
+
},
|
| 112 |
+
{
|
| 113 |
+
"name": "chain B-chain D interaction",
|
| 114 |
+
"agent_1": "chain B",
|
| 115 |
+
"agent_2": "chain D",
|
| 116 |
+
"selection_1": "chain B",
|
| 117 |
+
"selection_2": "chain C",
|
| 118 |
+
"type": "protein-protein"
|
| 119 |
+
},
|
| 120 |
+
{
|
| 121 |
+
"name": "chain B-chain E interaction",
|
| 122 |
+
"agent_1": "chain B",
|
| 123 |
+
"agent_2": "chain E",
|
| 124 |
+
"selection_1": "chain B",
|
| 125 |
+
"selection_2": "chain D",
|
| 126 |
+
"type": "protein-protein"
|
| 127 |
+
},
|
| 128 |
+
{
|
| 129 |
+
"name": "chain C-chain E interaction",
|
| 130 |
+
"agent_1": "chain C",
|
| 131 |
+
"agent_2": "chain E",
|
| 132 |
+
"selection_1": "chain B",
|
| 133 |
+
"selection_2": "chain E",
|
| 134 |
+
"type": "protein-protein"
|
| 135 |
+
},
|
| 136 |
+
{
|
| 137 |
+
"name": "chain C-chain F interaction",
|
| 138 |
+
"agent_1": "chain C",
|
| 139 |
+
"agent_2": "chain F",
|
| 140 |
+
"selection_1": "chain B",
|
| 141 |
+
"selection_2": "chain F",
|
| 142 |
+
"type": "protein-protein"
|
| 143 |
+
}
|
| 144 |
+
],
|
| 145 |
+
"PBC_SELECTION": null,
|
| 146 |
+
"CHAINNAMES": null,
|
| 147 |
+
"MEMBRANES": null,
|
| 148 |
+
"CUSTOMS": null,
|
| 149 |
+
"ORIENTATION": null,
|
| 150 |
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"PTM": [],
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data/files/A005B/records.jsonl
ADDED
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The diff for this file is too large to render.
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data/files/A005C/project.json
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@@ -0,0 +1,194 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A005C",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3K1R",
|
| 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 |
+
"3K1R"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9Y6N9",
|
| 31 |
+
"Q495M9"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"MDRKVAREFRHKVDFLIENDAEKDYLYDVLRMYHQTMDVAVLVGDLKLVINEPSRLPLFDAIRPLIPLKHQVEYDQLTPRRSRKLKEVRLDRLHPEGLGLSVRGGLEFGCGLFISHLIKGGQADSVGLQVGDEIVRINGYSISSCTHEEVINLIRTEKTVSIKVRHIGLIPVKSSPDEPLTWQYVDQFVSES",
|
| 38 |
+
"ETSPLETFLASLHMEDFAALLRQEKIDLEALMLCSDLDLRSISVPLGPREKILGAVRRRRQAMERPPALEDTEL"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Harmonin",
|
| 43 |
+
"PDZ 1",
|
| 44 |
+
"N-terminal domain",
|
| 45 |
+
"pre-mRNA splicing regulator USH1G",
|
| 46 |
+
"SAM"
|
| 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": 4314,
|
| 58 |
+
"SYSTRES": 266,
|
| 59 |
+
"PROTATS": 4314,
|
| 60 |
+
"PROTRES": 266,
|
| 61 |
+
"NUCLATS": 0,
|
| 62 |
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"NUCLRES": 0,
|
| 63 |
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"LIPIATS": 0,
|
| 64 |
+
"LIPIRES": 0,
|
| 65 |
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"CARBATS": 0,
|
| 66 |
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"CARBRES": 0,
|
| 67 |
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"SOLVATS": 0,
|
| 68 |
+
"SOLVRES": 0,
|
| 69 |
+
"COUNCAT": 0,
|
| 70 |
+
"COUNANI": 0,
|
| 71 |
+
"COUNION": 0,
|
| 72 |
+
"INTERACTIONS": [
|
| 73 |
+
{
|
| 74 |
+
"name": "chain A-chain B interaction",
|
| 75 |
+
"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
+
"selection_2": "chain B",
|
| 79 |
+
"type": "protein-protein"
|
| 80 |
+
}
|
| 81 |
+
],
|
| 82 |
+
"PBC_SELECTION": null,
|
| 83 |
+
"CHAINNAMES": null,
|
| 84 |
+
"MEMBRANES": null,
|
| 85 |
+
"CUSTOMS": null,
|
| 86 |
+
"ORIENTATION": null,
|
| 87 |
+
"PTM": [],
|
| 88 |
+
"MULTIMERIC": null,
|
| 89 |
+
"COLLECTIONS": "dynarepo",
|
| 90 |
+
"WARNINGS": [],
|
| 91 |
+
"BOXSIZEX": 10.3995,
|
| 92 |
+
"BOXSIZEY": 10.3995,
|
| 93 |
+
"BOXSIZEZ": 7.34743,
|
| 94 |
+
"mdName": "replica 1",
|
| 95 |
+
"mdAtoms": 4314,
|
| 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 |
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"pca_trajectory_04.bin",
|
| 112 |
+
"pca_trajectory_05.bin",
|
| 113 |
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"pca_trajectory_06.bin",
|
| 114 |
+
"pca_trajectory_07.bin",
|
| 115 |
+
"pca_trajectory_08.bin",
|
| 116 |
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"pca_trajectory_09.bin",
|
| 117 |
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"pca_trajectory_10.bin",
|
| 118 |
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"pca_trajectory_11.bin",
|
| 119 |
+
"pca_trajectory_12.bin",
|
| 120 |
+
"pca_trajectory_13.bin",
|
| 121 |
+
"structure.pdb",
|
| 122 |
+
"trajectory.xtc",
|
| 123 |
+
"clusters_00_screenshot_00.jpg",
|
| 124 |
+
"clusters_00_screenshot_01.jpg",
|
| 125 |
+
"clusters_00_screenshot_02.jpg",
|
| 126 |
+
"clusters_00_screenshot_03.jpg",
|
| 127 |
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"clusters_00_screenshot_04.jpg",
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| 128 |
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"clusters_00_screenshot_05.jpg",
|
| 129 |
+
"clusters_00_screenshot_06.jpg",
|
| 130 |
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"clusters_00_screenshot_07.jpg",
|
| 131 |
+
"clusters_00_screenshot_08.jpg",
|
| 132 |
+
"clusters_00_screenshot_09.jpg",
|
| 133 |
+
"clusters_00_screenshot_10.jpg",
|
| 134 |
+
"clusters_00_screenshot_11.jpg",
|
| 135 |
+
"clusters_00_screenshot_12.jpg",
|
| 136 |
+
"clusters_00_screenshot_13.jpg",
|
| 137 |
+
"clusters_00_screenshot_14.jpg",
|
| 138 |
+
"clusters_00_screenshot_15.jpg",
|
| 139 |
+
"clusters_00_screenshot_16.jpg",
|
| 140 |
+
"clusters_00_screenshot_17.jpg",
|
| 141 |
+
"clusters_00_screenshot_18.jpg",
|
| 142 |
+
"clusters_00_screenshot_19.jpg",
|
| 143 |
+
"clusters_00_screenshot_20.jpg",
|
| 144 |
+
"clusters_00_screenshot_21.jpg",
|
| 145 |
+
"clusters_00_screenshot_22.jpg",
|
| 146 |
+
"clusters_01_screenshot_00.jpg",
|
| 147 |
+
"clusters_01_screenshot_01.jpg",
|
| 148 |
+
"clusters_01_screenshot_02.jpg",
|
| 149 |
+
"clusters_01_screenshot_03.jpg",
|
| 150 |
+
"clusters_01_screenshot_04.jpg",
|
| 151 |
+
"clusters_01_screenshot_05.jpg",
|
| 152 |
+
"clusters_01_screenshot_06.jpg",
|
| 153 |
+
"clusters_01_screenshot_07.jpg",
|
| 154 |
+
"clusters_01_screenshot_08.jpg",
|
| 155 |
+
"clusters_01_screenshot_09.jpg",
|
| 156 |
+
"clusters_01_screenshot_10.jpg",
|
| 157 |
+
"clusters_01_screenshot_11.jpg",
|
| 158 |
+
"clusters_01_screenshot_12.jpg",
|
| 159 |
+
"clusters_01_screenshot_13.jpg",
|
| 160 |
+
"clusters_01_screenshot_14.jpg",
|
| 161 |
+
"clusters_01_screenshot_15.jpg",
|
| 162 |
+
"clusters_01_screenshot_16.jpg",
|
| 163 |
+
"clusters_01_screenshot_17.jpg",
|
| 164 |
+
"clusters_01_screenshot_18.jpg",
|
| 165 |
+
"clusters_01_screenshot_19.jpg",
|
| 166 |
+
"pocket_01.pdb",
|
| 167 |
+
"pocket_02.pdb",
|
| 168 |
+
"pocket_03.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
+
"clusters",
|
| 172 |
+
"clusters-00",
|
| 173 |
+
"clusters-01",
|
| 174 |
+
"dist-perres",
|
| 175 |
+
"energies",
|
| 176 |
+
"fluctuation",
|
| 177 |
+
"hbonds",
|
| 178 |
+
"interactions",
|
| 179 |
+
"pca",
|
| 180 |
+
"pockets",
|
| 181 |
+
"rgyr",
|
| 182 |
+
"rmsd-pairwise",
|
| 183 |
+
"rmsd-perres",
|
| 184 |
+
"rmsds",
|
| 185 |
+
"sasa",
|
| 186 |
+
"tmscores"
|
| 187 |
+
],
|
| 188 |
+
"mdIndex": 0,
|
| 189 |
+
"mdNumber": 1,
|
| 190 |
+
"refframe": 0,
|
| 191 |
+
"internalId": "68410b0a672b9b51ae0f19b4",
|
| 192 |
+
"creationDate": "2025-06-05T03:12:10.000Z",
|
| 193 |
+
"identifier": "A005C"
|
| 194 |
+
}
|
data/files/A005C/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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| 1 |
+
{"project_identifier": "A005C", "accession": "A005C", "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 3K1R", "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": ["3K1R"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9Y6N9", "Q495M9"], 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data/files/A005D/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005D",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3K2M",
|
| 6 |
+
"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",
|
| 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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"3K2M"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P00519",
|
| 31 |
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"P02751"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"GSSVSSVPTKLEVVAATPTSLLISWDAPMSSSSVYYYRITYGETGGNSPVQEFTVPYSSSTATISGLSPGVDYTITVYAWGEDSAGYMFMYSPISINYRTC",
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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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"Tyrosine-protein kinase ABL1",
|
| 43 |
+
"SH3",
|
| 44 |
+
"SH2",
|
| 45 |
+
"Fibronectin",
|
| 46 |
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"Fibronectin type-III 10",
|
| 47 |
+
"Fibronectin type-III 11",
|
| 48 |
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"Fibronectin type-III 12",
|
| 49 |
+
"Cell-attachment",
|
| 50 |
+
"Cell attachment site"
|
| 51 |
+
],
|
| 52 |
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"FRAMESTEP": 0.1,
|
| 53 |
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"TIMESTEP": 2,
|
| 54 |
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"TEMP": 310,
|
| 55 |
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"ENSEMBLE": "NPT",
|
| 56 |
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"FF": [
|
| 57 |
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"CHARMM36m"
|
| 58 |
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],
|
| 59 |
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"WAT": "TIP3P",
|
| 60 |
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"BOXTYPE": "Dodecahedron",
|
| 61 |
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"SYSTATS": 3051,
|
| 62 |
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"SYSTRES": 201,
|
| 63 |
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"PROTATS": 3051,
|
| 64 |
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"PROTRES": 201,
|
| 65 |
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"NUCLATS": 0,
|
| 66 |
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"NUCLRES": 0,
|
| 67 |
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"LIPIATS": 0,
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| 68 |
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"LIPIRES": 0,
|
| 69 |
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"CARBATS": 0,
|
| 70 |
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"CARBRES": 0,
|
| 71 |
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"SOLVATS": 0,
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| 72 |
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"SOLVRES": 0,
|
| 73 |
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"COUNCAT": 0,
|
| 74 |
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"COUNANI": 0,
|
| 75 |
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"COUNION": 0,
|
| 76 |
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"INTERACTIONS": [
|
| 77 |
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{
|
| 78 |
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"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
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}
|
| 85 |
+
],
|
| 86 |
+
"PBC_SELECTION": null,
|
| 87 |
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"CHAINNAMES": null,
|
| 88 |
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"MEMBRANES": null,
|
| 89 |
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"CUSTOMS": null,
|
| 90 |
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"ORIENTATION": null,
|
| 91 |
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"PTM": [],
|
| 92 |
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"MULTIMERIC": null,
|
| 93 |
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"COLLECTIONS": "dynarepo",
|
| 94 |
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"WARNINGS": [],
|
| 95 |
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"BOXSIZEX": 8.3966,
|
| 96 |
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"BOXSIZEY": 8.3966,
|
| 97 |
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"BOXSIZEZ": 5.92877,
|
| 98 |
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"mdName": "replica 1",
|
| 99 |
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"mdAtoms": 3051,
|
| 100 |
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"mdFrames": 5001
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| 101 |
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},
|
| 102 |
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"mds": [
|
| 103 |
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"replica 1",
|
| 104 |
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"replica 2",
|
| 105 |
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"replica 3"
|
| 106 |
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],
|
| 107 |
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"mdref": 0,
|
| 108 |
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"files": [
|
| 109 |
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"topology.tpr",
|
| 110 |
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"screenshot.jpg",
|
| 111 |
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"trajectory.bin",
|
| 112 |
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"pca_trajectory_01.bin",
|
| 113 |
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"pca_trajectory_02.bin",
|
| 114 |
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"pca_trajectory_03.bin",
|
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"clusters_01_screenshot_18.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb"
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],
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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": "68410cf3d5f6bca89496a30a",
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"creationDate": "2025-06-05T03:20:19.000Z",
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"identifier": "A005D"
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}
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data/files/A005D/records.jsonl
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{
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"accession": "A005E",
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"published": true,
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"metadata": {
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"NAME": "Dynarepo 3K6G",
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
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| 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 |
+
"3K6G"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q9NYB0",
|
| 31 |
+
"Q15554"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"TIGMMTLKAAFKTLSGAQDSEAAFAKLDQKDLV",
|
| 38 |
+
"VSQPEVGAAIKIIRQLMEKFNLDLSTVTQAFLKNSGELEATSAFLASGQRADGYPIWSRQDDIDLQKDDEDTREALVKKFGAQNVARRIEFRK"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Telomeric repeat-binding factor 2-interacting protein 1",
|
| 43 |
+
"Disordered",
|
| 44 |
+
"Nuclear localization signal",
|
| 45 |
+
"Telomeric repeat-binding factor 2"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 1979,
|
| 57 |
+
"SYSTRES": 126,
|
| 58 |
+
"PROTATS": 1979,
|
| 59 |
+
"PROTRES": 126,
|
| 60 |
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|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
|
| 63 |
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|
| 64 |
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|
| 65 |
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"CARBRES": 0,
|
| 66 |
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"SOLVATS": 0,
|
| 67 |
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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
"PBC_SELECTION": null,
|
| 82 |
+
"CHAINNAMES": null,
|
| 83 |
+
"MEMBRANES": null,
|
| 84 |
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"CUSTOMS": null,
|
| 85 |
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"ORIENTATION": null,
|
| 86 |
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"PTM": [],
|
| 87 |
+
"MULTIMERIC": null,
|
| 88 |
+
"COLLECTIONS": "dynarepo",
|
| 89 |
+
"WARNINGS": [],
|
| 90 |
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"BOXSIZEX": 7.37846,
|
| 91 |
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"BOXSIZEY": 7.37846,
|
| 92 |
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"BOXSIZEZ": 5.23351,
|
| 93 |
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"mdName": "replica 1",
