Tonic commited on
Commit
5e4b1c1
·
verified ·
1 Parent(s): 1967e7b

Add files using upload-large-folder tool

Browse files
This view is limited to 50 files because it contains too many changes.   See raw diff
.gitattributes CHANGED
@@ -57,3 +57,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
57
  # Video files - compressed
58
  *.mp4 filter=lfs diff=lfs merge=lfs -text
59
  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
57
  # Video files - compressed
58
  *.mp4 filter=lfs diff=lfs merge=lfs -text
59
  *.webm filter=lfs diff=lfs merge=lfs -text
60
+ all_records.jsonl filter=lfs diff=lfs merge=lfs -text
A000D/project.json ADDED
@@ -0,0 +1,191 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A000D",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1AY7",
6
+ "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns",
7
+ "AUTHORS": [
8
+ "Omid Mokhtari",
9
+ "Hamed Khakzad",
10
+ "Yasaman Karami"
11
+ ],
12
+ "GROUPS": [
13
+ "Delta team, Inria center at the University of Lorraine"
14
+ ],
15
+ "CONTACT": "yasaman.karami@inria.fr",
16
+ "PROGRAM": "GROMACS",
17
+ "VERSION": "2024.2",
18
+ "TYPE": "trajectory",
19
+ "METHOD": "Classical MD",
20
+ "LICENSE": "Apache License 2.0",
21
+ "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
22
+ "CITATION": "DynaRepo citation",
23
+ "THANKS": "DynaRepo Acknowledgements",
24
+ "LINKS": null,
25
+ "PDBIDS": [
26
+ "1AY7"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P05798",
31
+ "P11540"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC",
38
+ "KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Guanyl-specific ribonuclease Sa",
43
+ "Barstar"
44
+ ],
45
+ "FRAMESTEP": 0.1,
46
+ "TIMESTEP": 2,
47
+ "TEMP": 310,
48
+ "ENSEMBLE": "NPT",
49
+ "FF": [
50
+ "CHARMM36m"
51
+ ],
52
+ "WAT": "TIP3P",
53
+ "BOXTYPE": "Dodecahedron",
54
+ "SYSTATS": 2875,
55
+ "SYSTRES": 185,
56
+ "PROTATS": 2875,
57
+ "PROTRES": 185,
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": "protein-protein interaction B-A",
72
+ "agent_1": "protein B",
73
+ "agent_2": "protein A",
74
+ "selection_1": "chain A",
75
+ "selection_2": "chain B",
76
+ "type": "protein-protein"
77
+ }
78
+ ],
79
+ "PBC_SELECTION": null,
80
+ "CHAINNAMES": null,
81
+ "MEMBRANES": null,
82
+ "CUSTOMS": null,
83
+ "ORIENTATION": null,
84
+ "PTM": [],
85
+ "MULTIMERIC": null,
86
+ "COLLECTIONS": "dynarepo",
87
+ "WARNINGS": [],
88
+ "BOXSIZEX": 8.14692,
89
+ "BOXSIZEY": 8.14692,
90
+ "BOXSIZEZ": 5.75583,
91
+ "mdName": "replica 1",
92
+ "mdAtoms": 2875,
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
+ "pca_trajectory_13.bin",
118
+ "pca_trajectory_14.bin",
119
+ "pca_trajectory_15.bin",
120
+ "pca_trajectory_16.bin",
121
+ "pca_trajectory_17.bin",
122
+ "structure.pdb",
123
+ "trajectory.xtc",
124
+ "clusters_00_screenshot_00.jpg",
125
+ "clusters_00_screenshot_01.jpg",
126
+ "clusters_00_screenshot_02.jpg",
127
+ "clusters_00_screenshot_03.jpg",
128
+ "clusters_00_screenshot_04.jpg",
129
+ "clusters_00_screenshot_05.jpg",
130
+ "clusters_00_screenshot_06.jpg",
131
+ "clusters_00_screenshot_07.jpg",
132
+ "clusters_00_screenshot_08.jpg",
133
+ "clusters_00_screenshot_09.jpg",
134
+ "clusters_00_screenshot_10.jpg",
135
+ "clusters_00_screenshot_11.jpg",
136
+ "clusters_00_screenshot_12.jpg",
137
+ "clusters_00_screenshot_13.jpg",
138
+ "clusters_00_screenshot_14.jpg",
139
+ "clusters_00_screenshot_15.jpg",
140
+ "clusters_00_screenshot_16.jpg",
141
+ "clusters_00_screenshot_17.jpg",
142
+ "clusters_00_screenshot_18.jpg",
143
+ "clusters_00_screenshot_19.jpg",
144
+ "clusters_01_screenshot_00.jpg",
145
+ "clusters_01_screenshot_01.jpg",
146
+ "clusters_01_screenshot_02.jpg",
147
+ "clusters_01_screenshot_03.jpg",
148
+ "clusters_01_screenshot_04.jpg",
149
+ "clusters_01_screenshot_05.jpg",
150
+ "clusters_01_screenshot_06.jpg",
151
+ "clusters_01_screenshot_07.jpg",
152
+ "clusters_01_screenshot_08.jpg",
153
+ "clusters_01_screenshot_09.jpg",
154
+ "clusters_01_screenshot_10.jpg",
155
+ "clusters_01_screenshot_11.jpg",
156
+ "clusters_01_screenshot_12.jpg",
157
+ "clusters_01_screenshot_13.jpg",
158
+ "clusters_01_screenshot_14.jpg",
159
+ "clusters_01_screenshot_15.jpg",
160
+ "clusters_01_screenshot_16.jpg",
161
+ "pocket_01.pdb",
162
+ "pocket_02.pdb",
163
+ "pocket_03.pdb",
164
+ "pocket_04.pdb",
165
+ "pocket_05.pdb"
166
+ ],
167
+ "analyses": [
168
+ "clusters",
169
+ "clusters-00",
170
+ "clusters-01",
171
+ "dist-perres",
172
+ "energies",
173
+ "fluctuation",
174
+ "hbonds",
175
+ "interactions",
176
+ "pca",
177
+ "pockets",
178
+ "rgyr",
179
+ "rmsd-pairwise",
180
+ "rmsd-perres",
181
+ "rmsds",
182
+ "sasa",
183
+ "tmscores"
184
+ ],
185
+ "mdIndex": 0,
186
+ "mdNumber": 1,
187
+ "refframe": 0,
188
+ "internalId": "683f0058acc0a79ac6ea66e7",
189
+ "creationDate": "2025-06-03T14:02:00.000Z",
190
+ "identifier": "A000D"
191
+ }
A000D/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A000D", "accession": "A000D", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1AY7", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1AY7"], "FORCED_REFERENCES": null, "REFERENCES": ["P05798", "P11540"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC", "KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS"], "NUCLSEQ": [], "DOMAINS": ["Guanyl-specific ribonuclease Sa", "Barstar"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2875, "SYSTRES": 185, "PROTATS": 2875, "PROTRES": 185, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "protein-protein interaction B-A", "agent_1": "protein B", "agent_2": "protein A", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.14692, "BOXSIZEY": 8.14692, "BOXSIZEZ": 5.75583, "mdName": "replica 1", "mdAtoms": 2875, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A000D/files/topology.tpr", "length": 1068892, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A000D/files/screenshot.jpg", "length": 20396, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A000D/files/trajectory.bin", "length": 172534500, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 5001, "atoms": 2875}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_01.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_02.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_03.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_04.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_05.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_06.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_07.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_08.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_09.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_10.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_11.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_12.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_13.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_14.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_15.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_16.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_17.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "structure.pdb", "downloadUrl": "/projects/A000D/files/structure.pdb", "length": 232910, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A000D/files/trajectory.xtc", "length": 54760256, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_00.