|
| 94 |
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"mdAtoms": 1979,
|
| 95 |
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"mdFrames": 5001
|
| 96 |
+
},
|
| 97 |
+
"mds": [
|
| 98 |
+
"replica 1",
|
| 99 |
+
"replica 2",
|
| 100 |
+
"replica 3"
|
| 101 |
+
],
|
| 102 |
+
"mdref": 0,
|
| 103 |
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"files": [
|
| 104 |
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"topology.tpr",
|
| 105 |
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"screenshot.jpg",
|
| 106 |
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"trajectory.bin",
|
| 107 |
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"pca_trajectory_01.bin",
|
| 108 |
+
"pca_trajectory_02.bin",
|
| 109 |
+
"pca_trajectory_03.bin",
|
| 110 |
+
"pca_trajectory_04.bin",
|
| 111 |
+
"pca_trajectory_05.bin",
|
| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
+
"pca_trajectory_07.bin",
|
| 114 |
+
"pca_trajectory_08.bin",
|
| 115 |
+
"pca_trajectory_09.bin",
|
| 116 |
+
"pca_trajectory_10.bin",
|
| 117 |
+
"pca_trajectory_11.bin",
|
| 118 |
+
"pca_trajectory_12.bin",
|
| 119 |
+
"pca_trajectory_13.bin",
|
| 120 |
+
"pca_trajectory_14.bin",
|
| 121 |
+
"pca_trajectory_15.bin",
|
| 122 |
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"pca_trajectory_16.bin",
|
| 123 |
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"pca_trajectory_17.bin",
|
| 124 |
+
"pca_trajectory_18.bin",
|
| 125 |
+
"pca_trajectory_19.bin",
|
| 126 |
+
"pca_trajectory_20.bin",
|
| 127 |
+
"structure.pdb",
|
| 128 |
+
"trajectory.xtc",
|
| 129 |
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"clusters_00_screenshot_00.jpg",
|
| 130 |
+
"clusters_00_screenshot_01.jpg",
|
| 131 |
+
"clusters_00_screenshot_02.jpg",
|
| 132 |
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"clusters_00_screenshot_03.jpg",
|
| 133 |
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"clusters_00_screenshot_04.jpg",
|
| 134 |
+
"clusters_00_screenshot_05.jpg",
|
| 135 |
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"clusters_00_screenshot_06.jpg",
|
| 136 |
+
"clusters_00_screenshot_07.jpg",
|
| 137 |
+
"clusters_00_screenshot_08.jpg",
|
| 138 |
+
"clusters_00_screenshot_09.jpg",
|
| 139 |
+
"clusters_00_screenshot_10.jpg",
|
| 140 |
+
"clusters_00_screenshot_11.jpg",
|
| 141 |
+
"clusters_00_screenshot_12.jpg",
|
| 142 |
+
"clusters_00_screenshot_13.jpg",
|
| 143 |
+
"clusters_00_screenshot_14.jpg",
|
| 144 |
+
"clusters_00_screenshot_15.jpg",
|
| 145 |
+
"clusters_00_screenshot_16.jpg",
|
| 146 |
+
"clusters_00_screenshot_17.jpg",
|
| 147 |
+
"clusters_00_screenshot_18.jpg",
|
| 148 |
+
"clusters_00_screenshot_19.jpg",
|
| 149 |
+
"clusters_01_screenshot_00.jpg",
|
| 150 |
+
"clusters_01_screenshot_01.jpg",
|
| 151 |
+
"clusters_01_screenshot_02.jpg",
|
| 152 |
+
"clusters_01_screenshot_03.jpg",
|
| 153 |
+
"clusters_01_screenshot_04.jpg",
|
| 154 |
+
"clusters_01_screenshot_05.jpg",
|
| 155 |
+
"clusters_01_screenshot_06.jpg",
|
| 156 |
+
"clusters_01_screenshot_07.jpg",
|
| 157 |
+
"clusters_01_screenshot_08.jpg",
|
| 158 |
+
"clusters_01_screenshot_09.jpg",
|
| 159 |
+
"clusters_01_screenshot_10.jpg",
|
| 160 |
+
"clusters_01_screenshot_11.jpg",
|
| 161 |
+
"clusters_01_screenshot_12.jpg",
|
| 162 |
+
"clusters_01_screenshot_13.jpg",
|
| 163 |
+
"clusters_01_screenshot_14.jpg",
|
| 164 |
+
"clusters_01_screenshot_15.jpg",
|
| 165 |
+
"clusters_01_screenshot_16.jpg",
|
| 166 |
+
"clusters_01_screenshot_17.jpg",
|
| 167 |
+
"pocket_01.pdb",
|
| 168 |
+
"pocket_02.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
+
"clusters",
|
| 172 |
+
"clusters-00",
|
| 173 |
+
"clusters-01",
|
| 174 |
+
"dist-perres",
|
| 175 |
+
"energies",
|
| 176 |
+
"fluctuation",
|
| 177 |
+
"hbonds",
|
| 178 |
+
"interactions",
|
| 179 |
+
"pca",
|
| 180 |
+
"pockets",
|
| 181 |
+
"rgyr",
|
| 182 |
+
"rmsd-pairwise",
|
| 183 |
+
"rmsd-perres",
|
| 184 |
+
"rmsds",
|
| 185 |
+
"sasa",
|
| 186 |
+
"tmscores"
|
| 187 |
+
],
|
| 188 |
+
"mdIndex": 0,
|
| 189 |
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"mdNumber": 1,
|
| 190 |
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|
| 191 |
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|
| 192 |
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"creationDate": "2025-06-05T03:25:31.000Z",
|
| 193 |
+
"identifier": "A005E"
|
| 194 |
+
}
|
data/files/A005E/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005E", "accession": "A005E", "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 3K6G", "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": ["3K6G"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9NYB0", "Q15554"], 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data/files/A005F/project.json
ADDED
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| 1 |
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{
|
| 2 |
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"accession": "A005F",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 3K75",
|
| 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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],
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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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| 25 |
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|
| 26 |
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"3K75"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P18887",
|
| 31 |
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"P06766"
|
| 32 |
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],
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| 33 |
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|
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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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"DNA repair protein XRCC1",
|
| 43 |
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"DNA polymerase beta",
|
| 44 |
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"DNA-binding"
|
| 45 |
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],
|
| 46 |
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|
| 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": 6349,
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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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| 68 |
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| 69 |
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"COUNION": 0,
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| 70 |
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"INTERACTIONS": [
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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 |
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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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],
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| 80 |
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|
| 81 |
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| 83 |
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| 86 |
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| 87 |
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"COLLECTIONS": "dynarepo",
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| 88 |
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| 89 |
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| 90 |
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| 93 |
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},
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"mds": [
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| 97 |
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| 99 |
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|
| 100 |
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],
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| 101 |
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| 151 |
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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_15.jpg",
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"clusters_01_screenshot_16.jpg",
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"clusters_01_screenshot_18.jpg",
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"clusters_01_screenshot_19.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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| 166 |
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"pocket_04.pdb",
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| 167 |
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"pocket_05.pdb",
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| 168 |
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"pocket_06.pdb"
|
| 169 |
+
],
|
| 170 |
+
"analyses": [
|
| 171 |
+
"clusters",
|
| 172 |
+
"clusters-00",
|
| 173 |
+
"clusters-01",
|
| 174 |
+
"dist-perres",
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| 175 |
+
"energies",
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| 176 |
+
"fluctuation",
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| 177 |
+
"hbonds",
|
| 178 |
+
"interactions",
|
| 179 |
+
"pca",
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| 180 |
+
"pockets",
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| 181 |
+
"rgyr",
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| 182 |
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"rmsd-pairwise",
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| 183 |
+
"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": "68410fe4f671eb2879021607",
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"creationDate": "2025-06-05T03:32:52.000Z",
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+
"identifier": "A005F"
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}
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data/files/A005F/records.jsonl
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data/files/A005G/project.json
ADDED
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{
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"accession": "A005G",
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"published": true,
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"metadata": {
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| 5 |
+
"NAME": "Dynarepo 3K9M",
|
| 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 |
+
"3K9M"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P07858",
|
| 31 |
+
"P01040"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"LPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD",
|
| 38 |
+
"MIPGGLSEAKPATPEIQEIVDKVKPQLEEKTNETYGKLEAVQYKTQVVAGTNYYIKVRAGDNKYMHLKVFKSLPGQNEDLVLTGYQVDKNKDDELTGF"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Cathepsin B",
|
| 43 |
+
"Cathepsin B light chain",
|
| 44 |
+
"Cathepsin B heavy chain",
|
| 45 |
+
"Cystatin-A",
|
| 46 |
+
"Cystatin-A, N-terminally processed",
|
| 47 |
+
"Secondary area of contact",
|
| 48 |
+
"Reactive site"
|
| 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": 5304,
|
| 60 |
+
"SYSTRES": 352,
|
| 61 |
+
"PROTATS": 5304,
|
| 62 |
+
"PROTRES": 352,
|
| 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": 9.51914,
|
| 94 |
+
"BOXSIZEY": 9.51914,
|
| 95 |
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"BOXSIZEZ": 6.78236,
|
| 96 |
+
"mdName": "replica 1",
|
| 97 |
+
"mdAtoms": 5304,
|
| 98 |
+
"mdFrames": 5001
|
| 99 |
+
},
|
| 100 |
+
"mds": [
|
| 101 |
+
"replica 1",
|
| 102 |
+
"replica 2",
|
| 103 |
+
"replica 3"
|
| 104 |
+
],
|
| 105 |
+
"mdref": 0,
|
| 106 |
+
"files": [
|
| 107 |
+
"topology.tpr",
|
| 108 |
+
"screenshot.jpg",
|
| 109 |
+
"trajectory.bin",
|
| 110 |
+
"pca_trajectory_01.bin",
|
| 111 |
+
"pca_trajectory_02.bin",
|
| 112 |
+
"pca_trajectory_03.bin",
|
| 113 |
+
"pca_trajectory_04.bin",
|
| 114 |
+
"pca_trajectory_05.bin",
|
| 115 |
+
"pca_trajectory_06.bin",
|
| 116 |
+
"pca_trajectory_07.bin",
|
| 117 |
+
"pca_trajectory_08.bin",
|
| 118 |
+
"pca_trajectory_09.bin",
|
| 119 |
+
"pca_trajectory_10.bin",
|
| 120 |
+
"pca_trajectory_11.bin",
|
| 121 |
+
"pca_trajectory_12.bin",
|
| 122 |
+
"pca_trajectory_13.bin",
|
| 123 |
+
"pca_trajectory_14.bin",
|
| 124 |
+
"structure.pdb",
|
| 125 |
+
"trajectory.xtc",
|
| 126 |
+
"clusters_00_screenshot_00.jpg",
|
| 127 |
+
"clusters_00_screenshot_01.jpg",
|
| 128 |
+
"clusters_00_screenshot_02.jpg",
|
| 129 |
+
"clusters_00_screenshot_03.jpg",
|
| 130 |
+
"clusters_00_screenshot_04.jpg",
|
| 131 |
+
"clusters_00_screenshot_05.jpg",
|
| 132 |
+
"clusters_00_screenshot_06.jpg",
|
| 133 |
+
"clusters_00_screenshot_07.jpg",
|
| 134 |
+
"clusters_00_screenshot_08.jpg",
|
| 135 |
+
"clusters_00_screenshot_09.jpg",
|
| 136 |
+
"clusters_00_screenshot_10.jpg",
|
| 137 |
+
"clusters_00_screenshot_11.jpg",
|
| 138 |
+
"clusters_00_screenshot_12.jpg",
|
| 139 |
+
"clusters_00_screenshot_13.jpg",
|
| 140 |
+
"clusters_00_screenshot_14.jpg",
|
| 141 |
+
"clusters_00_screenshot_15.jpg",
|
| 142 |
+
"clusters_00_screenshot_16.jpg",
|
| 143 |
+
"clusters_00_screenshot_17.jpg",
|
| 144 |
+
"clusters_00_screenshot_18.jpg",
|
| 145 |
+
"clusters_00_screenshot_19.jpg",
|
| 146 |
+
"clusters_00_screenshot_20.jpg",
|
| 147 |
+
"clusters_01_screenshot_00.jpg",
|
| 148 |
+
"clusters_01_screenshot_01.jpg",
|
| 149 |
+
"clusters_01_screenshot_02.jpg",
|
| 150 |
+
"clusters_01_screenshot_03.jpg",
|
| 151 |
+
"clusters_01_screenshot_04.jpg",
|
| 152 |
+
"clusters_01_screenshot_05.jpg",
|
| 153 |
+
"clusters_01_screenshot_06.jpg",
|
| 154 |
+
"clusters_01_screenshot_07.jpg",
|
| 155 |
+
"clusters_01_screenshot_08.jpg",
|
| 156 |
+
"clusters_01_screenshot_09.jpg",
|
| 157 |
+
"clusters_01_screenshot_10.jpg",
|
| 158 |
+
"clusters_01_screenshot_11.jpg",
|
| 159 |
+
"clusters_01_screenshot_12.jpg",
|
| 160 |
+
"clusters_01_screenshot_13.jpg",
|
| 161 |
+
"clusters_01_screenshot_14.jpg",
|
| 162 |
+
"clusters_01_screenshot_15.jpg",
|
| 163 |
+
"clusters_01_screenshot_16.jpg",
|
| 164 |
+
"clusters_01_screenshot_17.jpg",
|
| 165 |
+
"pocket_01.pdb",
|
| 166 |
+
"pocket_02.pdb",
|
| 167 |
+
"pocket_03.pdb",
|
| 168 |
+
"pocket_04.pdb",
|
| 169 |
+
"pocket_05.pdb",
|
| 170 |
+
"pocket_06.pdb",
|
| 171 |
+
"pocket_07.pdb",
|
| 172 |
+
"pocket_08.pdb",
|
| 173 |
+
"pocket_09.pdb",
|
| 174 |
+
"pocket_10.pdb"
|
| 175 |
+
],
|
| 176 |
+
"analyses": [
|
| 177 |
+
"clusters",
|
| 178 |
+
"clusters-00",
|
| 179 |
+
"clusters-01",
|
| 180 |
+
"dist-perres",
|
| 181 |
+
"energies",
|
| 182 |
+
"fluctuation",
|
| 183 |
+
"hbonds",
|
| 184 |
+
"interactions",
|
| 185 |
+
"pca",
|
| 186 |
+
"pockets",
|
| 187 |
+
"rgyr",
|
| 188 |
+
"rmsd-pairwise",
|
| 189 |
+
"rmsd-perres",
|
| 190 |
+
"rmsds",
|
| 191 |
+
"sasa",
|
| 192 |
+
"tmscores"
|
| 193 |
+
],
|
| 194 |
+
"mdIndex": 0,
|
| 195 |
+
"mdNumber": 1,
|
| 196 |
+
"refframe": 0,
|
| 197 |
+
"internalId": "68411224dc6f84863699f306",
|
| 198 |
+
"creationDate": "2025-06-05T03:42:28.000Z",
|
| 199 |
+
"identifier": "A005G"
|
| 200 |
+
}
|
data/files/A005G/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005G", "accession": "A005G", "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 3K9M", "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": ["3K9M"], "FORCED_REFERENCES": null, "REFERENCES": ["P07858", "P01040"], 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data/files/A005H/project.json
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| 1 |
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{
|
| 2 |
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"accession": "A005H",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 3KNB",
|
| 6 |
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"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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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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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"3KNB"
|
| 27 |
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],
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| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"Q8WZ42",
|
| 31 |
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"O75147"
|
| 32 |
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],
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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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| 38 |
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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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"Titin",
|
| 43 |
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"Ig-like 152",
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| 44 |
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"Obscurin-like protein 1",
|
| 45 |
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"Ig-like 1",
|
| 46 |
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"Interaction with TTN"
|
| 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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],
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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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"SYSTATS": 2871,
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| 58 |
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"SYSTRES": 194,
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| 59 |
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| 60 |
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| 61 |
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| 62 |
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| 64 |
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| 65 |
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| 66 |
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| 67 |
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| 68 |
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| 69 |
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| 70 |
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|
| 71 |
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"COUNION": 0,
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| 72 |
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"INTERACTIONS": [
|
| 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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"PBC_SELECTION": null,
|
| 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": [],
|
| 91 |
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"BOXSIZEX": 7.94951,
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| 92 |
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| 93 |
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| 94 |
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| 95 |
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| 97 |
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},
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| 98 |
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"mds": [
|
| 99 |
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|
| 100 |
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"replica 2",
|
| 101 |
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|
| 102 |
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| 103 |
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| 104 |
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| 108 |
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| 109 |
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| 110 |
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| 111 |
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| 135 |
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"clusters_01_screenshot_17.jpg",
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"clusters_01_screenshot_18.jpg",
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"pocket_01.pdb",
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"pocket_02.pdb",
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"pocket_03.pdb",
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"pocket_04.pdb"
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],
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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": "684113f560a8c1eb227d6aad",
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"creationDate": "2025-06-05T03:50:13.000Z",
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"identifier": "A005H"
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}
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data/files/A005H/records.jsonl
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data/files/A005I/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A005I",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3KXF",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
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"3KXF"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01889",
|
| 31 |
+
"P61769",
|
| 32 |
+
"P01848",
|
| 33 |
+
"A0A5B9",
|
| 34 |
+
"P03206"
|
| 35 |
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],
|
| 36 |
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"INPUT_LIGANDS": null,
|
| 37 |
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"LIGANDS": [],
|
| 38 |
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"LIGANDNAMES": null,
|
| 39 |
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"PROTSEQ": [
|
| 40 |
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"GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYWDRNTAIFKANTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEARRAYLEGLCVEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP",
|
| 41 |
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"QKVTQAQTEISVVEDEDVTLDCVYETRDTTYYLFWYKQPPSGELVFLIRRNSFDEQNEISGRYSWNFQKSTSSFNFTITASQVVDSAVYFCALSGFYNTDKLIFGTGTRLQVFPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS",
|
| 42 |
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"LPEPLPQGQLTAY",
|
| 43 |
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"IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM",
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| 44 |
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"GVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASPGLAGEYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPEPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD"
|
| 45 |
+
],
|
| 46 |
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"NUCLSEQ": [],
|
| 47 |
+
"DOMAINS": [
|
| 48 |
+
"HLA class I histocompatibility antigen, B alpha chain",
|
| 49 |
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"Ig-like C1-type",
|
| 50 |
+
"Alpha-1",
|
| 51 |
+
"Alpha-2",
|
| 52 |
+
"Alpha-3",
|
| 53 |
+
"Connecting peptide",
|
| 54 |
+
"Bw6 motif",
|
| 55 |
+
"Beta-2-microglobulin",
|
| 56 |
+
"Beta-2-microglobulin form pI 5.3",
|
| 57 |
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"Ig-like C1-type",
|
| 58 |
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"T cell receptor alpha chain constant",
|
| 59 |
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"Ig-like C1-type",
|
| 60 |
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"Connecting peptide",
|
| 61 |
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"T cell receptor beta constant 2",
|
| 62 |
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"Ig-like C1-type",
|
| 63 |
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"Connecting peptide",
|
| 64 |
+
"Lytic switch protein BZLF1",
|
| 65 |
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"Transactivation"
|
| 66 |
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],
|
| 67 |
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"FRAMESTEP": 0.1,
|
| 68 |
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"TIMESTEP": 2,
|
| 69 |
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"TEMP": 310,
|
| 70 |
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"ENSEMBLE": "NPT",
|
| 71 |
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"FF": [
|
| 72 |
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"CHARMM36m"
|
| 73 |
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],
|
| 74 |
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"WAT": "TIP3P",
|
| 75 |
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"BOXTYPE": "Dodecahedron",
|
| 76 |
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"SYSTATS": 13083,
|
| 77 |
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|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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"NUCLRES": 0,
|
| 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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"COUNANI": 0,
|
| 90 |
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"COUNION": 0,
|
| 91 |
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"INTERACTIONS": [
|
| 92 |
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{
|
| 93 |
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"name": "chain A-chain B interaction",
|
| 94 |
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"agent_1": "chain A",
|
| 95 |
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"agent_2": "chain B",
|
| 96 |
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"selection_1": "chain A",
|
| 97 |
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"selection_2": "chain B",
|
| 98 |
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"type": "protein-protein"
|
| 99 |
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},
|
| 100 |
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{
|
| 101 |
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"name": "chain A-chain C interaction",
|
| 102 |
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"agent_1": "chain A",
|
| 103 |
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"agent_2": "chain C",
|
| 104 |
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"selection_1": "chain A",
|
| 105 |
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"selection_2": "chain C",
|
| 106 |
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"type": "protein-protein"
|
| 107 |
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},
|
| 108 |
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{
|
| 109 |
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"name": "chain A-chain D interaction",
|
| 110 |
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"agent_1": "chain A",
|
| 111 |
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|
| 112 |
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"selection_1": "chain A",
|
| 113 |
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"selection_2": "chain D",
|
| 114 |
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"type": "protein-protein"
|
| 115 |
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},
|
| 116 |
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{
|
| 117 |
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"name": "chain A-chain E interaction",
|
| 118 |
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"agent_1": "chain A",
|
| 119 |
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"agent_2": "chain E",
|
| 120 |
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"selection_1": "chain A",
|
| 121 |
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"selection_2": "chain E",
|
| 122 |
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"type": "protein-protein"
|
| 123 |
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},
|
| 124 |
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{
|
| 125 |
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"name": "chain C-chain D interaction",
|
| 126 |
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"agent_1": "chain C",
|
| 127 |
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"agent_2": "chain D",
|
| 128 |
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"selection_1": "chain B",
|
| 129 |
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"selection_2": "chain C",
|
| 130 |
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"type": "protein-protein"
|
| 131 |
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},
|
| 132 |
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{
|
| 133 |
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"name": "chain C-chain E interaction",
|
| 134 |
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"agent_1": "chain C",
|
| 135 |
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"agent_2": "chain E",
|
| 136 |
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"selection_1": "chain B",
|
| 137 |
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"selection_2": "chain D",
|
| 138 |
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"type": "protein-protein"
|
| 139 |
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},
|
| 140 |
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{
|
| 141 |
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"name": "chain D-chain E interaction",
|
| 142 |
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"agent_1": "chain D",
|
| 143 |
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"agent_2": "chain E",
|
| 144 |
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"selection_1": "chain B",
|
| 145 |
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|
| 146 |
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"type": "protein-protein"
|
| 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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|
| 156 |
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| 157 |
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|
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|
| 162 |
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"mdAtoms": 13083,
|
| 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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"mdref": 0,
|
| 171 |
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"files": [
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| 172 |
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| 173 |
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| 174 |
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|
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| 272 |
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|
| 273 |
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|
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|
| 275 |
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|
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"clusters_04_screenshot_05.jpg",
|
| 277 |
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|
| 278 |
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|
| 279 |
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|
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|
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|
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|
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|
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|
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|
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|
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| 305 |
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| 343 |
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| 344 |
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| 345 |
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|
| 346 |
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|
| 347 |
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|
| 348 |
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|
| 349 |
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|
| 350 |
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"clusters_07_screenshot_19.jpg",
|
| 351 |
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"pocket_01.pdb",
|
| 352 |
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"pocket_02.pdb",
|
| 353 |
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"pocket_03.pdb",
|
| 354 |
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"pocket_04.pdb",
|
| 355 |
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"pocket_05.pdb",
|
| 356 |
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"pocket_06.pdb",
|
| 357 |
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"pocket_07.pdb",
|
| 358 |
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"pocket_08.pdb",
|
| 359 |
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"pocket_09.pdb",
|
| 360 |
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"pocket_10.pdb"
|
| 361 |
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|
| 362 |
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|
| 363 |
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"clusters",
|
| 364 |
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|
| 365 |
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|
| 366 |