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_01.jpg", "length": 20067, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_02.jpg", "length": 19557, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_03.jpg", "length": 20172, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_04.jpg", "length": 20065, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_05.jpg", "length": 19864, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_06.jpg", "length": 20016, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_07.jpg", "length": 20199, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_08.jpg", "length": 19841, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_09.jpg", "length": 20222, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_10.jpg", "length": 19420, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_11.jpg", "length": 20220, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_12.jpg", "length": 19696, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_13.jpg", "length": 19857, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_14.jpg", "length": 20180, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_15.jpg", "length": 19934, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_16.jpg", "length": 20435, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_17.jpg", "length": 19814, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_18.jpg", "length": 19869, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_19.jpg", "length": 20119, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_00.jpg", "length": 19433, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_01.jpg", "length": 19996, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_02.jpg", "length": 19982, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_03.jpg", "length": 19926, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_04.jpg", "length": 19653, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_05.jpg", "length": 19727, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_06.jpg", "length": 20199, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_07.jpg", "length": 19792, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_08.jpg", "length": 19726, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_09.jpg", "length": 19363, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_10.jpg", "length": 19698, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_11.jpg", "length": 19769, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_12.jpg", "length": 19250, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_13.jpg", "length": 19823, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_14.jpg", "length": 19571, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_15.jpg", "length": 19903, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_16.jpg", "length": 19616, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A000D/files/pocket_01.pdb", "length": 11457, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A000D/files/pocket_02.pdb", "length": 8978, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A000D/files/pocket_03.pdb", "length": 8576, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A000D/files/pocket_04.pdb", "length": 4422, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A000D/files/pocket_05.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}]}
2
+ {"project_identifier": "A000D", "accession": "A000D", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1AY7", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1AY7"], "FORCED_REFERENCES": null, "REFERENCES": ["P05798", "P11540"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC", "KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS"], "NUCLSEQ": [], "DOMAINS": ["Guanyl-specific ribonuclease Sa", "Barstar"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2875, "SYSTRES": 185, "PROTATS": 2875, "PROTRES": 185, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "protein-protein interaction B-A", "agent_1": "protein B", "agent_2": "protein A", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.14692, "BOXSIZEY": 8.14692, "BOXSIZEZ": 5.75583, "mdName": "replica 1", "mdAtoms": 2875, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A000D/files/topology.tpr", "length": 1068892, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A000D/files/screenshot.jpg", "length": 20396, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A000D/files/trajectory.bin", "length": 172534500, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 5001, "atoms": 2875}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_01.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_02.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_03.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_04.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_05.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_06.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_07.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_08.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_09.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_10.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_11.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_12.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_13.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_14.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_15.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_16.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_17.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "structure.pdb", "downloadUrl": "/projects/A000D/files/structure.pdb", "length": 232910, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A000D/files/trajectory.xtc", "length": 54760256, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_00.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_01.jpg", "length": 20067, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_02.jpg", "length": 19557, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_03.jpg", "length": 20172, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_04.jpg", "length": 20065, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_05.jpg", "length": 19864, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_06.jpg", "length": 20016, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_07.jpg", "length": 20199, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_08.jpg", "length": 19841, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_09.jpg", "length": 20222, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_10.jpg", "length": 19420, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_11.jpg", "length": 20220, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_12.jpg", "length": 19696, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_13.jpg", "length": 19857, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_14.jpg", "length": 20180, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_15.jpg", "length": 19934, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_16.jpg", "length": 20435, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_17.jpg", "length": 19814, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_18.jpg", "length": 19869, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_19.jpg", "length": 20119, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_00.jpg", "length": 19433, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_01.jpg", "length": 19996, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_02.jpg", "length": 19982, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_03.jpg", "length": 19926, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_04.jpg", "length": 19653, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_05.jpg", "length": 19727, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_06.jpg", "length": 20199, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_07.jpg", "length": 19792, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_08.jpg", "length": 19726, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_09.jpg", "length": 19363, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_10.jpg", "length": 19698, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_11.jpg", "length": 19769, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_12.jpg", "length": 19250, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_13.jpg", "length": 19823, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_14.jpg", "length": 19571, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_15.jpg", "length": 19903, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_16.jpg", "length": 19616, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A000D/files/pocket_01.pdb", "length": 11457, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A000D/files/pocket_02.pdb", "length": 8978, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A000D/files/pocket_03.pdb", "length": 8576, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A000D/files/pocket_04.pdb", "length": 4422, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A000D/files/pocket_05.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}]}
3
+ {"project_identifier": "A000D", "accession": "A000D", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 1AY7", "DESCRIPTION": "PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "yasaman.karami@inria.fr", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["1AY7"], "FORCED_REFERENCES": null, "REFERENCES": ["P05798", "P11540"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHEYTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC", "KKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDCLTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGCDITIILS"], "NUCLSEQ": [], "DOMAINS": ["Guanyl-specific ribonuclease Sa", "Barstar"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2875, "SYSTRES": 185, "PROTATS": 2875, "PROTRES": 185, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "protein-protein interaction B-A", "agent_1": "protein B", "agent_2": "protein A", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.14692, "BOXSIZEY": 8.14692, "BOXSIZEZ": 5.75583, "mdName": "replica 1", "mdAtoms": 2875, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A000D/files/topology.tpr", "length": 1068892, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A000D/files/screenshot.jpg", "length": 20396, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A000D/files/trajectory.bin", "length": 172534500, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 5001, "atoms": 2875}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_01.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_02.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_03.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_04.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_05.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_06.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_07.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_08.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_09.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_10.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_11.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_12.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_13.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_14.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_15.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_16.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A000D/files/pca_trajectory_17.bin", "length": 133200, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0, "frames": 20, "atoms": 555}}, {"name": "structure.pdb", "downloadUrl": "/projects/A000D/files/structure.pdb", "length": 232910, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A000D/files/trajectory.xtc", "length": 54760256, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_00.jpg", "length": 19697, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_01.jpg", "length": 20067, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_02.jpg", "length": 19557, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_03.jpg", "length": 20172, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_04.jpg", "length": 20065, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_05.jpg", "length": 19864, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_06.jpg", "length": 20016, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_07.jpg", "length": 20199, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_08.jpg", "length": 19841, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_09.jpg", "length": 20222, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_10.jpg", "length": 19420, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_11.jpg", "length": 20220, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_12.jpg", "length": 19696, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_13.jpg", "length": 19857, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_14.jpg", "length": 20180, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_15.jpg", "length": 19934, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_16.jpg", "length": 20435, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_17.jpg", "length": 19814, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_18.jpg", "length": 19869, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A000D/files/clusters_00_screenshot_19.jpg", "length": 20119, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_00.jpg", "length": 19433, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_01.jpg", "length": 19996, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_02.jpg", "length": 19982, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_03.jpg", "length": 19926, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_04.jpg", "length": 19653, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_05.jpg", "length": 19727, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_06.jpg", "length": 20199, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_07.jpg", "length": 19792, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_08.jpg", "length": 19726, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_09.jpg", "length": 19363, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_10.jpg", "length": 19698, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_11.jpg", "length": 19769, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_12.jpg", "length": 19250, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_13.jpg", "length": 19823, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_14.jpg", "length": 19571, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_15.jpg", "length": 19903, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A000D/files/clusters_01_screenshot_16.jpg", "length": 19616, "contentType": "application/octet-stream", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A000D/files/pocket_01.pdb", "length": 11457, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A000D/files/pocket_02.pdb", "length": 8978, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A000D/files/pocket_03.pdb", "length": 8576, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A000D/files/pocket_04.pdb", "length": 4422, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A000D/files/pocket_05.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f0058acc0a79ac6ea66e7", "md": 0}}]}