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|
| 367 |
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|
| 368 |
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|
| 369 |
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|
| 370 |
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|
| 371 |
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"clusters-07",
|
| 372 |
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|
| 373 |
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|
| 374 |
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|
| 375 |
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|
| 376 |
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|
| 377 |
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|
| 378 |
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|
| 379 |
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|
| 380 |
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"rmsd-pairwise",
|
| 381 |
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|
| 382 |
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"rmsds",
|
| 383 |
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"sasa",
|
| 384 |
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"tmscores"
|
| 385 |
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|
| 386 |
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|
| 391 |
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"identifier": "A005I"
|
| 392 |
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}
|
data/files/A005I/records.jsonl
ADDED
|
The diff for this file is too large to render.
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|
|
|
data/files/A005J/project.json
ADDED
|
@@ -0,0 +1,256 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005J",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3LK2",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"3LK2"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P13127",
|
| 31 |
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"P14315",
|
| 32 |
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"Q5VZK9"
|
| 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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"SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNKTGSGTMNLGGSLTRQMEKDETVSDSSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVNGL",
|
| 39 |
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|
| 40 |
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|
| 41 |
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],
|
| 42 |
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"NUCLSEQ": [],
|
| 43 |
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"DOMAINS": [
|
| 44 |
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"F-actin-capping protein subunit alpha-1",
|
| 45 |
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"F-actin-capping protein subunit beta isoforms 1 and 2",
|
| 46 |
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"F-actin-uncapping protein LRRC16A",
|
| 47 |
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"Disordered",
|
| 48 |
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"Inhibits capping activity of CAPZA2"
|
| 49 |
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],
|
| 50 |
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|
| 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 |
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"CHARMM36m"
|
| 56 |
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],
|
| 57 |
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"WAT": "TIP3P",
|
| 58 |
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"BOXTYPE": "Dodecahedron",
|
| 59 |
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"SYSTATS": 8667,
|
| 60 |
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"SYSTRES": 545,
|
| 61 |
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"PROTATS": 8667,
|
| 62 |
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"PROTRES": 545,
|
| 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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|
| 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 |
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"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,
|
| 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": [],
|
| 109 |
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"BOXSIZEX": 12.0635,
|
| 110 |
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"BOXSIZEY": 12.0635,
|
| 111 |
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|
| 112 |
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"mdName": "replica 1",
|
| 113 |
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|
| 114 |
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|
| 115 |
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},
|
| 116 |
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"mds": [
|
| 117 |
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"replica 1",
|
| 118 |
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|
| 119 |
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|
| 120 |
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],
|
| 121 |
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"mdref": 0,
|
| 122 |
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"files": [
|
| 123 |
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|
| 124 |
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"screenshot.jpg",
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"trajectory.bin",
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"pca_trajectory_01.bin",
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"pca_trajectory_02.bin",
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"pca_trajectory_11.bin",
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"pca_trajectory_12.bin",
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"structure.pdb",
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"trajectory.xtc",
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"clusters_00_screenshot_00.jpg",
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"clusters_03_screenshot_13.jpg",
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"clusters_03_screenshot_14.jpg",
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"clusters_03_screenshot_15.jpg",
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"clusters_03_screenshot_16.jpg",
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"clusters_03_screenshot_17.jpg",
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"clusters_03_screenshot_18.jpg",
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"clusters_03_screenshot_19.jpg",
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"clusters_03_screenshot_20.jpg",
|
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+
"clusters_03_screenshot_21.jpg",
|
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+
"pocket_01.pdb",
|
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+
"pocket_02.pdb",
|
| 221 |
+
"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",
|
| 228 |
+
"pocket_10.pdb"
|
| 229 |
+
],
|
| 230 |
+
"analyses": [
|
| 231 |
+
"clusters",
|
| 232 |
+
"clusters-00",
|
| 233 |
+
"clusters-01",
|
| 234 |
+
"clusters-02",
|
| 235 |
+
"clusters-03",
|
| 236 |
+
"dist-perres",
|
| 237 |
+
"energies",
|
| 238 |
+
"fluctuation",
|
| 239 |
+
"hbonds",
|
| 240 |
+
"interactions",
|
| 241 |
+
"pca",
|
| 242 |
+
"pockets",
|
| 243 |
+
"rgyr",
|
| 244 |
+
"rmsd-pairwise",
|
| 245 |
+
"rmsd-perres",
|
| 246 |
+
"rmsds",
|
| 247 |
+
"sasa",
|
| 248 |
+
"tmscores"
|
| 249 |
+
],
|
| 250 |
+
"mdIndex": 0,
|
| 251 |
+
"mdNumber": 1,
|
| 252 |
+
"refframe": 1,
|
| 253 |
+
"internalId": "68411a96ea17fcf453a76a29",
|
| 254 |
+
"creationDate": "2025-06-05T04:18:30.000Z",
|
| 255 |
+
"identifier": "A005J"
|
| 256 |
+
}
|
data/files/A005J/records.jsonl
ADDED
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{"project_identifier": "A005J", "accession": "A005J", "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 3LK2", "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": ["3LK2"], "FORCED_REFERENCES": null, "REFERENCES": 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data/files/A005K/project.json
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005K",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3NVQ",
|
| 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 |
+
"3NVQ"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O75326",
|
| 31 |
+
"O60486"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GHLRSGPRIFAVWKGHVGQDRVDFGQTEPHTVLFHEPGSSSVWVGGRGKVYLFDFPEGKNASVRTVNIGSTKGSCLDKRDCENYITLLERRSEGLLACGTNARHPSCWNLVNGTVVPLGEMRGYAPFSPDENSLVLFEGDEVYSTIRKQEYNGKIPRFRRIRGESELYTSDTVMQNPQFIKATIVHQDQAYDDKIYYFFREDNPDKNPEAPLNVSRVAQLCRGDQGGESSLSVSKWNTFLKAMLVCSDAATNKNFNRLQDVFLLPDPSGQWRDTRVYGVFSNPWNYSAVCVYSLGDIDKVFRTSSLKGYHSSLPNPRPGKCLPDQQPIPTETFQVADRHPEVAQRVEPMGPLKTPLFHSKYHYQKVAVHRMQASHGETFHVLYLTTDRGTIHKVVEPGEQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLYVSSQWEVSQVPLDLCEVYGGGCHGCLMSRDPYCGWDQGRCISIYSSERSVLQSINPAEPHKECPNPKPDKAPLQKVSLAPNSRYYLSCPMESRHATYSWRHKENVEQSCEPGHQSPNCILFIENLTAQQYGHYFCEAQEGSYFREAQHWQLLPED",
|
| 38 |
+
"ADEPVWRSEQAIGAIAASQEDGVFVASGSCLDQLDYSLEHSLSRLYRDQAGNCTEPVSLAPPARPRPGSSFSKLLLPYREGAAGLGGLLLTGWTFDRGACEVRPLGNLSRNSLRNGTEVVSCHPQGSTAGVVYRAGRNNRWYLAVAATYVLPEPETASRCNPAASDHDTAIALKDTEGRSLATQELGRLKLCEGAGSLHFVDAFLWNGSIYFPYYPYNYTSGAATGWPSMARIAQSTEVLFQGQASLDCGHGHPDGRRLLLSSSLVEALDVWAGVFSAAAGEGQERRSPTTTALCLFRMSEIQARAKRVSWDFKTAESHCKEGDQPERVQPIASSTLIHSDLTSVYGTVVMNRTVLFLGTGDGQLLKVILGENLTSNCPEVIYEIKEETPVFYKLVPDPVKNIYIYLTAGKEVRRIRVANCNKHKSCSECLTATDPHCGWCHSLQRCTFQGDCVHSENLENWLDISSGAKKCPG"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Semaphorin-7A",
|
| 43 |
+
"Sema",
|
| 44 |
+
"Ig-like C2-type",
|
| 45 |
+
"Interaction with integrins",
|
| 46 |
+
"Cell attachment site",
|
| 47 |
+
"Plexin-C1",
|
| 48 |
+
"Sema"
|
| 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": 32656,
|
| 60 |
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"SYSTRES": 2124,
|
| 61 |
+
"PROTATS": 32656,
|
| 62 |
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"PROTRES": 2124,
|
| 63 |
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"NUCLATS": 0,
|
| 64 |
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"NUCLRES": 0,
|
| 65 |
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"LIPIATS": 0,
|
| 66 |
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"LIPIRES": 0,
|
| 67 |
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"CARBATS": 0,
|
| 68 |
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"CARBRES": 0,
|
| 69 |
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"SOLVATS": 0,
|
| 70 |
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"SOLVRES": 0,
|
| 71 |
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"COUNCAT": 0,
|
| 72 |
+
"COUNANI": 0,
|
| 73 |
+
"COUNION": 0,
|
| 74 |
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"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 |
+
"name": "chain A-chain C interaction",
|
| 85 |
+
"agent_1": "chain A",
|
| 86 |
+
"agent_2": "chain C",
|
| 87 |
+
"selection_1": "chain A",
|
| 88 |
+
"selection_2": "chain C",
|
| 89 |
+
"type": "protein-protein"
|
| 90 |
+
},
|
| 91 |
+
{
|
| 92 |
+
"name": "chain C-chain D interaction",
|
| 93 |
+
"agent_1": "chain C",
|
| 94 |
+
"agent_2": "chain D",
|
| 95 |
+
"selection_1": "chain A",
|
| 96 |
+
"selection_2": "chain D",
|
| 97 |
+
"type": "protein-protein"
|
| 98 |
+
}
|
| 99 |
+
],
|
| 100 |
+
"PBC_SELECTION": null,
|
| 101 |
+
"CHAINNAMES": null,
|
| 102 |
+
"MEMBRANES": null,
|
| 103 |
+
"CUSTOMS": null,
|
| 104 |
+
"ORIENTATION": null,
|
| 105 |
+
"PTM": [],
|
| 106 |
+
"MULTIMERIC": null,
|
| 107 |
+
"COLLECTIONS": "dynarepo",
|
| 108 |
+
"WARNINGS": [],
|
| 109 |
+
"BOXSIZEX": 18.8379,
|
| 110 |
+
"BOXSIZEY": 18.8379,
|
| 111 |
+
"BOXSIZEZ": 13.3084,
|
| 112 |
+
"mdName": "replica 1",
|
| 113 |
+
"mdAtoms": 32656,
|
| 114 |
+
"mdFrames": 5001
|
| 115 |
+
},
|
| 116 |
+
"mds": [
|
| 117 |
+
"replica 1",
|
| 118 |
+
"replica 2",
|
| 119 |
+
"replica 3"
|
| 120 |
+
],
|
| 121 |
+
"mdref": 0,
|
| 122 |
+
"files": [
|
| 123 |
+
"topology.tpr",
|
| 124 |
+
"screenshot.jpg",
|
| 125 |
+
"trajectory.bin",
|
| 126 |
+
"pca_trajectory_01.bin",
|
| 127 |
+
"pca_trajectory_02.bin",
|
| 128 |
+
"pca_trajectory_03.bin",
|
| 129 |
+
"pca_trajectory_04.bin",
|
| 130 |
+
"pca_trajectory_05.bin",
|
| 131 |
+
"structure.pdb",
|
| 132 |
+
"trajectory.xtc",
|
| 133 |
+
"clusters_00_screenshot_00.jpg",
|
| 134 |
+
"clusters_00_screenshot_01.jpg",
|
| 135 |
+
"clusters_00_screenshot_02.jpg",
|
| 136 |
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"clusters_00_screenshot_03.jpg",
|
| 137 |
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"clusters_00_screenshot_04.jpg",
|
| 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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"clusters_00_screenshot_07.jpg",
|
| 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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"clusters_00_screenshot_10.jpg",
|
| 144 |
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"clusters_00_screenshot_11.jpg",
|
| 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_01_screenshot_00.jpg",
|
| 154 |
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"clusters_01_screenshot_01.jpg",
|
| 155 |
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"clusters_01_screenshot_02.jpg",
|
| 156 |
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"clusters_01_screenshot_03.jpg",
|
| 157 |
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"clusters_01_screenshot_04.jpg",
|
| 158 |
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"clusters_01_screenshot_05.jpg",
|
| 159 |
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"clusters_01_screenshot_06.jpg",
|
| 160 |
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"clusters_01_screenshot_07.jpg",
|
| 161 |
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"clusters_01_screenshot_08.jpg",
|
| 162 |
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"clusters_01_screenshot_09.jpg",
|
| 163 |
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"clusters_01_screenshot_10.jpg",
|
| 164 |
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"clusters_01_screenshot_11.jpg",
|
| 165 |
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"clusters_01_screenshot_12.jpg",
|
| 166 |
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"clusters_01_screenshot_13.jpg",
|
| 167 |
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"clusters_01_screenshot_14.jpg",
|
| 168 |
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"clusters_01_screenshot_15.jpg",
|
| 169 |
+
"clusters_01_screenshot_16.jpg",
|
| 170 |
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"clusters_01_screenshot_17.jpg",
|
| 171 |
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"clusters_01_screenshot_18.jpg",
|
| 172 |
+
"clusters_01_screenshot_19.jpg",
|
| 173 |
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"clusters_01_screenshot_20.jpg",
|
| 174 |
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"clusters_01_screenshot_21.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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"clusters_02_screenshot_05.jpg",
|
| 181 |
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"clusters_02_screenshot_06.jpg",
|
| 182 |
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"clusters_02_screenshot_07.jpg",
|
| 183 |
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"clusters_02_screenshot_08.jpg",
|
| 184 |
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"clusters_02_screenshot_09.jpg",
|
| 185 |
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"clusters_02_screenshot_10.jpg",
|
| 186 |
+
"clusters_02_screenshot_11.jpg",
|
| 187 |
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"clusters_02_screenshot_12.jpg",
|
| 188 |
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"clusters_02_screenshot_13.jpg",
|
| 189 |
+
"clusters_02_screenshot_14.jpg",
|
| 190 |
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"clusters_02_screenshot_15.jpg",
|
| 191 |
+
"clusters_02_screenshot_16.jpg",
|
| 192 |
+
"clusters_02_screenshot_17.jpg",
|
| 193 |
+
"clusters_02_screenshot_18.jpg",
|
| 194 |
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"clusters_02_screenshot_19.jpg",
|
| 195 |
+
"clusters_02_screenshot_20.jpg",
|
| 196 |
+
"clusters_02_screenshot_21.jpg",
|
| 197 |
+
"clusters_02_screenshot_22.jpg",
|
| 198 |
+
"clusters_03_screenshot_00.jpg",
|
| 199 |
+
"clusters_03_screenshot_01.jpg",
|
| 200 |
+
"clusters_03_screenshot_02.jpg",
|
| 201 |
+
"clusters_03_screenshot_03.jpg",
|
| 202 |
+
"clusters_03_screenshot_04.jpg",
|
| 203 |
+
"clusters_03_screenshot_05.jpg",
|
| 204 |
+
"clusters_03_screenshot_06.jpg",
|
| 205 |
+
"clusters_03_screenshot_07.jpg",
|
| 206 |
+
"clusters_03_screenshot_08.jpg",
|
| 207 |
+
"clusters_03_screenshot_09.jpg",
|
| 208 |
+
"clusters_03_screenshot_10.jpg",
|
| 209 |
+
"clusters_03_screenshot_11.jpg",
|
| 210 |
+
"clusters_03_screenshot_12.jpg",
|
| 211 |
+
"clusters_03_screenshot_13.jpg",
|
| 212 |
+
"clusters_03_screenshot_14.jpg",
|
| 213 |
+
"clusters_03_screenshot_15.jpg",
|
| 214 |
+
"clusters_03_screenshot_16.jpg",
|
| 215 |
+
"clusters_03_screenshot_17.jpg",
|
| 216 |
+
"pocket_01.pdb",
|
| 217 |
+
"pocket_02.pdb",
|
| 218 |
+
"pocket_03.pdb",
|
| 219 |
+
"pocket_04.pdb",
|
| 220 |
+
"pocket_05.pdb",
|
| 221 |
+
"pocket_06.pdb"
|
| 222 |
+
],
|
| 223 |
+
"analyses": [
|
| 224 |
+
"clusters",
|
| 225 |
+
"clusters-00",
|
| 226 |
+
"clusters-01",
|
| 227 |
+
"clusters-02",
|
| 228 |
+
"clusters-03",
|
| 229 |
+
"dist-perres",
|
| 230 |
+
"energies",
|
| 231 |
+
"fluctuation",
|
| 232 |
+
"hbonds",
|
| 233 |
+
"interactions",
|
| 234 |
+
"pca",
|
| 235 |
+
"pockets",
|
| 236 |
+
"rgyr",
|
| 237 |
+
"rmsd-pairwise",
|
| 238 |
+
"rmsd-perres",
|
| 239 |
+
"rmsds",
|
| 240 |
+
"sasa",
|
| 241 |
+
"tmscores"
|
| 242 |
+
],
|
| 243 |
+
"mdIndex": 0,
|
| 244 |
+
"mdNumber": 1,
|
| 245 |
+
"refframe": 0,
|
| 246 |
+
"internalId": "68412004840da755eba6027f",
|
| 247 |
+
"creationDate": "2025-06-05T04:41:40.000Z",
|
| 248 |
+
"identifier": "A005K"
|
| 249 |
+
}
|
data/files/A005K/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005K", "accession": "A005K", "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 3NVQ", "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": ["3NVQ"], "FORCED_REFERENCES": null, "REFERENCES": 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|
|
|
| 1 |
+
{
|
| 2 |
+
"accession": "A005L",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3O4O",
|
| 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 |
+
"3O4O"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P01584",
|
| 31 |
+
"P27930",
|
| 32 |
+
"Q9NPH3"
|
| 33 |
+
],
|
| 34 |
+
"INPUT_LIGANDS": null,
|
| 35 |
+
"LIGANDS": [],
|
| 36 |
+
"LIGANDNAMES": null,
|
| 37 |
+
"PROTSEQ": [
|
| 38 |
+
"CDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKFNYSTAHSAGLTLIWYWTRQDRDLEEPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTTYCSKVAFPLEVVQKDSCFNSPMKLPVHKLYIEYGIQRITCPNVDGYFPSSVKPTITWYMGCYKIQNFNNVIPEGMNLSFLIALISNNGNYTCVVTYPENGRTFHLTRTLTVKVVGSPKNAVPPVIHSPNDHVVYEKEPGEELLIPCTVYFSFLMDSRNEVWWTIDGKKPDDITIDVTINESISHSRTEDETRTQILSIKKVTSEDLKRSYVCHARSAKGEVAKAAK",
|
| 39 |
+
"APVRSLNCTLRDSQQKSLVMSGPYELKALHLQGQDMEQQVVFSMSFVQGEESNDKIPVALGLKEKNLYLSCVLKDDKPTLQLESVDPKNYPKKKMEKRFVFNKIEINNKLEFESAQFPNWYISTSQAENMPVFLGGTKGGQDITDFTMQFVS",
|
| 40 |
+
"CRFRGRHYKREFRLEGEPVALRCPQVPYWLWASVSPRINLTWHKNDSARTVPGEEETRMWAQDGALWLLPALQEDSGTYVCTTRNASYCDKMSIELRVFENTDAFLPFISYPQILTLSTSGVLVCPDLSEFTRDKTDVKIQWYKDSLLLDKDNEKFLSVRGTTHLLVHDVALEDAGYYRCVLTFAHEGQQYNITRSIELRIKKKKEETIPVIISPLKTISASLGSRLTIPCKVFLGTGTPLTTMLWWTANDTHIESAYPGGRVTEGPRQEYSENNENYIEVPLIFDPVTREDLHMDFKCVVHNTLSFQTLRTTVKE"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Interleukin-1 beta",
|
| 45 |
+
"Involved in interaction with TMED10 C-terminus",
|
| 46 |
+
"Involved in receptor binding",
|
| 47 |
+
"Important for interaction with integrin",
|
| 48 |
+
"Interleukin-1 receptor type 2, membrane form",
|
| 49 |
+
"Ig-like C2-type 1",
|
| 50 |
+
"Ig-like C2-type 2",
|
| 51 |
+
"Ig-like C2-type 3",
|
| 52 |
+
"Contains proteolytic cleavage site",
|
| 53 |
+
"Interleukin-1 receptor accessory protein",
|
| 54 |
+
"Ig-like C2-type 1",
|
| 55 |
+
"Ig-like C2-type 2",
|
| 56 |
+
"Ig-like C2-type 3",
|
| 57 |
+
"Essential for interaction with PTPRD"
|
| 58 |
+
],
|
| 59 |
+
"FRAMESTEP": 0.1,
|
| 60 |
+
"TIMESTEP": 2,
|
| 61 |
+
"TEMP": 310,
|
| 62 |
+
"ENSEMBLE": "NPT",
|
| 63 |
+
"FF": [
|
| 64 |
+
"CHARMM36m"
|
| 65 |
+
],
|
| 66 |
+
"WAT": "TIP3P",
|
| 67 |
+
"BOXTYPE": "Dodecahedron",
|
| 68 |
+
"SYSTATS": 12709,
|
| 69 |
+
"SYSTRES": 791,
|
| 70 |
+
"PROTATS": 12709,
|
| 71 |
+
"PROTRES": 791,
|
| 72 |
+
"NUCLATS": 0,
|
| 73 |
+
"NUCLRES": 0,
|
| 74 |
+
"LIPIATS": 0,
|
| 75 |
+
"LIPIRES": 0,
|
| 76 |
+
"CARBATS": 0,
|
| 77 |
+
"CARBRES": 0,
|
| 78 |
+
"SOLVATS": 0,
|
| 79 |
+
"SOLVRES": 0,
|
| 80 |
+
"COUNCAT": 0,
|
| 81 |
+
"COUNANI": 0,
|
| 82 |
+
"COUNION": 0,
|
| 83 |
+
"INTERACTIONS": [
|
| 84 |
+
{
|
| 85 |
+
"name": "chain A-chain B interaction",
|
| 86 |
+
"agent_1": "chain A",
|
| 87 |
+
"agent_2": "chain B",
|
| 88 |
+
"selection_1": "chain A",
|
| 89 |
+
"selection_2": "chain B",
|
| 90 |
+
"type": "protein-protein"
|
| 91 |
+
},
|
| 92 |
+
{
|
| 93 |
+
"name": "chain A-chain C interaction",
|
| 94 |
+
"agent_1": "chain A",
|
| 95 |
+
"agent_2": "chain C",
|
| 96 |
+
"selection_1": "chain A",
|
| 97 |
+
"selection_2": "chain C",
|
| 98 |
+
"type": "protein-protein"
|
| 99 |
+
},
|
| 100 |
+
{
|
| 101 |
+
"name": "chain B-chain C interaction",
|
| 102 |
+
"agent_1": "chain B",
|
| 103 |
+
"agent_2": "chain C",
|
| 104 |
+
"selection_1": "chain B",
|
| 105 |
+
"selection_2": "chain C",
|
| 106 |
+
"type": "protein-protein"
|
| 107 |
+
}
|
| 108 |
+
],
|
| 109 |
+
"PBC_SELECTION": null,
|
| 110 |
+
"CHAINNAMES": null,
|
| 111 |
+
"MEMBRANES": null,
|
| 112 |
+
"CUSTOMS": null,
|
| 113 |
+
"ORIENTATION": null,
|
| 114 |
+
"PTM": [],
|
| 115 |
+
"MULTIMERIC": null,
|
| 116 |
+
"COLLECTIONS": "dynarepo",
|
| 117 |
+
"WARNINGS": [],
|
| 118 |
+
"BOXSIZEX": 13.1186,
|
| 119 |
+
"BOXSIZEY": 13.1186,
|
| 120 |
+
"BOXSIZEZ": 9.28164,
|
| 121 |
+
"mdName": "replica 1",
|
| 122 |
+
"mdAtoms": 12709,
|
| 123 |
+
"mdFrames": 5001
|
| 124 |
+
},
|
| 125 |
+
"mds": [
|
| 126 |
+
"replica 1",
|
| 127 |
+
"replica 2",
|
| 128 |
+
"replica 3"
|
| 129 |
+
],
|
| 130 |
+
"mdref": 0,
|
| 131 |
+
"files": [
|
| 132 |
+
"topology.tpr",
|
| 133 |
+
"screenshot.jpg",
|
| 134 |
+
"trajectory.bin",
|
| 135 |
+
"pca_trajectory_01.bin",
|
| 136 |
+
"pca_trajectory_02.bin",
|
| 137 |
+
"pca_trajectory_03.bin",
|
| 138 |
+
"pca_trajectory_04.bin",
|
| 139 |
+
"pca_trajectory_05.bin",
|
| 140 |
+
"pca_trajectory_06.bin",
|
| 141 |
+
"structure.pdb",
|
| 142 |
+
"trajectory.xtc",
|
| 143 |
+
"clusters_00_screenshot_00.jpg",
|
| 144 |
+
"clusters_00_screenshot_01.jpg",
|
| 145 |
+
"clusters_00_screenshot_02.jpg",
|
| 146 |
+
"clusters_00_screenshot_03.jpg",
|
| 147 |
+
"clusters_00_screenshot_04.jpg",
|
| 148 |
+
"clusters_00_screenshot_05.jpg",
|
| 149 |
+
"clusters_00_screenshot_06.jpg",
|
| 150 |
+
"clusters_00_screenshot_07.jpg",
|
| 151 |
+
"clusters_00_screenshot_08.jpg",
|
| 152 |
+
"clusters_00_screenshot_09.jpg",
|
| 153 |
+
"clusters_00_screenshot_10.jpg",
|
| 154 |
+
"clusters_00_screenshot_11.jpg",
|
| 155 |
+
"clusters_00_screenshot_12.jpg",
|
| 156 |
+
"clusters_00_screenshot_13.jpg",
|
| 157 |
+
"clusters_00_screenshot_14.jpg",
|
| 158 |
+
"clusters_00_screenshot_15.jpg",
|
| 159 |
+
"clusters_00_screenshot_16.jpg",
|
| 160 |
+
"clusters_00_screenshot_17.jpg",
|
| 161 |
+
"clusters_00_screenshot_18.jpg",
|
| 162 |
+
"clusters_00_screenshot_19.jpg",
|
| 163 |
+
"clusters_01_screenshot_00.jpg",
|
| 164 |
+
"clusters_01_screenshot_01.jpg",
|
| 165 |
+
"clusters_01_screenshot_02.jpg",
|
| 166 |
+
"clusters_01_screenshot_03.jpg",
|
| 167 |
+
"clusters_01_screenshot_04.jpg",
|
| 168 |
+
"clusters_01_screenshot_05.jpg",
|
| 169 |
+
"clusters_01_screenshot_06.jpg",
|
| 170 |
+
"clusters_01_screenshot_07.jpg",
|
| 171 |
+
"clusters_01_screenshot_08.jpg",
|
| 172 |
+
"clusters_01_screenshot_09.jpg",
|
| 173 |
+
"clusters_01_screenshot_10.jpg",
|
| 174 |
+
"clusters_01_screenshot_11.jpg",
|
| 175 |
+
"clusters_01_screenshot_12.jpg",
|
| 176 |
+
"clusters_01_screenshot_13.jpg",
|
| 177 |
+
"clusters_01_screenshot_14.jpg",
|
| 178 |
+
"clusters_01_screenshot_15.jpg",
|
| 179 |
+
"clusters_01_screenshot_16.jpg",
|
| 180 |
+
"clusters_01_screenshot_17.jpg",
|
| 181 |
+
"clusters_01_screenshot_18.jpg",
|
| 182 |
+
"clusters_01_screenshot_19.jpg",
|
| 183 |
+
"clusters_02_screenshot_00.jpg",
|
| 184 |
+
"clusters_02_screenshot_01.jpg",
|
| 185 |
+
"clusters_02_screenshot_02.jpg",
|
| 186 |
+
"clusters_02_screenshot_03.jpg",
|
| 187 |
+
"clusters_02_screenshot_04.jpg",
|
| 188 |
+
"clusters_02_screenshot_05.jpg",
|
| 189 |
+
"clusters_02_screenshot_06.jpg",
|
| 190 |
+
"clusters_02_screenshot_07.jpg",
|
| 191 |
+
"clusters_02_screenshot_08.jpg",
|
| 192 |
+
"clusters_02_screenshot_09.jpg",
|
| 193 |
+
"clusters_02_screenshot_10.jpg",
|
| 194 |
+
"clusters_02_screenshot_11.jpg",
|
| 195 |
+
"clusters_02_screenshot_12.jpg",
|
| 196 |
+
"clusters_02_screenshot_13.jpg",
|
| 197 |
+
"clusters_02_screenshot_14.jpg",
|
| 198 |
+
"clusters_02_screenshot_15.jpg",
|
| 199 |
+
"clusters_02_screenshot_16.jpg",
|
| 200 |
+
"clusters_02_screenshot_17.jpg",
|
| 201 |
+
"clusters_02_screenshot_18.jpg",
|
| 202 |
+
"clusters_02_screenshot_19.jpg",
|
| 203 |
+
"clusters_02_screenshot_20.jpg",
|
| 204 |
+
"clusters_03_screenshot_00.jpg",
|
| 205 |
+
"clusters_03_screenshot_01.jpg",
|
| 206 |
+
"clusters_03_screenshot_02.jpg",
|
| 207 |
+
"clusters_03_screenshot_03.jpg",
|
| 208 |
+
"clusters_03_screenshot_04.jpg",
|
| 209 |
+
"clusters_03_screenshot_05.jpg",
|
| 210 |
+
"clusters_03_screenshot_06.jpg",
|
| 211 |
+
"clusters_03_screenshot_07.jpg",
|
| 212 |
+
"clusters_03_screenshot_08.jpg",
|
| 213 |
+
"clusters_03_screenshot_09.jpg",
|
| 214 |
+
"clusters_03_screenshot_10.jpg",
|
| 215 |
+
"clusters_03_screenshot_11.jpg",
|
| 216 |
+
"clusters_03_screenshot_12.jpg",
|
| 217 |
+
"clusters_03_screenshot_13.jpg",
|
| 218 |
+
"clusters_03_screenshot_14.jpg",
|
| 219 |
+
"clusters_03_screenshot_15.jpg",
|
| 220 |
+
"clusters_03_screenshot_16.jpg",
|
| 221 |
+
"clusters_03_screenshot_17.jpg",
|
| 222 |
+
"clusters_03_screenshot_18.jpg",
|
| 223 |
+
"clusters_03_screenshot_19.jpg",
|
| 224 |
+
"pocket_01.pdb",
|
| 225 |
+
"pocket_02.pdb",
|
| 226 |
+
"pocket_03.pdb",
|
| 227 |
+
"pocket_04.pdb",
|
| 228 |
+
"pocket_05.pdb",
|
| 229 |
+
"pocket_06.pdb"
|
| 230 |
+
],
|
| 231 |
+
"analyses": [
|
| 232 |
+
"mem-map",
|
| 233 |
+
"clusters",
|
| 234 |
+
"clusters-00",
|
| 235 |
+
"clusters-01",
|
| 236 |
+
"clusters-02",
|
| 237 |
+
"clusters-03",
|
| 238 |
+
"dist-perres",
|
| 239 |
+
"energies",
|
| 240 |
+
"fluctuation",
|
| 241 |
+
"hbonds",
|
| 242 |
+
"interactions",
|
| 243 |
+
"pca",
|
| 244 |
+
"pockets",
|
| 245 |
+
"rgyr",
|
| 246 |
+
"rmsd-pairwise",
|
| 247 |
+
"rmsd-perres",
|
| 248 |
+
"rmsds",
|
| 249 |
+
"sasa",
|
| 250 |
+
"tmscores"
|
| 251 |
+
],
|
| 252 |
+
"mdIndex": 0,
|
| 253 |
+
"mdNumber": 1,
|
| 254 |
+
"refframe": 0,
|
| 255 |
+
"internalId": "6841274042b52be2345f009c",
|
| 256 |
+
"creationDate": "2025-06-05T05:12:32.000Z",
|
| 257 |
+
"identifier": "A005L"
|
| 258 |
+
}
|
data/files/A005L/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005M",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3O6Q",
|
| 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 |
+
"3O6Q"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"O34853",
|
| 31 |
+
"O34800"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"DTREILEENNEMLHMYLNRLKTYQYLLKNEPIHVYYGSIDAYAEGIDKLLKTYADKMNLTASLCHYSTQADKDRLTEHMDDPADVQTRLDRKDVYYDQYGKVVLIPFTIETQNYVIKLTSDSIVTEFDYLLFTSLTSIYDLVLP",
|
| 38 |
+
"CEPRAAKPFKILKKRSTTSVASYQVSPHTARIFKENERLIDEY",
|
| 39 |
+
"CEPRAAKPFKILKKRSTTSVASYQVSPHTARIFKENERLIDEYK",
|
| 40 |
+
"TDTREILEENNEMLHMYLNRLKTYQYLLKNEPIHVYYGSIDAYAEGIDKLLKTYADKMNLTASLCHYSTQADKDRLTEHMDDPADVQTRLDRKDVYYDQYGKVVLIPFTIETQNYVIKLTSDSIVTEFDYLLFTSLTSIYDLVLP"
|
| 41 |
+
],
|
| 42 |
+
"NUCLSEQ": [],
|
| 43 |
+
"DOMAINS": [
|
| 44 |
+
"Stage II sporulation protein SA",
|
| 45 |
+
"Stage II sporulation protein SB"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 6194,
|
| 57 |
+
"SYSTRES": 376,
|
| 58 |
+
"PROTATS": 6194,
|
| 59 |
+
"PROTRES": 376,
|
| 60 |
+
"NUCLATS": 0,
|
| 61 |
+
"NUCLRES": 0,
|
| 62 |
+
"LIPIATS": 0,
|
| 63 |
+
"LIPIRES": 0,
|
| 64 |
+
"CARBATS": 0,
|
| 65 |
+
"CARBRES": 0,
|
| 66 |
+
"SOLVATS": 0,
|
| 67 |
+
"SOLVRES": 0,
|
| 68 |
+
"COUNCAT": 0,
|
| 69 |
+
"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"name": "chain A-chain C interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain C",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain C",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "chain A-chain D interaction",
|
| 90 |
+
"agent_1": "chain A",
|
| 91 |
+
"agent_2": "chain D",
|
| 92 |
+
"selection_1": "chain A",
|
| 93 |
+
"selection_2": "chain D",
|
| 94 |
+
"type": "protein-protein"
|
| 95 |
+
},
|
| 96 |
+
{
|
| 97 |
+
"name": "chain B-chain C interaction",
|
| 98 |
+
"agent_1": "chain B",
|
| 99 |
+
"agent_2": "chain C",
|
| 100 |
+
"selection_1": "chain B",
|
| 101 |
+
"selection_2": "chain C",
|
| 102 |
+
"type": "protein-protein"
|
| 103 |
+
},
|
| 104 |
+
{
|
| 105 |
+
"name": "chain B-chain D interaction",
|
| 106 |
+
"agent_1": "chain B",
|
| 107 |
+
"agent_2": "chain D",
|
| 108 |
+
"selection_1": "chain B",
|
| 109 |
+
"selection_2": "chain D",
|
| 110 |
+
"type": "protein-protein"
|
| 111 |
+
},
|
| 112 |
+
{
|
| 113 |
+
"name": "chain C-chain D interaction",
|
| 114 |
+
"agent_1": "chain C",
|
| 115 |
+
"agent_2": "chain D",
|
| 116 |
+
"selection_1": "chain C",
|
| 117 |
+
"selection_2": "chain D",
|
| 118 |
+
"type": "protein-protein"
|
| 119 |
+
}
|
| 120 |
+
],
|
| 121 |
+
"PBC_SELECTION": null,
|
| 122 |
+
"CHAINNAMES": null,
|
| 123 |
+
"MEMBRANES": null,
|
| 124 |
+
"CUSTOMS": null,
|
| 125 |
+
"ORIENTATION": null,
|
| 126 |
+
"PTM": [],
|
| 127 |
+
"MULTIMERIC": null,
|
| 128 |
+
"COLLECTIONS": "dynarepo",
|
| 129 |
+
"WARNINGS": [],
|
| 130 |
+
"BOXSIZEX": 9.48606,
|
| 131 |
+
"BOXSIZEY": 9.48606,
|
| 132 |
+
"BOXSIZEZ": 6.75086,
|
| 133 |
+
"mdName": "replica 1",
|
| 134 |
+
"mdAtoms": 6194,
|
| 135 |
+
"mdFrames": 5001
|
| 136 |
+
},
|
| 137 |
+
"mds": [
|
| 138 |
+
"replica 1",
|
| 139 |
+
"replica 2",
|
| 140 |
+
"replica 3"
|
| 141 |
+
],
|
| 142 |
+
"mdref": 0,
|
| 143 |
+
"files": [
|
| 144 |
+
"topology.tpr",
|
| 145 |
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"screenshot.jpg",
|
| 146 |
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"trajectory.bin",
|
| 147 |
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|
| 148 |
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| 149 |
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| 163 |
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|
| 164 |
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|
| 165 |
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"structure.pdb",
|
| 166 |
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|
| 167 |
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|
| 168 |
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|
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| 294 |
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| 295 |
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| 296 |
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| 297 |
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| 300 |
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"clusters_06_screenshot_18.jpg",
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| 302 |
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"pocket_01.pdb",
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| 303 |
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"pocket_02.pdb",
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| 304 |
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"pocket_03.pdb",
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| 305 |
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"pocket_04.pdb",
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| 306 |
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| 307 |
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|
| 308 |
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| 309 |
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|
| 310 |
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"pocket_09.pdb",
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| 311 |
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|
| 312 |
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| 314 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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data/files/A005M/records.jsonl
ADDED
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The diff for this file is too large to render.