A000J/project.json ADDED
@@ -0,0 +1,196 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A000J",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1E3U",
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
+ "1E3U"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P14489"
31
+ ],
32
+ "INPUT_LIGANDS": null,
33
+ "LIGANDS": [],
34
+ "LIGANDNAMES": null,
35
+ "PROTSEQ": [
36
+ "ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII",
37
+ "ITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG"
38
+ ],
39
+ "NUCLSEQ": [],
40
+ "DOMAINS": [
41
+ "Beta-lactamase OXA-10"
42
+ ],
43
+ "FRAMESTEP": 0.1,
44
+ "TIMESTEP": 2,
45
+ "TEMP": 310,
46
+ "ENSEMBLE": "NPT",
47
+ "FF": [
48
+ "CHARMM36m"
49
+ ],
50
+ "WAT": "TIP3P",
51
+ "BOXTYPE": "Dodecahedron",
52
+ "SYSTATS": 7716,
53
+ "SYSTRES": 488,
54
+ "PROTATS": 7716,
55
+ "PROTRES": 488,
56
+ "NUCLATS": 0,
57
+ "NUCLRES": 0,
58
+ "LIPIATS": 0,
59
+ "LIPIRES": 0,
60
+ "CARBATS": 0,
61
+ "CARBRES": 0,
62
+ "SOLVATS": 0,
63
+ "SOLVRES": 0,
64
+ "COUNCAT": 0,
65
+ "COUNANI": 0,
66
+ "COUNION": 0,
67
+ "INTERACTIONS": [
68
+ {
69
+ "name": "protein-protein interaction B-A",
70
+ "agent_1": "protein B",
71
+ "agent_2": "protein A",
72
+ "selection_1": "chain A",
73
+ "selection_2": "chain B",
74
+ "type": "protein-protein"
75
+ }
76
+ ],
77
+ "PBC_SELECTION": null,
78
+ "CHAINNAMES": null,
79
+ "MEMBRANES": null,
80
+ "CUSTOMS": null,
81
+ "ORIENTATION": null,
82
+ "PTM": [],
83
+ "MULTIMERIC": null,
84
+ "COLLECTIONS": "dynarepo",
85
+ "WARNINGS": [],
86
+ "BOXSIZEX": 10.3656,
87
+ "BOXSIZEY": 10.3656,
88
+ "BOXSIZEZ": 7.33423,
89
+ "mdName": "replica 1",
90
+ "mdAtoms": 7716,
91
+ "mdFrames": 5001
92
+ },
93
+ "mds": [
94
+ "replica 1",
95
+ "replica 2",
96
+ "replica 3"
97
+ ],
98
+ "mdref": 0,
99
+ "files": [
100
+ "topology.tpr",
101
+ "screenshot.jpg",
102
+ "trajectory.bin",
103
+ "pca_trajectory_01.bin",
104
+ "pca_trajectory_02.bin",
105
+ "pca_trajectory_03.bin",
106
+ "pca_trajectory_04.bin",
107
+ "pca_trajectory_05.bin",
108
+ "pca_trajectory_06.bin",
109
+ "pca_trajectory_07.bin",
110
+ "pca_trajectory_08.bin",
111
+ "pca_trajectory_09.bin",
112
+ "pca_trajectory_10.bin",
113
+ "pca_trajectory_11.bin",
114
+ "pca_trajectory_12.bin",
115
+ "pca_trajectory_13.bin",
116
+ "pca_trajectory_14.bin",
117
+ "pca_trajectory_15.bin",
118
+ "pca_trajectory_16.bin",
119
+ "structure.pdb",
120
+ "trajectory.xtc",
121
+ "clusters_00_screenshot_00.jpg",
122
+ "clusters_00_screenshot_01.jpg",
123
+ "clusters_00_screenshot_02.jpg",
124
+ "clusters_00_screenshot_03.jpg",
125
+ "clusters_00_screenshot_04.jpg",
126
+ "clusters_00_screenshot_05.jpg",
127
+ "clusters_00_screenshot_06.jpg",
128
+ "clusters_00_screenshot_07.jpg",
129
+ "clusters_00_screenshot_08.jpg",
130
+ "clusters_00_screenshot_09.jpg",
131
+ "clusters_00_screenshot_10.jpg",
132
+ "clusters_00_screenshot_11.jpg",
133
+ "clusters_00_screenshot_12.jpg",
134
+ "clusters_00_screenshot_13.jpg",
135
+ "clusters_00_screenshot_14.jpg",
136
+ "clusters_00_screenshot_15.jpg",
137
+ "clusters_00_screenshot_16.jpg",
138
+ "clusters_00_screenshot_17.jpg",
139
+ "clusters_00_screenshot_18.jpg",
140
+ "clusters_00_screenshot_19.jpg",
141
+ "clusters_01_screenshot_00.jpg",
142
+ "clusters_01_screenshot_01.jpg",
143
+ "clusters_01_screenshot_02.jpg",
144
+ "clusters_01_screenshot_03.jpg",
145
+ "clusters_01_screenshot_04.jpg",
146
+ "clusters_01_screenshot_05.jpg",
147
+ "clusters_01_screenshot_06.jpg",
148
+ "clusters_01_screenshot_07.jpg",
149
+ "clusters_01_screenshot_08.jpg",
150
+ "clusters_01_screenshot_09.jpg",
151
+ "clusters_01_screenshot_10.jpg",
152
+ "clusters_01_screenshot_11.jpg",
153
+ "clusters_01_screenshot_12.jpg",
154
+ "clusters_01_screenshot_13.jpg",
155
+ "clusters_01_screenshot_14.jpg",
156
+ "clusters_01_screenshot_15.jpg",
157
+ "clusters_01_screenshot_16.jpg",
158
+ "clusters_01_screenshot_17.jpg",
159
+ "clusters_01_screenshot_18.jpg",
160
+ "clusters_01_screenshot_19.jpg",
161
+ "pocket_01.pdb",
162
+ "pocket_02.pdb",
163
+ "pocket_03.pdb",
164
+ "pocket_04.pdb",
165
+ "pocket_05.pdb",
166
+ "pocket_06.pdb",
167
+ "pocket_07.pdb",
168
+ "pocket_08.pdb",
169
+ "pocket_09.pdb",
170
+ "pocket_10.pdb"
171
+ ],
172
+ "analyses": [
173
+ "clusters",
174
+ "clusters-00",
175
+ "clusters-01",
176
+ "dist-perres",
177
+ "energies",
178
+ "fluctuation",
179
+ "hbonds",
180
+ "interactions",
181
+ "pca",
182
+ "pockets",
183
+ "rgyr",
184
+ "rmsd-pairwise",
185
+ "rmsd-perres",
186
+ "rmsds",
187
+ "sasa",
188
+ "tmscores"
189
+ ],
190
+ "mdIndex": 0,
191
+ "mdNumber": 1,
192
+ "refframe": 0,
193
+ "internalId": "683f1fbaa4df910e8af0c108",
194
+ "creationDate": "2025-06-03T16:15:54.000Z",
195
+ "identifier": "A000J"
196
+ }
A000Z/project.json ADDED
@@ -0,0 +1,344 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A000Z",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1I5K",
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
+ "1I5K"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P00747",
31
+ "P49054"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "EKLTADAELQRLKNERHEEAELERLK",
38
+ "EECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRC",
39
+ "ECMHGSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRDLRPWCFTTDPNKRWEYCDIPRC"
40
+ ],
41
+ "NUCLSEQ": [],
42
+ "DOMAINS": [
43
+ "Plasminogen",
44
+ "Plasmin heavy chain A",
45
+ "Angiostatin",
46
+ "Plasmin heavy chain A, short form",
47
+ "Kringle 2",
48
+ "Plasminogen-binding group A streptococcal M-like protein PAM",
49
+ "Able to bind plasminogen",
50
+ "2 X approximate tandem repeats, type a",
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": 3391,
63
+ "SYSTRES": 211,
64
+ "PROTATS": 3391,
65
+ "PROTRES": 211,
66
+ "NUCLATS": 0,
67
+ "NUCLRES": 0,
68
+ "LIPIATS": 0,
69
+ "LIPIRES": 0,
70
+ "CARBATS": 0,
71
+ "CARBRES": 0,
72
+ "SOLVATS": 0,
73
+ "SOLVRES": 0,
74
+ "COUNCAT": 0,
75
+ "COUNANI": 0,
76
+ "COUNION": 0,
77
+ "INTERACTIONS": [
78
+ {
79
+ "name": "protein-protein interaction C-B",
80
+ "agent_1": "protein C",
81
+ "agent_2": "protein B",
82
+ "selection_1": "chain A",
83
+ "selection_2": "chain B",
84
+ "type": "protein-protein"
85
+ },
86
+ {
87
+ "name": "protein-protein interaction C-D",
88
+ "agent_1": "protein C",
89
+ "agent_2": "protein D",
90
+ "selection_1": "chain A",
91
+ "selection_2": "chain C",
92
+ "type": "protein-protein"
93
+ },
94
+ {
95
+ "name": "protein-protein interaction C-A",
96
+ "agent_1": "protein C",
97
+ "agent_2": "protein A",
98
+ "selection_1": "chain A",
99
+ "selection_2": "chain D",
100
+ "type": "protein-protein"
101
+ },
102
+ {
103
+ "name": "protein-protein interaction B-D",
104
+ "agent_1": "protein B",
105
+ "agent_2": "protein D",
106
+ "selection_1": "chain B",
107
+ "selection_2": "chain C",
108
+ "type": "protein-protein"
109
+ },
110
+ {
111
+ "name": "protein-protein interaction B-A",
112
+ "agent_1": "protein B",
113
+ "agent_2": "protein A",
114
+ "selection_1": "chain B",
115
+ "selection_2": "chain D",
116
+ "type": "protein-protein"
117
+ },
118
+ {
119
+ "name": "protein-protein interaction D-A",
120
+ "agent_1": "protein D",
121
+ "agent_2": "protein A",
122
+ "selection_1": "chain C",
123
+ "selection_2": "chain D",
124
+ "type": "protein-protein"
125
+ }
126
+ ],
127
+ "PBC_SELECTION": null,
128
+ "CHAINNAMES": null,
129
+ "MEMBRANES": null,
130
+ "CUSTOMS": null,
131
+ "ORIENTATION": null,
132
+ "PTM": [],
133
+ "MULTIMERIC": null,
134
+ "COLLECTIONS": "dynarepo",
135
+ "WARNINGS": [],
136
+ "BOXSIZEX": 9.13395,
137
+ "BOXSIZEY": 9.13395,
138
+ "BOXSIZEZ": 6.42953,
139
+ "mdName": "replica 1",
140
+ "mdAtoms": 3391,
141
+ "mdFrames": 5001
142
+ },
143
+ "mds": [
144
+ "replica 1",
145
+ "replica 2",
146
+ "replica 3"
147
+ ],
148
+ "mdref": 0,
149
+ "files": [
150
+ "topology.tpr",
151
+ "screenshot.jpg",
152
+ "trajectory.bin",
153
+ "pca_trajectory_01.bin",
154
+ "pca_trajectory_02.bin",
155
+ "pca_trajectory_03.bin",
156
+ "structure.pdb",
157
+ "trajectory.xtc",
158
+ "clusters_00_screenshot_00.jpg",
159
+ "clusters_00_screenshot_01.jpg",
160
+ "clusters_00_screenshot_02.jpg",
161
+ "clusters_00_screenshot_03.jpg",
162
+ "clusters_00_screenshot_04.jpg",
163
+ "clusters_00_screenshot_05.jpg",
164
+ "clusters_00_screenshot_06.jpg",
165
+ "clusters_00_screenshot_07.jpg",
166
+ "clusters_00_screenshot_08.jpg",
167
+ "clusters_00_screenshot_09.jpg",
168
+ "clusters_00_screenshot_10.jpg",
169
+ "clusters_00_screenshot_11.jpg",
170
+ "clusters_00_screenshot_12.jpg",
171
+ "clusters_00_screenshot_13.jpg",
172
+ "clusters_00_screenshot_14.jpg",
173
+ "clusters_00_screenshot_15.jpg",
174
+ "clusters_00_screenshot_16.jpg",
175
+ "clusters_00_screenshot_17.jpg",
176
+ "clusters_00_screenshot_18.jpg",
177
+ "clusters_00_screenshot_19.jpg",
178
+ "clusters_00_screenshot_20.jpg",
179
+ "clusters_01_screenshot_00.jpg",
180
+ "clusters_01_screenshot_01.jpg",
181
+ "clusters_01_screenshot_02.jpg",
182
+ "clusters_01_screenshot_03.jpg",
183
+ "clusters_01_screenshot_04.jpg",
184
+ "clusters_01_screenshot_05.jpg",
185
+ "clusters_01_screenshot_06.jpg",
186
+ "clusters_01_screenshot_07.jpg",
187
+ "clusters_01_screenshot_08.jpg",
188
+ "clusters_01_screenshot_09.jpg",
189
+ "clusters_01_screenshot_10.jpg",
190
+ "clusters_01_screenshot_11.jpg",
191
+ "clusters_01_screenshot_12.jpg",
192
+ "clusters_01_screenshot_13.jpg",
193
+ "clusters_01_screenshot_14.jpg",
194
+ "clusters_01_screenshot_15.jpg",
195
+ "clusters_01_screenshot_16.jpg",
196
+ "clusters_01_screenshot_17.jpg",
197
+ "clusters_01_screenshot_18.jpg",
198
+ "clusters_01_screenshot_19.jpg",
199
+ "clusters_01_screenshot_20.jpg",
200
+ "clusters_01_screenshot_21.jpg",
201
+ "clusters_01_screenshot_22.jpg",
202
+ "clusters_01_screenshot_23.jpg",
203
+ "clusters_02_screenshot_00.jpg",
204
+ "clusters_02_screenshot_01.jpg",
205
+ "clusters_02_screenshot_02.jpg",
206
+ "clusters_02_screenshot_03.jpg",
207
+ "clusters_02_screenshot_04.jpg",
208
+ "clusters_02_screenshot_05.jpg",
209
+ "clusters_02_screenshot_06.jpg",
210
+ "clusters_02_screenshot_07.jpg",
211
+ "clusters_02_screenshot_08.jpg",
212
+ "clusters_02_screenshot_09.jpg",
213
+ "clusters_02_screenshot_10.jpg",
214
+ "clusters_02_screenshot_11.jpg",
215
+ "clusters_02_screenshot_12.jpg",
216
+ "clusters_02_screenshot_13.jpg",
217
+ "clusters_02_screenshot_14.jpg",
218
+ "clusters_02_screenshot_15.jpg",
219
+ "clusters_02_screenshot_16.jpg",
220
+ "clusters_02_screenshot_17.jpg",
221
+ "clusters_02_screenshot_18.jpg",
222
+ "clusters_02_screenshot_19.jpg",
223
+ "clusters_02_screenshot_20.jpg",
224
+ "clusters_02_screenshot_21.jpg",
225
+ "clusters_03_screenshot_00.jpg",
226
+ "clusters_03_screenshot_01.jpg",
227
+ "clusters_03_screenshot_02.jpg",
228
+ "clusters_03_screenshot_03.jpg",
229
+ "clusters_03_screenshot_04.jpg",
230
+ "clusters_03_screenshot_05.jpg",
231
+ "clusters_03_screenshot_06.jpg",
232
+ "clusters_03_screenshot_07.jpg",
233
+ "clusters_03_screenshot_08.jpg",
234
+ "clusters_03_screenshot_09.jpg",
235
+ "clusters_03_screenshot_10.jpg",
236
+ "clusters_03_screenshot_11.jpg",
237
+ "clusters_03_screenshot_12.jpg",
238
+ "clusters_03_screenshot_13.jpg",
239
+ "clusters_03_screenshot_14.jpg",
240
+ "clusters_03_screenshot_15.jpg",
241
+ "clusters_03_screenshot_16.jpg",
242
+ "clusters_03_screenshot_17.jpg",
243
+ "clusters_03_screenshot_18.jpg",
244
+ "clusters_03_screenshot_19.jpg",
245
+ "clusters_03_screenshot_20.jpg",
246
+ "clusters_04_screenshot_00.jpg",
247
+ "clusters_04_screenshot_01.jpg",
248
+ "clusters_04_screenshot_02.jpg",
249
+ "clusters_04_screenshot_03.jpg",
250
+ "clusters_04_screenshot_04.jpg",
251
+ "clusters_04_screenshot_05.jpg",
252
+ "clusters_04_screenshot_06.jpg",
253
+ "clusters_04_screenshot_07.jpg",
254
+ "clusters_04_screenshot_08.jpg",
255
+ "clusters_04_screenshot_09.jpg",
256
+ "clusters_04_screenshot_10.jpg",
257
+ "clusters_04_screenshot_11.jpg",
258
+ "clusters_04_screenshot_12.jpg",
259
+ "clusters_04_screenshot_13.jpg",
260
+ "clusters_04_screenshot_14.jpg",
261
+ "clusters_04_screenshot_15.jpg",
262
+ "clusters_04_screenshot_16.jpg",
263
+ "clusters_04_screenshot_17.jpg",
264
+ "clusters_04_screenshot_18.jpg",
265
+ "clusters_04_screenshot_19.jpg",
266
+ "clusters_04_screenshot_20.jpg",
267
+ "clusters_05_screenshot_00.jpg",
268
+ "clusters_05_screenshot_01.jpg",
269
+ "clusters_05_screenshot_02.jpg",
270
+ "clusters_05_screenshot_03.jpg",
271
+ "clusters_05_screenshot_04.jpg",
272
+ "clusters_05_screenshot_05.jpg",
273
+ "clusters_05_screenshot_06.jpg",
274
+ "clusters_05_screenshot_07.jpg",
275
+ "clusters_05_screenshot_08.jpg",
276
+ "clusters_05_screenshot_09.jpg",
277
+ "clusters_05_screenshot_10.jpg",
278
+ "clusters_05_screenshot_11.jpg",
279
+ "clusters_05_screenshot_12.jpg",
280
+ "clusters_05_screenshot_13.jpg",
281
+ "clusters_05_screenshot_14.jpg",
282
+ "clusters_05_screenshot_15.jpg",
283
+ "clusters_05_screenshot_16.jpg",
284
+ "clusters_05_screenshot_17.jpg",
285
+ "clusters_05_screenshot_18.jpg",
286
+ "clusters_05_screenshot_19.jpg",
287
+ "clusters_05_screenshot_20.jpg",
288
+ "clusters_05_screenshot_21.jpg",
289
+ "clusters_05_screenshot_22.jpg",
290
+ "clusters_05_screenshot_23.jpg",
291
+ "clusters_06_screenshot_00.jpg",
292
+ "clusters_06_screenshot_01.jpg",
293
+ "clusters_06_screenshot_02.jpg",
294
+ "clusters_06_screenshot_03.jpg",
295
+ "clusters_06_screenshot_04.jpg",
296
+ "clusters_06_screenshot_05.jpg",
297
+ "clusters_06_screenshot_06.jpg",
298
+ "clusters_06_screenshot_07.jpg",
299
+ "clusters_06_screenshot_08.jpg",
300
+ "clusters_06_screenshot_09.jpg",
301
+ "clusters_06_screenshot_10.jpg",
302
+ "clusters_06_screenshot_11.jpg",
303
+ "clusters_06_screenshot_12.jpg",
304
+ "clusters_06_screenshot_13.jpg",
305
+ "clusters_06_screenshot_14.jpg",
306
+ "clusters_06_screenshot_15.jpg",
307
+ "clusters_06_screenshot_16.jpg",
308
+ "clusters_06_screenshot_17.jpg",
309
+ "clusters_06_screenshot_18.jpg",
310