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data/files/A005N/project.json
ADDED
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| 1 |
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{
|
| 2 |
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"accession": "A005N",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 3OAK",
|
| 6 |
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|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
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| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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| 20 |
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"LICENSE": "Apache License 2.0",
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| 24 |
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{
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|
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| 76 |
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|
| 159 |
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"clusters_01_screenshot_16.jpg",
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"clusters_01_screenshot_17.jpg",
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| 161 |
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"clusters_01_screenshot_18.jpg",
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| 162 |
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"pocket_01.pdb",
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| 163 |
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"pocket_02.pdb",
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"pocket_03.pdb",
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| 165 |
+
"pocket_04.pdb",
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| 166 |
+
"pocket_05.pdb",
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| 167 |
+
"pocket_06.pdb"
|
| 168 |
+
],
|
| 169 |
+
"analyses": [
|
| 170 |
+
"clusters",
|
| 171 |
+
"clusters-00",
|
| 172 |
+
"clusters-01",
|
| 173 |
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"dist-perres",
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| 174 |
+
"energies",
|
| 175 |
+
"fluctuation",
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| 176 |
+
"hbonds",
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| 177 |
+
"interactions",
|
| 178 |
+
"pca",
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| 179 |
+
"pockets",
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| 180 |
+
"rgyr",
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| 181 |
+
"rmsd-pairwise",
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| 182 |
+
"rmsd-perres",
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| 183 |
+
"rmsds",
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| 184 |
+
"sasa",
|
| 185 |
+
"tmscores"
|
| 186 |
+
],
|
| 187 |
+
"mdIndex": 0,
|
| 188 |
+
"mdNumber": 1,
|
| 189 |
+
"refframe": 0,
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| 190 |
+
"internalId": "68412c6983fa9b46f31901b4",
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| 191 |
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"creationDate": "2025-06-05T05:34:33.000Z",
|
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+
"identifier": "A005N"
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}
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data/files/A005N/records.jsonl
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data/files/A005O/project.json
ADDED
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| 1 |
+
{
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| 2 |
+
"accession": "A005O",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3OGO",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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|
| 23 |
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|
| 24 |
+
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|
| 25 |
+
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|
| 26 |
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"3OGO"
|
| 27 |
+
],
|
| 28 |
+
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|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P42212",
|
| 31 |
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"P0DOX5"
|
| 32 |
+
],
|
| 33 |
+
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|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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|
| 38 |
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"QVQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVSS"
|
| 39 |
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],
|
| 40 |
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"NUCLSEQ": [],
|
| 41 |
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"DOMAINS": [
|
| 42 |
+
"Green fluorescent protein",
|
| 43 |
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"Immunoglobulin gamma-1 heavy chain",
|
| 44 |
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"Ig-like 1",
|
| 45 |
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"Variable (V) domain, involved in antigen recognition"
|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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|
| 51 |
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|
| 52 |
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"CHARMM36m"
|
| 53 |
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],
|
| 54 |
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"WAT": "TIP3P",
|
| 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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|
| 70 |
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|
| 71 |
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"INTERACTIONS": [
|
| 72 |
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{
|
| 73 |
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"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
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}
|
| 80 |
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],
|
| 81 |
+
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|
| 82 |
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|
| 83 |
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|
| 84 |
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|
| 85 |
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| 86 |
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|
| 87 |
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|
| 88 |
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|
| 89 |
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|
| 90 |
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|
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| 92 |
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|
| 96 |
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},
|
| 97 |
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"mds": [
|
| 98 |
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"replica 1",
|
| 99 |
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"replica 2",
|
| 100 |
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"replica 3"
|
| 101 |
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],
|
| 102 |
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"mdref": 0,
|
| 103 |
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"files": [
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| 104 |
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| 105 |
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"screenshot.jpg",
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| 106 |
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"trajectory.bin",
|
| 107 |
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"pca_trajectory_01.bin",
|
| 108 |
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"pca_trajectory_02.bin",
|
| 109 |
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"pca_trajectory_03.bin",
|
| 110 |
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"pca_trajectory_04.bin",
|
| 111 |
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"pca_trajectory_05.bin",
|
| 112 |
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"pca_trajectory_06.bin",
|
| 113 |
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"structure.pdb",
|
| 114 |
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"trajectory.xtc",
|
| 115 |
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"clusters_00_screenshot_00.jpg",
|
| 116 |
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|
| 117 |
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"clusters_00_screenshot_02.jpg",
|
| 118 |
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|
| 119 |
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| 120 |
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| 121 |
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"clusters_00_screenshot_06.jpg",
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| 122 |
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"clusters_00_screenshot_07.jpg",
|
| 123 |
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|
| 124 |
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"clusters_00_screenshot_09.jpg",
|
| 125 |
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"clusters_00_screenshot_10.jpg",
|
| 126 |
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"clusters_00_screenshot_11.jpg",
|
| 127 |
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"clusters_00_screenshot_12.jpg",
|
| 128 |
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"clusters_00_screenshot_13.jpg",
|
| 129 |
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"clusters_00_screenshot_14.jpg",
|
| 130 |
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"clusters_00_screenshot_15.jpg",
|
| 131 |
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"clusters_00_screenshot_16.jpg",
|
| 132 |
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"clusters_00_screenshot_17.jpg",
|
| 133 |
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"clusters_00_screenshot_18.jpg",
|
| 134 |
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"clusters_00_screenshot_19.jpg",
|
| 135 |
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"clusters_00_screenshot_20.jpg",
|
| 136 |
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"clusters_01_screenshot_00.jpg",
|
| 137 |
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"clusters_01_screenshot_01.jpg",
|
| 138 |
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"clusters_01_screenshot_02.jpg",
|
| 139 |
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"clusters_01_screenshot_03.jpg",
|
| 140 |
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"clusters_01_screenshot_04.jpg",
|
| 141 |
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"clusters_01_screenshot_05.jpg",
|
| 142 |
+
"clusters_01_screenshot_06.jpg",
|
| 143 |
+
"clusters_01_screenshot_07.jpg",
|
| 144 |
+
"clusters_01_screenshot_08.jpg",
|
| 145 |
+
"clusters_01_screenshot_09.jpg",
|
| 146 |
+
"clusters_01_screenshot_10.jpg",
|
| 147 |
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"clusters_01_screenshot_11.jpg",
|
| 148 |
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"clusters_01_screenshot_12.jpg",
|
| 149 |
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"clusters_01_screenshot_13.jpg",
|
| 150 |
+
"clusters_01_screenshot_14.jpg",
|
| 151 |
+
"clusters_01_screenshot_15.jpg",
|
| 152 |
+
"clusters_01_screenshot_16.jpg",
|
| 153 |
+
"clusters_01_screenshot_17.jpg",
|
| 154 |
+
"clusters_01_screenshot_18.jpg",
|
| 155 |
+
"clusters_01_screenshot_19.jpg",
|
| 156 |
+
"clusters_01_screenshot_20.jpg"
|
| 157 |
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],
|
| 158 |
+
"analyses": [
|
| 159 |
+
"mem-map",
|
| 160 |
+
"clusters",
|
| 161 |
+
"clusters-00",
|
| 162 |
+
"clusters-01",
|
| 163 |
+
"dist-perres",
|
| 164 |
+
"energies",
|
| 165 |
+
"fluctuation",
|
| 166 |
+
"hbonds",
|
| 167 |
+
"interactions",
|
| 168 |
+
"pca",
|
| 169 |
+
"rgyr",
|
| 170 |
+
"rmsd-pairwise",
|
| 171 |
+
"rmsd-perres",
|
| 172 |
+
"rmsds",
|
| 173 |
+
"sasa",
|
| 174 |
+
"tmscores"
|
| 175 |
+
],
|
| 176 |
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"mdIndex": 0,
|
| 177 |
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"mdNumber": 1,
|
| 178 |
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|
| 179 |
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"internalId": "68412e65b8c430bbbadc48d3",
|
| 180 |
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"creationDate": "2025-06-05T05:43:01.000Z",
|
| 181 |
+
"identifier": "A005O"
|
| 182 |
+
}
|
data/files/A005O/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005O", "accession": "A005O", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 3OGO", "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": ["3OGO"], "FORCED_REFERENCES": null, "REFERENCES": ["P42212", "P0DOX5"], 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|
| 3 |
+
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| 1 |
+
{
|
| 2 |
+
"accession": "A005P",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3ONA",
|
| 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 |
+
"3ONA"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q7TDW8",
|
| 31 |
+
"P78423"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"CNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALT",
|
| 38 |
+
"GSFNSIDVEINMYPVNKTSCNSSIGSSSTISTSELTITLTHEDCTPVFIGDYYSVVDKLATSGFFTNDKVHQDLTTQCKINLEIKCNSGRESRQLTPTTKVYLMPHSETVTVVGDCLSNLDVYIVYANTDAIYSDMDVVAYHTSYILNVDHIPPNDCE"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Fractalkine",
|
| 43 |
+
"Processed fractalkine",
|
| 44 |
+
"Chemokine and involved in interaction with ITGAV:ITGB3 and ITGA4:ITGB1"
|
| 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": 3445,
|
| 56 |
+
"SYSTRES": 224,
|
| 57 |
+
"PROTATS": 3445,
|
| 58 |
+
"PROTRES": 224,
|
| 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": 8.35838,
|
| 90 |
+
"BOXSIZEY": 8.35838,
|
| 91 |
+
"BOXSIZEZ": 5.90241,
|
| 92 |
+
"mdName": "replica 1",
|
| 93 |
+
"mdAtoms": 3445,
|
| 94 |
+
"mdFrames": 5001
|
| 95 |
+
},
|
| 96 |
+
"mds": [
|
| 97 |
+
"replica 1",
|
| 98 |
+
"replica 2",
|
| 99 |
+
"replica 3"
|
| 100 |
+
],
|
| 101 |
+
"mdref": 0,
|
| 102 |
+
"files": [
|
| 103 |
+
"topology.tpr",
|
| 104 |
+
"screenshot.jpg",
|
| 105 |
+
"trajectory.bin",
|
| 106 |
+
"pca_trajectory_01.bin",
|
| 107 |
+
"pca_trajectory_02.bin",
|
| 108 |
+
"pca_trajectory_03.bin",
|
| 109 |
+
"pca_trajectory_04.bin",
|
| 110 |
+
"pca_trajectory_05.bin",
|
| 111 |
+
"pca_trajectory_06.bin",
|
| 112 |
+
"pca_trajectory_07.bin",
|
| 113 |
+
"pca_trajectory_08.bin",
|
| 114 |
+
"pca_trajectory_09.bin",
|
| 115 |
+
"pca_trajectory_10.bin",
|
| 116 |
+
"pca_trajectory_11.bin",
|
| 117 |
+
"pca_trajectory_12.bin",
|
| 118 |
+
"pca_trajectory_13.bin",
|
| 119 |
+
"pca_trajectory_14.bin",
|
| 120 |
+
"pca_trajectory_15.bin",
|
| 121 |
+
"pca_trajectory_16.bin",
|
| 122 |
+
"pca_trajectory_17.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_01_screenshot_00.jpg",
|
| 143 |
+
"clusters_01_screenshot_01.jpg",
|
| 144 |
+
"clusters_01_screenshot_02.jpg",
|
| 145 |
+
"clusters_01_screenshot_03.jpg",
|
| 146 |
+
"clusters_01_screenshot_04.jpg",
|
| 147 |
+
"clusters_01_screenshot_05.jpg",
|
| 148 |
+
"clusters_01_screenshot_06.jpg",
|
| 149 |
+
"clusters_01_screenshot_07.jpg",
|
| 150 |
+
"clusters_01_screenshot_08.jpg",
|
| 151 |
+
"clusters_01_screenshot_09.jpg",
|
| 152 |
+
"clusters_01_screenshot_10.jpg",
|
| 153 |
+
"clusters_01_screenshot_11.jpg",
|
| 154 |
+
"clusters_01_screenshot_12.jpg",
|
| 155 |
+
"clusters_01_screenshot_13.jpg",
|
| 156 |
+
"clusters_01_screenshot_14.jpg",
|
| 157 |
+
"clusters_01_screenshot_15.jpg",
|
| 158 |
+
"clusters_01_screenshot_16.jpg",
|
| 159 |
+
"clusters_01_screenshot_17.jpg",
|
| 160 |
+
"clusters_01_screenshot_18.jpg",
|
| 161 |
+
"clusters_01_screenshot_19.jpg",
|
| 162 |
+
"pocket_01.pdb",
|
| 163 |
+
"pocket_02.pdb",
|
| 164 |
+
"pocket_03.pdb",
|
| 165 |
+
"pocket_04.pdb",
|
| 166 |
+
"pocket_05.pdb",
|
| 167 |
+
"pocket_06.pdb",
|
| 168 |
+
"pocket_07.pdb",
|
| 169 |
+
"pocket_08.pdb",
|
| 170 |
+
"pocket_09.pdb",
|
| 171 |
+
"pocket_10.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": "6841302dd5c183614e856381",
|
| 195 |
+
"creationDate": "2025-06-05T05:50:37.000Z",