+ "clusters_06_screenshot_19.jpg",
311
+ "clusters_06_screenshot_20.jpg",
312
+ "clusters_06_screenshot_21.jpg",
313
+ "clusters_06_screenshot_22.jpg",
314
+ "clusters_06_screenshot_23.jpg"
315
+ ],
316
+ "analyses": [
317
+ "clusters",
318
+ "clusters-00",
319
+ "clusters-01",
320
+ "clusters-02",
321
+ "clusters-03",
322
+ "clusters-04",
323
+ "clusters-05",
324
+ "clusters-06",
325
+ "dist-perres",
326
+ "energies",
327
+ "fluctuation",
328
+ "hbonds",
329
+ "interactions",
330
+ "pca",
331
+ "rgyr",
332
+ "rmsd-pairwise",
333
+ "rmsd-perres",
334
+ "rmsds",
335
+ "sasa",
336
+ "tmscores"
337
+ ],
338
+ "mdIndex": 0,
339
+ "mdNumber": 1,
340
+ "refframe": 0,
341
+ "internalId": "683f32e0c2e0ade273d7fd0f",
342
+ "creationDate": "2025-06-03T17:37:36.000Z",
343
+ "identifier": "A000Z"
344
+ }
A000Z/records.jsonl ADDED
The diff for this file is too large to render. See raw diff
 
A0016/project.json ADDED
@@ -0,0 +1,318 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0016",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1JWH",
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
+ "1JWH"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P68400",
31
+ "P67870"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS",
38
+ "EVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYXPRVYXENQPMLPIGLSDIPGEAMVKLYXPKXMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHPMAYQLQLQAAS",
39
+ "SGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS",
40
+ "SSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYXPRVYXENQPMLPIGLSDIPGEAMVKLYXPKXMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHPMAYQLQLQAAS"
41
+ ],
42
+ "NUCLSEQ": [],
43
+ "DOMAINS": [
44
+ "Casein kinase II subunit alpha",
45
+ "Protein kinase",
46
+ "Interaction with beta subunit",
47
+ "Casein kinase II subunit beta",
48
+ "Interaction with alpha subunit",
49
+ "KSSR motif"
50
+ ],
51
+ "FRAMESTEP": 0.1,
52
+ "TIMESTEP": 2,
53
+ "TEMP": 310,
54
+ "ENSEMBLE": "NPT",
55
+ "FF": [
56
+ "CHARMM36m"
57
+ ],
58
+ "WAT": "TIP3P",
59
+ "BOXTYPE": "Dodecahedron",
60
+ "SYSTATS": 17609,
61
+ "SYSTRES": 1075,
62
+ "PROTATS": 17609,
63
+ "PROTRES": 1075,
64
+ "NUCLATS": 0,
65
+ "NUCLRES": 0,
66
+ "LIPIATS": 0,
67
+ "LIPIRES": 0,
68
+ "CARBATS": 0,
69
+ "CARBRES": 0,
70
+ "SOLVATS": 0,
71
+ "SOLVRES": 0,
72
+ "COUNCAT": 0,
73
+ "COUNANI": 0,
74
+ "COUNION": 0,
75
+ "INTERACTIONS": [
76
+ {
77
+ "name": "protein-protein interaction A-D",
78
+ "agent_1": "protein A",
79
+ "agent_2": "protein D",
80
+ "selection_1": "chain A",
81
+ "selection_2": "chain B",
82
+ "type": "protein-protein"
83
+ },
84
+ {
85
+ "name": "protein-protein interaction A-C",
86
+ "agent_1": "protein A",
87
+ "agent_2": "protein C",
88
+ "selection_1": "chain A",
89
+ "selection_2": "chain C",
90
+ "type": "protein-protein"
91
+ },
92
+ {
93
+ "name": "protein-protein interaction B-D",
94
+ "agent_1": "protein B",
95
+ "agent_2": "protein D",
96
+ "selection_1": "chain A",
97
+ "selection_2": "chain D",
98
+ "type": "protein-protein"
99
+ },
100
+ {
101
+ "name": "protein-protein interaction B-C",
102
+ "agent_1": "protein B",
103
+ "agent_2": "protein C",
104
+ "selection_1": "chain B",
105
+ "selection_2": "chain C",
106
+ "type": "protein-protein"
107
+ },
108
+ {
109
+ "name": "protein-protein interaction D-C",
110
+ "agent_1": "protein D",
111
+ "agent_2": "protein C",
112
+ "selection_1": "chain B",
113
+ "selection_2": "chain D",
114
+ "type": "protein-protein"
115
+ }
116
+ ],
117
+ "PBC_SELECTION": null,
118
+ "CHAINNAMES": null,
119
+ "MEMBRANES": null,
120
+ "CUSTOMS": null,
121
+ "ORIENTATION": null,
122
+ "PTM": [],
123
+ "MULTIMERIC": null,
124
+ "COLLECTIONS": "dynarepo",
125
+ "WARNINGS": [],
126
+ "BOXSIZEX": 18.2153,
127
+ "BOXSIZEY": 18.2153,
128
+ "BOXSIZEZ": 12.8434,
129
+ "mdName": "replica 1",
130
+ "mdAtoms": 17609,
131
+ "mdFrames": 5001
132
+ },
133
+ "mds": [
134
+ "replica 1",
135
+ "replica 2",
136
+ "replica 3"
137
+ ],
138
+ "mdref": 0,
139
+ "files": [
140
+ "topology.tpr",
141
+ "screenshot.jpg",
142
+ "trajectory.bin",
143
+ "pca_trajectory_01.bin",
144
+ "pca_trajectory_02.bin",
145
+ "pca_trajectory_03.bin",
146
+ "pca_trajectory_04.bin",
147
+ "pca_trajectory_05.bin",
148
+ "pca_trajectory_06.bin",
149
+ "pca_trajectory_07.bin",
150
+ "pca_trajectory_08.bin",
151
+ "pca_trajectory_09.bin",
152
+ "pca_trajectory_10.bin",
153
+ "structure.pdb",
154
+ "trajectory.xtc",
155
+ "clusters_00_screenshot_00.jpg",
156
+ "clusters_00_screenshot_01.jpg",
157
+ "clusters_00_screenshot_02.jpg",
158
+ "clusters_00_screenshot_03.jpg",
159
+ "clusters_00_screenshot_04.jpg",
160
+ "clusters_00_screenshot_05.jpg",
161
+ "clusters_00_screenshot_06.jpg",
162
+ "clusters_00_screenshot_07.jpg",
163
+ "clusters_00_screenshot_08.jpg",
164
+ "clusters_00_screenshot_09.jpg",
165
+ "clusters_00_screenshot_10.jpg",
166
+ "clusters_00_screenshot_11.jpg",
167
+ "clusters_00_screenshot_12.jpg",
168
+ "clusters_00_screenshot_13.jpg",
169
+ "clusters_00_screenshot_14.jpg",
170
+ "clusters_00_screenshot_15.jpg",
171
+ "clusters_00_screenshot_16.jpg",
172
+ "clusters_00_screenshot_17.jpg",
173
+ "clusters_00_screenshot_18.jpg",
174
+ "clusters_00_screenshot_19.jpg",
175
+ "clusters_01_screenshot_00.jpg",
176
+ "clusters_01_screenshot_01.jpg",
177
+ "clusters_01_screenshot_02.jpg",
178
+ "clusters_01_screenshot_03.jpg",
179
+ "clusters_01_screenshot_04.jpg",
180
+ "clusters_01_screenshot_05.jpg",
181
+ "clusters_01_screenshot_06.jpg",
182
+ "clusters_01_screenshot_07.jpg",
183
+ "clusters_01_screenshot_08.jpg",
184
+ "clusters_01_screenshot_09.jpg",
185
+ "clusters_01_screenshot_10.jpg",
186
+ "clusters_01_screenshot_11.jpg",
187
+ "clusters_01_screenshot_12.jpg",
188
+ "clusters_01_screenshot_13.jpg",
189
+ "clusters_01_screenshot_14.jpg",
190
+ "clusters_01_screenshot_15.jpg",
191
+ "clusters_01_screenshot_16.jpg",
192
+ "clusters_01_screenshot_17.jpg",
193
+ "clusters_01_screenshot_18.jpg",
194
+ "clusters_01_screenshot_19.jpg",
195
+ "clusters_01_screenshot_20.jpg",
196
+ "clusters_02_screenshot_00.jpg",
197
+ "clusters_02_screenshot_01.jpg",
198
+ "clusters_02_screenshot_02.jpg",
199
+ "clusters_02_screenshot_03.jpg",
200
+ "clusters_02_screenshot_04.jpg",
201
+ "clusters_02_screenshot_05.jpg",
202
+ "clusters_02_screenshot_06.jpg",
203
+ "clusters_02_screenshot_07.jpg",
204
+ "clusters_02_screenshot_08.jpg",
205
+ "clusters_02_screenshot_09.jpg",
206
+ "clusters_02_screenshot_10.jpg",
207
+ "clusters_02_screenshot_11.jpg",
208
+ "clusters_02_screenshot_12.jpg",
209
+ "clusters_02_screenshot_13.jpg",
210
+ "clusters_02_screenshot_14.jpg",
211
+ "clusters_02_screenshot_15.jpg",
212
+ "clusters_02_screenshot_16.jpg",
213
+ "clusters_02_screenshot_17.jpg",
214
+ "clusters_02_screenshot_18.jpg",
215
+ "clusters_02_screenshot_19.jpg",
216
+ "clusters_02_screenshot_20.jpg",
217
+ "clusters_03_screenshot_00.jpg",
218
+ "clusters_03_screenshot_01.jpg",
219
+ "clusters_03_screenshot_02.jpg",
220
+ "clusters_03_screenshot_03.jpg",
221
+ "clusters_03_screenshot_04.jpg",
222
+ "clusters_03_screenshot_05.jpg",
223
+ "clusters_03_screenshot_06.jpg",
224
+ "clusters_03_screenshot_07.jpg",
225
+ "clusters_03_screenshot_08.jpg",
226
+ "clusters_03_screenshot_09.jpg",
227
+ "clusters_03_screenshot_10.jpg",
228
+ "clusters_03_screenshot_11.jpg",
229
+ "clusters_03_screenshot_12.jpg",