|
| 196 |
+
"identifier": "A005P"
|
| 197 |
+
}
|
data/files/A005P/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
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| 1 |
+
{"project_identifier": "A005P", "accession": "A005P", "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 3ONA", "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": ["3ONA"], "FORCED_REFERENCES": null, "REFERENCES": ["Q7TDW8", "P78423"], 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"CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.35838, "BOXSIZEY": 8.35838, "BOXSIZEZ": 5.90241, "mdName": "replica 1", "mdAtoms": 3445, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A005P/files/topology.tpr", "length": 1222292, "contentType": "application/octet-stream", "metadata": {"project": "6841302dd5c183614e856381", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A005P/files/screenshot.jpg", "length": 19713, "contentType": "application/octet-stream", "metadata": {"project": "6841302dd5c183614e856381", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A005P/files/trajectory.bin", "length": 206741340, "contentType": "application/octet-stream", "metadata": {"project": "6841302dd5c183614e856381", "md": 0, "frames": 5001, "atoms": 3445}}, {"name": "pca_trajectory_01.bin", "downloadUrl": 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| 3 |
+
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005Q",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3ONL",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "yasaman.karami@inria.fr",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"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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"3ONL"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P47160",
|
| 31 |
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"Q04338"
|
| 32 |
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],
|
| 33 |
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"INPUT_LIGANDS": null,
|
| 34 |
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"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
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"PROTSEQ": [
|
| 37 |
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"NYTEMEGKVREATNNEPWGASSTLMDQISQGTYNFREREEILSMIFRRFTEKAGSEWRQIYKALQLLDYLIKHGSERFIDDTRNSINLIRILETFHYIDSQGRDQGINVRTRVKALIELLSDDNKIRAERKKARET",
|
| 38 |
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"SVDPNYTEMEGKVREATNNEPWGASSTLMDQISQGTYNFREREEILSMIFRRFTEKAGSEWRQIYKALQLLDYLIKHGSERFIDDTRNSINLIRILETFHYIDSQGRDQGINVRTRVKALIELLSDDNKIRAERKKARET",
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| 39 |
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"SLLISYESDFKTTLEQAKASLAEAPSQPLSQRNTTLKHVEQQQDELFDLLDQMDVEVNNSIGDASERATYKAKLREWKKTIQSDIKRPLQSLVDS"
|
| 40 |
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],
|
| 41 |
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"NUCLSEQ": [],
|
| 42 |
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"DOMAINS": [
|
| 43 |
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"Epsin-3",
|
| 44 |
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"ENTH",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"t-SNARE VTI1"
|
| 47 |
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],
|
| 48 |
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"FRAMESTEP": 0.1,
|
| 49 |
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"TIMESTEP": 2,
|
| 50 |
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"TEMP": 310,
|
| 51 |
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"ENSEMBLE": "NPT",
|
| 52 |
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"FF": [
|
| 53 |
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"CHARMM36m"
|
| 54 |
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],
|
| 55 |
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"WAT": "TIP3P",
|
| 56 |
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"BOXTYPE": "Dodecahedron",
|
| 57 |
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"SYSTATS": 6089,
|
| 58 |
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"SYSTRES": 371,
|
| 59 |
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"PROTATS": 6089,
|
| 60 |
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"PROTRES": 371,
|
| 61 |
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"NUCLATS": 0,
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| 62 |
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"NUCLRES": 0,
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| 63 |
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"LIPIATS": 0,
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| 64 |
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| 65 |
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| 66 |
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| 67 |
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| 68 |
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| 69 |
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"COUNCAT": 0,
|
| 70 |
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"COUNANI": 0,
|
| 71 |
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"COUNION": 0,
|
| 72 |
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"INTERACTIONS": [
|
| 73 |
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{
|
| 74 |
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"name": "chain A-chain B interaction",
|
| 75 |
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"agent_1": "chain A",
|
| 76 |
+
"agent_2": "chain B",
|
| 77 |
+
"selection_1": "chain A",
|
| 78 |
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"selection_2": "chain B",
|
| 79 |
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"type": "protein-protein"
|
| 80 |
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},
|
| 81 |
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{
|
| 82 |
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"name": "chain A-chain C interaction",
|
| 83 |
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"agent_1": "chain A",
|
| 84 |
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"agent_2": "chain C",
|
| 85 |
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"selection_1": "chain A",
|
| 86 |
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"selection_2": "chain C",
|
| 87 |
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"type": "protein-protein"
|
| 88 |
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}
|
| 89 |
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],
|
| 90 |
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"PBC_SELECTION": null,
|
| 91 |
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"CHAINNAMES": null,
|
| 92 |
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|
| 93 |
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| 94 |
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| 95 |
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"PTM": [],
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| 96 |
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| 97 |
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"COLLECTIONS": "dynarepo",
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| 98 |
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"WARNINGS": [],
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| 99 |
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"BOXSIZEX": 10.9321,
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| 100 |
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"BOXSIZEY": 10.9321,
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| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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},
|
| 106 |
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"mds": [
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| 108 |
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|
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|
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|
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"clusters_01_screenshot_01.jpg",
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|
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|
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|
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|
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|
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|
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|
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|
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"clusters_02_screenshot_15.jpg",
|
| 184 |
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|
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"clusters_02_screenshot_17.jpg",
|
| 186 |
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"clusters_02_screenshot_18.jpg",
|
| 187 |
+
"pocket_01.pdb",
|
| 188 |
+
"pocket_02.pdb",
|
| 189 |
+
"pocket_03.pdb",
|
| 190 |
+
"pocket_04.pdb",
|
| 191 |
+
"pocket_05.pdb",
|
| 192 |
+
"pocket_06.pdb",
|
| 193 |
+
"pocket_07.pdb",
|
| 194 |
+
"pocket_08.pdb",
|
| 195 |
+
"pocket_09.pdb"
|
| 196 |
+
],
|
| 197 |
+
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|
| 198 |
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"clusters",
|
| 199 |
+
"clusters-00",
|
| 200 |
+
"clusters-01",
|
| 201 |
+
"clusters-02",
|
| 202 |
+
"dist-perres",
|
| 203 |
+
"energies",
|
| 204 |
+
"fluctuation",
|
| 205 |
+
"hbonds",
|
| 206 |
+
"interactions",
|
| 207 |
+
"pca",
|
| 208 |
+
"pockets",
|
| 209 |
+
"rgyr",
|
| 210 |
+
"rmsd-pairwise",
|
| 211 |
+
"rmsd-perres",
|
| 212 |
+
"rmsds",
|
| 213 |
+
"sasa",
|
| 214 |
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"tmscores"
|
| 215 |
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],
|
| 216 |
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"mdIndex": 0,
|
| 217 |
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"mdNumber": 1,
|
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|
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"internalId": "6841321239c46d9de5877a38",
|
| 220 |
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"creationDate": "2025-06-05T05:58:42.000Z",
|
| 221 |
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"identifier": "A005Q"
|
| 222 |
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}
|
data/files/A005Q/records.jsonl
ADDED
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data/files/A005R/project.json
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| 1 |
+
{
|
| 2 |
+
"accession": "A005R",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3ONW",
|
| 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 |
+
"3ONW"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P63096",
|
| 31 |
+
"O43566"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"REVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYLLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNN",
|
| 38 |
+
"IEGLVELLNRVQSSGAHDQRGLLRKEDLVLPEFLQ"
|
| 39 |
+
],
|
| 40 |
+
"NUCLSEQ": [],
|
| 41 |
+
"DOMAINS": [
|
| 42 |
+
"Guanine nucleotide-binding protein G(i) subunit alpha-1",
|
| 43 |
+
"G-alpha",
|
| 44 |
+
"G1 motif",
|
| 45 |
+
"G2 motif",
|
| 46 |
+
"G3 motif",
|
| 47 |
+
"G4 motif",
|
| 48 |
+
"G5 motif",
|
| 49 |
+
"Regulator of G-protein signaling 14",
|
| 50 |
+
"GoLoco",
|
| 51 |
+
"Disordered"
|
| 52 |
+
],
|
| 53 |
+
"FRAMESTEP": 0.1,
|
| 54 |
+
"TIMESTEP": 2,
|
| 55 |
+
"TEMP": 310,
|
| 56 |
+
"ENSEMBLE": "NPT",
|
| 57 |
+
"FF": [
|
| 58 |
+
"CHARMM36m"
|
| 59 |
+
],
|
| 60 |
+
"WAT": "TIP3P",
|
| 61 |
+
"BOXTYPE": "Dodecahedron",
|
| 62 |
+
"SYSTATS": 5638,
|
| 63 |
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"SYSTRES": 351,
|
| 64 |
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|
| 65 |
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"PROTRES": 351,
|
| 66 |
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"NUCLATS": 0,
|
| 67 |
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"NUCLRES": 0,
|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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"CARBRES": 0,
|
| 72 |
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|
| 73 |
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|
| 74 |
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|
| 75 |
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"COUNANI": 0,
|
| 76 |
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"COUNION": 0,
|
| 77 |
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"INTERACTIONS": [
|
| 78 |
+
{
|
| 79 |
+
"name": "chain A-chain B interaction",
|
| 80 |
+
"agent_1": "chain A",
|
| 81 |
+
"agent_2": "chain B",
|
| 82 |
+
"selection_1": "chain A",
|
| 83 |
+
"selection_2": "chain B",
|
| 84 |
+
"type": "protein-protein"
|
| 85 |
+
}
|
| 86 |
+
],
|
| 87 |
+
"PBC_SELECTION": null,
|
| 88 |
+
"CHAINNAMES": null,
|
| 89 |
+
"MEMBRANES": null,
|
| 90 |
+
"CUSTOMS": null,
|
| 91 |
+
"ORIENTATION": null,
|
| 92 |
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"PTM": [],
|
| 93 |
+
"MULTIMERIC": null,
|
| 94 |
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"COLLECTIONS": "dynarepo",
|
| 95 |
+
"WARNINGS": [],
|
| 96 |
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"BOXSIZEX": 9.24264,
|
| 97 |
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"BOXSIZEY": 9.24264,
|
| 98 |
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"BOXSIZEZ": 6.59642,
|
| 99 |
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"mdName": "replica 1",
|
| 100 |
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"mdAtoms": 5638,
|
| 101 |
+
"mdFrames": 5001
|
| 102 |
+
},
|
| 103 |
+
"mds": [
|
| 104 |
+
"replica 1",
|
| 105 |
+
"replica 2",
|
| 106 |
+
"replica 3"
|
| 107 |
+
],
|
| 108 |
+
"mdref": 0,
|
| 109 |
+
"files": [
|
| 110 |
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"topology.tpr",
|
| 111 |
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"screenshot.jpg",
|
| 112 |
+
"trajectory.bin",
|
| 113 |
+
"pca_trajectory_01.bin",
|
| 114 |
+
"pca_trajectory_02.bin",
|
| 115 |
+
"pca_trajectory_03.bin",
|
| 116 |
+
"pca_trajectory_04.bin",
|
| 117 |
+
"pca_trajectory_05.bin",
|
| 118 |
+
"pca_trajectory_06.bin",
|
| 119 |
+
"pca_trajectory_07.bin",
|
| 120 |
+
"pca_trajectory_08.bin",
|
| 121 |
+
"pca_trajectory_09.bin",
|
| 122 |
+
"pca_trajectory_10.bin",
|
| 123 |
+
"pca_trajectory_11.bin",
|
| 124 |
+
"pca_trajectory_12.bin",
|
| 125 |
+
"pca_trajectory_13.bin",
|
| 126 |
+
"pca_trajectory_14.bin",
|
| 127 |
+
"pca_trajectory_15.bin",
|
| 128 |
+
"pca_trajectory_16.bin",
|
| 129 |
+
"structure.pdb",
|
| 130 |
+
"trajectory.xtc",
|
| 131 |
+
"clusters_00_screenshot_00.jpg",
|
| 132 |
+
"clusters_00_screenshot_01.jpg",
|
| 133 |
+
"clusters_00_screenshot_02.jpg",
|
| 134 |
+
"clusters_00_screenshot_03.jpg",
|
| 135 |
+
"clusters_00_screenshot_04.jpg",
|
| 136 |
+
"clusters_00_screenshot_05.jpg",
|
| 137 |
+
"clusters_00_screenshot_06.jpg",
|
| 138 |
+
"clusters_00_screenshot_07.jpg",
|
| 139 |
+
"clusters_00_screenshot_08.jpg",
|
| 140 |
+
"clusters_00_screenshot_09.jpg",
|
| 141 |
+
"clusters_00_screenshot_10.jpg",
|
| 142 |
+
"clusters_00_screenshot_11.jpg",
|
| 143 |
+
"clusters_00_screenshot_12.jpg",
|
| 144 |
+
"clusters_00_screenshot_13.jpg",
|
| 145 |
+
"clusters_00_screenshot_14.jpg",
|
| 146 |
+
"clusters_00_screenshot_15.jpg",
|
| 147 |
+
"clusters_00_screenshot_16.jpg",
|
| 148 |
+
"clusters_00_screenshot_17.jpg",
|
| 149 |
+
"clusters_00_screenshot_18.jpg",
|
| 150 |
+
"clusters_00_screenshot_19.jpg",
|
| 151 |
+
"clusters_01_screenshot_00.jpg",
|
| 152 |
+
"clusters_01_screenshot_01.jpg",
|
| 153 |
+
"clusters_01_screenshot_02.jpg",
|
| 154 |
+
"clusters_01_screenshot_03.jpg",
|
| 155 |
+
"clusters_01_screenshot_04.jpg",
|
| 156 |
+
"clusters_01_screenshot_05.jpg",
|
| 157 |
+
"clusters_01_screenshot_06.jpg",
|
| 158 |
+
"clusters_01_screenshot_07.jpg",
|
| 159 |
+
"clusters_01_screenshot_08.jpg",
|
| 160 |
+
"clusters_01_screenshot_09.jpg",
|
| 161 |
+
"clusters_01_screenshot_10.jpg",
|
| 162 |
+
"clusters_01_screenshot_11.jpg",
|
| 163 |
+
"clusters_01_screenshot_12.jpg",
|
| 164 |
+
"clusters_01_screenshot_13.jpg",
|
| 165 |
+
"clusters_01_screenshot_14.jpg",
|
| 166 |
+
"clusters_01_screenshot_15.jpg",
|
| 167 |
+
"clusters_01_screenshot_16.jpg",
|
| 168 |
+
"clusters_01_screenshot_17.jpg",
|
| 169 |
+
"clusters_01_screenshot_18.jpg",
|
| 170 |
+
"pocket_01.pdb",
|
| 171 |
+
"pocket_02.pdb",
|
| 172 |
+
"pocket_03.pdb",
|
| 173 |
+
"pocket_04.pdb",
|
| 174 |
+
"pocket_05.pdb",
|
| 175 |
+
"pocket_06.pdb",
|
| 176 |
+
"pocket_07.pdb",
|
| 177 |
+
"pocket_08.pdb",
|
| 178 |
+
"pocket_09.pdb"
|
| 179 |
+
],
|
| 180 |
+
"analyses": [
|
| 181 |
+
"clusters",
|
| 182 |
+
"clusters-00",
|
| 183 |
+
"clusters-01",
|
| 184 |
+
"dist-perres",
|
| 185 |
+
"energies",
|
| 186 |
+
"fluctuation",
|
| 187 |
+
"hbonds",
|
| 188 |
+
"interactions",
|
| 189 |
+
"pca",
|
| 190 |
+
"pockets",
|
| 191 |
+
"rgyr",
|
| 192 |
+
"rmsd-pairwise",
|
| 193 |
+
"rmsd-perres",
|
| 194 |
+
"rmsds",
|
| 195 |
+
"sasa",
|
| 196 |
+
"tmscores"
|
| 197 |
+
],
|
| 198 |
+
"mdIndex": 0,
|
| 199 |
+
"mdNumber": 1,
|
| 200 |
+
"refframe": 0,
|
| 201 |
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"internalId": "68413458e07b99349fdfded5",
|
| 202 |
+
"creationDate": "2025-06-05T06:08:24.000Z",
|
| 203 |
+
"identifier": "A005R"
|
| 204 |
+
}
|
data/files/A005R/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A005R", "accession": "A005R", "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 3ONW", "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": ["3ONW"], "FORCED_REFERENCES": null, "REFERENCES": ["P63096", "O43566"], 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data/files/A005S/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005S",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3OWT",
|
| 6 |
+
"DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"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 |
+
"3OWT"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P11938",
|
| 31 |
+
"P06701"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
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"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"DFSNEDIYDNIDPDTISFPPKIATTDLFLPLFFHFGSTRQFMDKLHEVISGDYEPSQAEKLVQDLCDETGIRKNFSTSILTCLSGDLMVFPRYFLNMFKDNVNPPPNVPGIWTHDDDESLKSNDQEQIRKLVKKHGTGRMEMRKRFFE",
|
| 38 |
+
"KMIDFATLSKLKKKYQIILD",
|
| 39 |
+
"FSNEDIYDNIDPDTISFPPKIATTDLFLPLFFHFGSTRQFMDKLHEVISGDYEPSQAEKLVQDLCDETGIRKNFSTSILTCLSGDLMVFPRYFLNMFKDNVNPPPNVPGIWTHDDDESLKSNDQEQIRKLVKKHGTGRMEMRKRFFEK"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"DNA-binding protein RAP1",
|
| 44 |
+
"Activation domain",
|
| 45 |
+
"Regulatory protein SIR3"
|
| 46 |
+
],
|
| 47 |
+
"FRAMESTEP": 0.1,
|
| 48 |
+
"TIMESTEP": 2,
|
| 49 |
+
"TEMP": 310,
|
| 50 |
+
"ENSEMBLE": "NPT",
|
| 51 |
+
"FF": [
|
| 52 |
+
"CHARMM36m"
|
| 53 |
+
],
|
| 54 |
+
"WAT": "TIP3P",
|
| 55 |
+
"BOXTYPE": "Dodecahedron",
|
| 56 |
+
"SYSTATS": 5125,
|
| 57 |
+
"SYSTRES": 316,
|
| 58 |
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"PROTATS": 5125,
|
| 59 |
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"PROTRES": 316,
|
| 60 |
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"NUCLATS": 0,
|
| 61 |
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"NUCLRES": 0,
|
| 62 |
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"LIPIATS": 0,
|
| 63 |
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"LIPIRES": 0,
|
| 64 |
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"CARBATS": 0,
|
| 65 |
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"CARBRES": 0,
|
| 66 |
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"SOLVATS": 0,
|
| 67 |
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"SOLVRES": 0,
|
| 68 |
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"COUNCAT": 0,
|
| 69 |
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"COUNANI": 0,
|
| 70 |
+
"COUNION": 0,
|
| 71 |
+
"INTERACTIONS": [
|
| 72 |
+
{
|
| 73 |
+
"name": "chain A-chain B interaction",
|
| 74 |
+
"agent_1": "chain A",
|
| 75 |
+
"agent_2": "chain B",
|
| 76 |
+
"selection_1": "chain A",
|
| 77 |
+
"selection_2": "chain B",
|
| 78 |
+
"type": "protein-protein"
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"name": "chain A-chain C interaction",
|
| 82 |
+
"agent_1": "chain A",
|
| 83 |
+
"agent_2": "chain C",
|
| 84 |
+
"selection_1": "chain A",
|
| 85 |
+
"selection_2": "chain C",
|
| 86 |
+
"type": "protein-protein"
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "chain B-chain C interaction",
|
| 90 |
+
"agent_1": "chain B",
|
| 91 |
+
"agent_2": "chain C",
|
| 92 |
+
"selection_1": "chain B",
|
| 93 |
+
"selection_2": "chain C",
|
| 94 |
+
"type": "protein-protein"
|
| 95 |
+
}
|
| 96 |
+
],
|
| 97 |
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"PBC_SELECTION": null,
|
| 98 |
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"CHAINNAMES": null,
|
| 99 |
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"MEMBRANES": null,
|
| 100 |
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"CUSTOMS": null,
|
| 101 |
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"ORIENTATION": null,
|
| 102 |
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"PTM": [],
|
| 103 |
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"MULTIMERIC": null,
|
| 104 |
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"COLLECTIONS": "dynarepo",
|
| 105 |
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"WARNINGS": [],
|
| 106 |
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"BOXSIZEX": 9.88632,
|
| 107 |
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"BOXSIZEY": 9.88632,
|
| 108 |
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"BOXSIZEZ": 7.02756,
|
| 109 |
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"mdName": "replica 1",
|
| 110 |
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"mdAtoms": 5125,
|
| 111 |
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"mdFrames": 5001
|
| 112 |
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},
|
| 113 |
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"mds": [
|
| 114 |
+
"replica 1",
|
| 115 |
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"replica 2",
|
| 116 |
+
"replica 3"
|
| 117 |
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],
|
| 118 |
+
"mdref": 0,
|
| 119 |
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"files": [
|
| 120 |
+
"topology.tpr",
|
| 121 |
+
"screenshot.jpg",
|
| 122 |
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"trajectory.bin",
|
| 123 |
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"pca_trajectory_01.bin",
|
| 124 |
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"pca_trajectory_02.bin",
|
| 125 |
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"pca_trajectory_03.bin",
|
| 126 |
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"pca_trajectory_04.bin",
|
| 127 |
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"pca_trajectory_05.bin",
|
| 128 |
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"pca_trajectory_06.bin",
|
| 129 |
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"clusters_03_screenshot_19.jpg",
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"pocket_01.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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"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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|
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"identifier": "A005S"
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}
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data/files/A005S/records.jsonl
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data/files/A005T/project.json
ADDED
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A005T",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 3P8M",
|
| 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 |
+
"3P8M"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"Q96FJ2",
|
| 31 |
+
"P03069"
|
| 32 |
+
],
|
| 33 |
+
"INPUT_LIGANDS": null,
|
| 34 |
+
"LIGANDS": [],
|
| 35 |
+
"LIGANDNAMES": null,
|
| 36 |
+
"PROTSEQ": [
|
| 37 |
+
"GSVSRGTQTEGGSGMKQLEDKVEELLSKNYHLENEVARLKKLV",
|
| 38 |
+
"DRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG",
|
| 39 |
+
"SVSRGTQTEGGSGMKQLEDKVEELLSKNYHLENEVARLKKLV"
|
| 40 |
+
],
|
| 41 |
+
"NUCLSEQ": [],
|
| 42 |
+
"DOMAINS": [
|
| 43 |
+
"Dynein light chain 2, cytoplasmic",
|
| 44 |
+
"Interaction with myosin V motor complex",
|
| 45 |
+
"General control transcription factor GCN4",
|
| 46 |
+
"bZIP",
|
| 47 |
+
"Disordered",
|
| 48 |
+
"Basic motif",
|
| 49 |
+
"Leucine-zipper",
|
| 50 |
+
"Nuclear localization signal"
|
| 51 |
+
],
|
| 52 |
+
"FRAMESTEP": 0.1,
|
| 53 |
+
"TIMESTEP": 2,
|
| 54 |
+
"TEMP": 310,
|
| 55 |
+
"ENSEMBLE": "NPT",
|
| 56 |
+
"FF": [
|
| 57 |
+
"CHARMM36m"
|
| 58 |
+
],
|
| 59 |
+
"WAT": "TIP3P",
|
| 60 |
+
"BOXTYPE": "Dodecahedron",
|
| 61 |
+
"SYSTATS": 4161,
|
| 62 |
+
"SYSTRES": 259,
|
| 63 |
+
"PROTATS": 4161,
|
| 64 |
+
"PROTRES": 259,
|
| 65 |
+
"NUCLATS": 0,
|
| 66 |
+
"NUCLRES": 0,
|
| 67 |
+
"LIPIATS": 0,
|
| 68 |
+
"LIPIRES": 0,
|
| 69 |
+
"CARBATS": 0,
|
| 70 |
+
"CARBRES": 0,
|
| 71 |
+
"SOLVATS": 0,
|
| 72 |
+
"SOLVRES": 0,
|
| 73 |
+
"COUNCAT": 0,
|
| 74 |
+
"COUNANI": 0,
|
| 75 |
+
"COUNION": 0,
|
| 76 |
+
"INTERACTIONS": [
|
| 77 |
+
{
|
| 78 |
+
"name": "chain A-chain B interaction",
|
| 79 |
+
"agent_1": "chain A",
|
| 80 |
+
"agent_2": "chain B",
|
| 81 |
+
"selection_1": "chain A",
|
| 82 |
+
"selection_2": "chain B",
|
| 83 |
+
"type": "protein-protein"
|
| 84 |
+
},
|
| 85 |
+
{
|
| 86 |
+
"name": "chain A-chain C interaction",
|
| 87 |
+
"agent_1": "chain A",
|
| 88 |
+
"agent_2": "chain C",
|
| 89 |
+
"selection_1": "chain A",
|
| 90 |
+
"selection_2": "chain C",
|
| 91 |
+
"type": "protein-protein"
|
| 92 |
+
},
|
| 93 |
+
{
|
| 94 |
+
"name": "chain A-chain D interaction",
|
| 95 |
+
"agent_1": "chain A",
|
| 96 |
+
"agent_2": "chain D",
|
| 97 |
+
"selection_1": "chain A",
|
| 98 |
+
"selection_2": "chain D",
|
| 99 |
+
"type": "protein-protein"
|
| 100 |
+
},
|
| 101 |
+
{
|
| 102 |
+
"name": "chain B-chain C interaction",
|
| 103 |
+
"agent_1": "chain B",
|
| 104 |
+
"agent_2": "chain C",
|
| 105 |
+
"selection_1": "chain B",
|
| 106 |
+
"selection_2": "chain C",
|
| 107 |
+
"type": "protein-protein"
|
| 108 |
+
},
|
| 109 |
+
{
|
| 110 |
+
"name": "chain B-chain D interaction",
|
| 111 |
+
"agent_1": "chain B",
|
| 112 |
+
"agent_2": "chain D",
|
| 113 |
+
"selection_1": "chain B",
|
| 114 |
+
"selection_2": "chain D",
|
| 115 |
+
"type": "protein-protein"
|
| 116 |
+
},
|
| 117 |
+
{
|
| 118 |
+
"name": "chain C-chain D interaction",
|
| 119 |
+
"agent_1": "chain C",
|
| 120 |
+
"agent_2": "chain D",
|
| 121 |
+
"selection_1": "chain C",
|
| 122 |
+
"selection_2": "chain D",
|
| 123 |
+
"type": "protein-protein"
|
| 124 |
+
}
|
| 125 |
+
],
|
| 126 |
+
"PBC_SELECTION": null,
|
| 127 |
+
"CHAINNAMES": null,
|
| 128 |
+
"MEMBRANES": null,
|
| 129 |
+
"CUSTOMS": null,
|
| 130 |
+
"ORIENTATION": null,
|
| 131 |
+
"PTM": [],
|
| 132 |
+
"MULTIMERIC": null,
|
| 133 |
+
"COLLECTIONS": "dynarepo",
|
| 134 |
+
"WARNINGS": [],
|
| 135 |
+
"BOXSIZEX": 10.8841,
|
| 136 |
+
"BOXSIZEY": 10.8841,
|
| 137 |
+
"BOXSIZEZ": 7.71429,
|
| 138 |
+
"mdName": "replica 1",
|
| 139 |
+
"mdAtoms": 4161,
|
| 140 |
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"mdFrames": 5001
|
| 141 |
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},
|
| 142 |
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"mds": [
|
| 143 |
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"replica 1",
|
| 144 |
+
"replica 2",
|
| 145 |
+
"replica 3"
|
| 146 |
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],
|
| 147 |
+
"mdref": 0,
|
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data/files/A005T/records.jsonl
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data/files/A005U/project.json
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| 1 |
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{
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| 2 |
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| 5 |
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"NAME": "Dynarepo 3P9W",
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| 6 |
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| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
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| 12 |
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|
| 13 |
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|
| 14 |
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],
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| 15 |
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|
| 16 |
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"PROGRAM": "GROMACS",
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| 17 |
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| 18 |
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"TYPE": "trajectory",
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"METHOD": "Classical MD",
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"LICENSE": "Apache License 2.0",
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| 44 |
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],
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| 76 |
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| 77 |
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{
|
| 78 |
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"name": "chain A-chain B interaction",
|
| 79 |
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"agent_1": "chain A",
|
| 80 |
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"agent_2": "chain B",
|
| 81 |
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"selection_1": "chain A",
|
| 82 |
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"selection_2": "chain B",
|
| 83 |
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"type": "protein-protein"
|
| 84 |
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|
| 85 |
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|
| 86 |
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|
| 87 |
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|
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| 91 |
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|
| 92 |
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|
| 106 |
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| 107 |
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| 108 |
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| 113 |
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|
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|
| 115 |
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|
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|
| 118 |
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|
| 119 |
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|
| 120 |
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|
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|
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| 147 |
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|
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|
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| 151 |
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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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"clusters_01_screenshot_20.jpg",
|
| 163 |
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"pocket_01.pdb"
|
| 164 |
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|
| 165 |
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|
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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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|
| 171 |
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"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 |
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"rmsd-perres",
|
| 179 |
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"rmsds",
|
| 180 |
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|
| 181 |
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|
| 182 |
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|
| 188 |
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"identifier": "A005U"
|
| 189 |
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|
data/files/A005U/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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