230
+ "clusters_03_screenshot_13.jpg",
231
+ "clusters_03_screenshot_14.jpg",
232
+ "clusters_03_screenshot_15.jpg",
233
+ "clusters_03_screenshot_16.jpg",
234
+ "clusters_03_screenshot_17.jpg",
235
+ "clusters_03_screenshot_18.jpg",
236
+ "clusters_03_screenshot_19.jpg",
237
+ "clusters_03_screenshot_20.jpg",
238
+ "clusters_03_screenshot_21.jpg",
239
+ "clusters_04_screenshot_00.jpg",
240
+ "clusters_04_screenshot_01.jpg",
241
+ "clusters_04_screenshot_02.jpg",
242
+ "clusters_04_screenshot_03.jpg",
243
+ "clusters_04_screenshot_04.jpg",
244
+ "clusters_04_screenshot_05.jpg",
245
+ "clusters_04_screenshot_06.jpg",
246
+ "clusters_04_screenshot_07.jpg",
247
+ "clusters_04_screenshot_08.jpg",
248
+ "clusters_04_screenshot_09.jpg",
249
+ "clusters_04_screenshot_10.jpg",
250
+ "clusters_04_screenshot_11.jpg",
251
+ "clusters_04_screenshot_12.jpg",
252
+ "clusters_04_screenshot_13.jpg",
253
+ "clusters_04_screenshot_14.jpg",
254
+ "clusters_04_screenshot_15.jpg",
255
+ "clusters_04_screenshot_16.jpg",
256
+ "clusters_04_screenshot_17.jpg",
257
+ "clusters_04_screenshot_18.jpg",
258
+ "clusters_04_screenshot_19.jpg",
259
+ "clusters_05_screenshot_00.jpg",
260
+ "clusters_05_screenshot_01.jpg",
261
+ "clusters_05_screenshot_02.jpg",
262
+ "clusters_05_screenshot_03.jpg",
263
+ "clusters_05_screenshot_04.jpg",
264
+ "clusters_05_screenshot_05.jpg",
265
+ "clusters_05_screenshot_06.jpg",
266
+ "clusters_05_screenshot_07.jpg",
267
+ "clusters_05_screenshot_08.jpg",
268
+ "clusters_05_screenshot_09.jpg",
269
+ "clusters_05_screenshot_10.jpg",
270
+ "clusters_05_screenshot_11.jpg",
271
+ "clusters_05_screenshot_12.jpg",
272
+ "clusters_05_screenshot_13.jpg",
273
+ "clusters_05_screenshot_14.jpg",
274
+ "clusters_05_screenshot_15.jpg",
275
+ "clusters_05_screenshot_16.jpg",
276
+ "clusters_05_screenshot_17.jpg",
277
+ "clusters_05_screenshot_18.jpg",
278
+ "clusters_05_screenshot_19.jpg",
279
+ "pocket_01.pdb",
280
+ "pocket_02.pdb",
281
+ "pocket_03.pdb",
282
+ "pocket_04.pdb",
283
+ "pocket_05.pdb",
284
+ "pocket_06.pdb",
285
+ "pocket_07.pdb",
286
+ "pocket_08.pdb",
287
+ "pocket_09.pdb",
288
+ "pocket_10.pdb"
289
+ ],
290
+ "analyses": [
291
+ "clusters",
292
+ "clusters-00",
293
+ "clusters-01",
294
+ "clusters-02",
295
+ "clusters-03",
296
+ "clusters-04",
297
+ "clusters-05",
298
+ "dist-perres",
299
+ "energies",
300
+ "fluctuation",
301
+ "hbonds",
302
+ "interactions",
303
+ "pca",
304
+ "pockets",
305
+ "rgyr",
306
+ "rmsd-pairwise",
307
+ "rmsd-perres",
308
+ "rmsds",
309
+ "sasa",
310
+ "tmscores"
311
+ ],
312
+ "mdIndex": 0,
313
+ "mdNumber": 1,
314
+ "refframe": 2,
315
+ "internalId": "683f3fd4e82f4ec7d5ececad",
316
+ "creationDate": "2025-06-03T18:32:52.000Z",
317
+ "identifier": "A0016"
318
+ }
A0016/records.jsonl ADDED
The diff for this file is too large to render. See raw diff
 
A001D/project.json ADDED
@@ -0,0 +1,306 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A001D",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1LJ2",
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
+ "1LJ2"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P03536",
31
+ "Q04637"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "KTIRIRDPNQGGKDITEEIMSG",
38
+ "PKRERKTIRIRDPNQGGKDITEEIMSG",
39
+ "HSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSF",
40
+ "MHSLQNVIPQQQAHIAELQVYNNKLERDLQNKIGSLTSSIEWYLRSMELDPEIKADIEQQINSIDAINPLHAFDDLESVIRNLISDYDKLFLMFKGLIQRSNYQYSFGSE"
41
+ ],
42
+ "NUCLSEQ": [],
43
+ "DOMAINS": [
44
+ "Non-structural protein 3",
45
+ "Dimerization",
46
+ "Interaction with host ZC3H7B",
47
+ "Interaction with host EIF4G1",
48
+ "Eukaryotic translation initiation factor 4 gamma 1",
49
+ "Disordered",
50
+ "PABPC1-binding"
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": 4321,
62
+ "SYSTRES": 265,
63
+ "PROTATS": 4321,
64
+ "PROTRES": 265,
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
+ "PBC_SELECTION": null,
119
+ "CHAINNAMES": null,
120
+ "MEMBRANES": null,
121
+ "CUSTOMS": null,
122
+ "ORIENTATION": null,
123
+ "PTM": [],
124
+ "MULTIMERIC": null,
125
+ "COLLECTIONS": "dynarepo",
126
+ "WARNINGS": [],
127
+ "BOXSIZEX": 12.1659,
128
+ "BOXSIZEY": 12.1659,
129
+ "BOXSIZEZ": 8.6127,
130
+ "mdName": "replica 1",
131
+ "mdAtoms": 4321,
132
+ "mdFrames": 5001
133
+ },
134
+ "mds": [
135
+ "replica 1",
136
+ "replica 2",
137
+ "replica 3"
138
+ ],
139
+ "mdref": 0,
140
+ "files": [
141
+ "topology.tpr",
142
+ "screenshot.jpg",
143
+ "trajectory.bin",
144
+ "pca_trajectory_01.bin",
145
+ "pca_trajectory_02.bin",
146
+ "pca_trajectory_03.bin",
147
+ "pca_trajectory_04.bin",
148
+ "pca_trajectory_05.bin",
149
+ "pca_trajectory_06.bin",
150
+ "pca_trajectory_07.bin",
151
+ "pca_trajectory_08.bin",
152
+ "pca_trajectory_09.bin",
153
+ "pca_trajectory_10.bin",
154
+ "pca_trajectory_11.bin",
155
+ "pca_trajectory_12.bin",
156
+ "pca_trajectory_13.bin",
157
+ "structure.pdb",
158
+ "trajectory.xtc",
159
+ "clusters_00_screenshot_00.jpg",
160
+ "clusters_00_screenshot_01.jpg",
161
+ "clusters_00_screenshot_02.jpg",
162
+ "clusters_00_screenshot_03.jpg",
163
+ "clusters_00_screenshot_04.jpg",
164
+ "clusters_00_screenshot_05.jpg",
165
+ "clusters_00_screenshot_06.jpg",
166
+ "clusters_00_screenshot_07.jpg",
167
+ "clusters_00_screenshot_08.jpg",
168
+ "clusters_00_screenshot_09.jpg",
169
+ "clusters_00_screenshot_10.jpg",
170
+ "clusters_00_screenshot_11.jpg",
171
+ "clusters_00_screenshot_12.jpg",
172
+ "clusters_00_screenshot_13.jpg",
173
+ "clusters_00_screenshot_14.jpg",
174
+ "clusters_00_screenshot_15.jpg",
175
+ "clusters_00_screenshot_16.jpg",
176
+ "clusters_00_screenshot_17.jpg",
177
+ "clusters_00_screenshot_18.jpg",
178
+ "clusters_00_screenshot_19.jpg",
179
+ "clusters_00_screenshot_20.jpg",
180
+ "clusters_01_screenshot_00.jpg",
181
+ "clusters_01_screenshot_01.jpg",
182
+ "clusters_01_screenshot_02.jpg",
183
+ "clusters_01_screenshot_03.jpg",
184
+ "clusters_01_screenshot_04.jpg",
185
+ "clusters_01_screenshot_05.jpg",
186
+ "clusters_01_screenshot_06.jpg",
187
+ "clusters_01_screenshot_07.jpg",
188
+ "clusters_01_screenshot_08.jpg",
189
+ "clusters_01_screenshot_09.jpg",
190
+ "clusters_01_screenshot_10.jpg",
191
+ "clusters_01_screenshot_11.jpg",
192
+ "clusters_01_screenshot_12.jpg",
193
+ "clusters_01_screenshot_13.jpg",
194
+ "clusters_01_screenshot_14.jpg",
195
+ "clusters_01_screenshot_15.jpg",
196
+ "clusters_01_screenshot_16.jpg",
197
+ "clusters_01_screenshot_17.jpg",
198
+ "clusters_01_screenshot_18.jpg",
199
+ "clusters_01_screenshot_19.jpg",
200
+ "clusters_02_screenshot_00.jpg",
201
+ "clusters_02_screenshot_01.jpg",
202
+ "clusters_02_screenshot_02.jpg",
203
+ "clusters_02_screenshot_03.jpg",
204
+ "clusters_02_screenshot_04.jpg",
205
+ "clusters_02_screenshot_05.jpg",
206
+ "clusters_02_screenshot_06.jpg",
207
+ "clusters_02_screenshot_07.jpg",
208
+ "clusters_02_screenshot_08.jpg",
209
+ "clusters_02_screenshot_09.jpg",
210
+ "clusters_02_screenshot_10.jpg",
211
+ "clusters_02_screenshot_11.jpg",
212
+ "clusters_02_screenshot_12.jpg",
213
+ "clusters_02_screenshot_13.jpg",
214
+ "clusters_02_screenshot_14.jpg",
215
+ "clusters_02_screenshot_15.jpg",
216
+ "clusters_02_screenshot_16.jpg",
217
+ "clusters_02_screenshot_17.jpg",
218
+ "clusters_02_screenshot_18.jpg",
219
+ "clusters_02_screenshot_19.jpg",
220
+ "clusters_03_screenshot_00.jpg",
221
+ "clusters_03_screenshot_01.jpg",
222
+ "clusters_03_screenshot_02.jpg",
223
+ "clusters_03_screenshot_03.jpg",
224
+ "clusters_03_screenshot_04.jpg",
225
+ "clusters_03_screenshot_05.jpg",
226
+ "clusters_03_screenshot_06.jpg",
227
+ "clusters_03_screenshot_07.jpg",
228
+ "clusters_03_screenshot_08.jpg",
229
+ "clusters_03_screenshot_09.jpg",
230
+ "clusters_03_screenshot_10.jpg",
231
+ "clusters_03_screenshot_11.jpg",
232
+ "clusters_03_screenshot_12.jpg",
233
+ "clusters_03_screenshot_13.jpg",
234
+ "clusters_03_screenshot_14.jpg",
235
+ "clusters_03_screenshot_15.jpg",
236
+ "clusters_03_screenshot_16.jpg",
237
+ "clusters_03_screenshot_17.jpg",
238
+ "clusters_03_screenshot_18.jpg",
239
+ "clusters_03_screenshot_19.jpg",
240
+ "clusters_03_screenshot_20.jpg",
241
+ "clusters_04_screenshot_00.jpg",
242
+ "clusters_04_screenshot_01.jpg",
243
+ "clusters_04_screenshot_02.jpg",
244
+ "clusters_04_screenshot_03.jpg",
245
+ "clusters_04_screenshot_04.jpg",
246
+ "clusters_04_screenshot_05.jpg",
247
+ "clusters_04_screenshot_06.jpg",
248
+ "clusters_04_screenshot_07.jpg",
249
+ "clusters_04_screenshot_08.jpg",
250
+ "clusters_04_screenshot_09.jpg",
251
+ "clusters_04_screenshot_10.jpg",
252
+ "clusters_04_screenshot_11.jpg",
253
+ "clusters_04_screenshot_12.jpg",
254
+ "clusters_04_screenshot_13.jpg",
255
+ "clusters_04_screenshot_14.jpg",
256
+ "clusters_04_screenshot_15.jpg",
257
+ "clusters_04_screenshot_16.jpg",
258
+ "clusters_04_screenshot_17.jpg",
259
+ "clusters_05_screenshot_00.jpg",
260
+ "clusters_05_screenshot_01.jpg",
261
+ "clusters_05_screenshot_02.jpg",
262
+ "clusters_05_screenshot_03.jpg",
263
+ "clusters_05_screenshot_04.jpg",
264
+ "clusters_05_screenshot_05.jpg",
265
+ "clusters_05_screenshot_06.jpg",
266
+ "clusters_05_screenshot_07.jpg",
267
+ "clusters_05_screenshot_08.jpg",
268
+ "clusters_05_screenshot_09.jpg",
269
+ "clusters_05_screenshot_10.jpg",
270
+ "clusters_05_screenshot_11.jpg",
271
+ "clusters_05_screenshot_12.jpg",
272
+ "clusters_05_screenshot_13.jpg",
273
+ "clusters_05_screenshot_14.jpg",
274
+ "clusters_05_screenshot_15.jpg",
275
+ "clusters_05_screenshot_16.jpg",
276
+ "clusters_05_screenshot_17.jpg",
277
+ "clusters_05_screenshot_18.jpg"
278
+ ],
279
+ "analyses": [
280
+ "clusters",
281
+ "clusters-00",
282
+ "clusters-01",
283
+ "clusters-02",
284
+ "clusters-03",
285
+ "clusters-04",
286
+ "clusters-05",
287
+ "dist-perres",
288
+ "energies",
289
+ "fluctuation",
290
+ "hbonds",
291
+ "interactions",
292
+ "pca",
293
+ "rgyr",
294
+ "rmsd-pairwise",
295
+ "rmsd-perres",
296
+ "rmsds",
297
+ "sasa",
298
+ "tmscores"
299
+ ],
300
+ "mdIndex": 0,
301
+ "mdNumber": 1,
302
+ "refframe": 0,
303
+ "internalId": "683f4db5bcf7c4a2946bd706",
304
+ "creationDate": "2025-06-03T19:32:05.000Z",
305
+ "identifier": "A001D"
306
+ }
A001D/records.jsonl ADDED
The diff for this file is too large to render. See raw diff
 
A001I/project.json ADDED
@@ -0,0 +1,189 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A001I",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1MQ8",
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
+ "1MQ8"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P05362",
31
+ "P20701"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "VDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI",
38
+ "QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQT"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Intercellular adhesion molecule 1",
43
+ "Ig-like C2-type 1",
44
+ "Ig-like C2-type 2",
45
+ "Cell attachment site; atypical",
46
+ "Integrin alpha-L",
47
+ "VWFA"
48
+ ],
49
+ "FRAMESTEP": 0.1,
50
+ "TIMESTEP": 2,
51
+ "TEMP": 310,
52
+ "ENSEMBLE": "NPT",
53
+ "FF": [
54
+ "CHARMM36m"
55
+ ],
56
+ "WAT": "TIP3P",
57
+ "BOXTYPE": "Dodecahedron",
58
+ "SYSTATS": 5705,
59
+ "SYSTRES": 361,
60
+ "PROTATS": 5705,
61
+ "PROTRES": 361,
62
+ "NUCLATS": 0,
63
+ "NUCLRES": 0,
64
+ "LIPIATS": 0,
65
+ "LIPIRES": 0,
66
+ "CARBATS": 0,
67
+ "CARBRES": 0,
68
+ "SOLVATS": 0,
69
+ "SOLVRES": 0,
70
+ "COUNCAT": 0,
71
+ "COUNANI": 0,
72
+ "COUNION": 0,
73
+ "INTERACTIONS": [
74
+ {
75
+ "name": "chain A-chain B interaction",
76
+ "agent_1": "chain A",
77
+ "agent_2": "chain B",
78
+ "selection_1": "chain A",
79
+ "selection_2": "chain B",
80
+ "type": "protein-protein"
81
+ }
82
+ ],
83
+ "PBC_SELECTION": null,
84
+ "CHAINNAMES": null,
85
+ "MEMBRANES": null,
86
+ "CUSTOMS": null,
87
+ "ORIENTATION": null,
88
+ "PTM": [],
89
+ "MULTIMERIC": null,
90
+ "COLLECTIONS": "dynarepo",
91
+ "WARNINGS": [],
92
+ "BOXSIZEX": 11.9032,
93
+ "BOXSIZEY": 11.9032,
94
+ "BOXSIZEZ": 8.40875,
95
+ "mdName": "replica 1",
96
+ "mdAtoms": 5705,
97
+ "mdFrames": 5001
98
+ },
99
+ "mds": [
100
+ "replica 1",
101
+ "replica 2",
102
+ "replica 3"
103
+ ],
104
+ "mdref": 0,
105
+ "files": [
106
+ "topology.tpr",
107
+ "screenshot.jpg",
108
+ "trajectory.bin",
109
+ "pca_trajectory_01.bin",
110
+ "pca_trajectory_02.bin",
111
+ "pca_trajectory_03.bin",
112
+ "pca_trajectory_04.bin",
113
+ "pca_trajectory_05.bin",
114
+ "pca_trajectory_06.bin",
115
+ "pca_trajectory_07.bin",
116
+ "pca_trajectory_08.bin",
117
+ "structure.pdb",
118
+ "trajectory.xtc",
119
+ "clusters_00_screenshot_00.jpg",
120
+ "clusters_00_screenshot_01.jpg",
121
+ "clusters_00_screenshot_02.jpg",
122
+ "clusters_00_screenshot_03.jpg",
123
+ "clusters_00_screenshot_04.jpg",
124
+ "clusters_00_screenshot_05.jpg",
125
+ "clusters_00_screenshot_06.jpg",
126
+ "clusters_00_screenshot_07.jpg",
127
+ "clusters_00_screenshot_08.jpg",
128
+ "clusters_00_screenshot_09.jpg",
129
+ "clusters_00_screenshot_10.jpg",
130
+ "clusters_00_screenshot_11.jpg",
131
+ "clusters_00_screenshot_12.jpg",
132
+ "clusters_00_screenshot_13.jpg",
133
+ "clusters_00_screenshot_14.jpg",
134
+ "clusters_00_screenshot_15.jpg",
135
+ "clusters_00_screenshot_16.jpg",
136
+ "clusters_00_screenshot_17.jpg",
137
+ "clusters_00_screenshot_18.jpg",
138
+ "clusters_00_screenshot_19.jpg",
139
+ "clusters_00_screenshot_20.jpg",
140
+ "clusters_00_screenshot_21.jpg",
141
+ "clusters_01_screenshot_00.jpg",
142
+ "clusters_01_screenshot_01.jpg",
143
+ "clusters_01_screenshot_02.jpg",
144
+ "clusters_01_screenshot_03.jpg",
145
+ "clusters_01_screenshot_04.jpg",
146
+ "clusters_01_screenshot_05.jpg",
147
+ "clusters_01_screenshot_06.jpg",
148
+ "clusters_01_screenshot_07.jpg",
149
+ "clusters_01_screenshot_08.jpg",
150
+ "clusters_01_screenshot_09.jpg",
151
+ "clusters_01_screenshot_10.jpg",
152
+ "clusters_01_screenshot_11.jpg",
153
+ "clusters_01_screenshot_12.jpg",
154
+ "clusters_01_screenshot_13.jpg",
155
+ "clusters_01_screenshot_14.jpg",
156
+ "clusters_01_screenshot_15.jpg",
157
+ "clusters_01_screenshot_16.jpg",
158
+ "clusters_01_screenshot_17.jpg",
159
+ "clusters_01_screenshot_18.jpg",
160
+ "clusters_01_screenshot_19.jpg",
161
+ "clusters_01_screenshot_20.jpg",
162
+ "pocket_01.pdb",
163
+ "pocket_02.pdb"
164
+ ],
165
+ "analyses": [
166
+ "clusters",
167
+ "clusters-00",
168
+ "clusters-01",
169
+ "dist-perres",
170
+ "energies",
171
+ "fluctuation",
172
+ "hbonds",
173
+ "interactions",
174
+ "pca",
175
+ "pockets",
176
+ "rgyr",
177
+ "rmsd-pairwise",
178
+ "rmsd-perres",
179
+ "rmsds",
180
+ "sasa",
181
+ "tmscores"
182
+ ],
183
+ "mdIndex": 0,
184
+ "mdNumber": 1,
185
+ "refframe": 0,
186
+ "internalId": "683f53a1b9e3119e941968bb",
187
+ "creationDate": "2025-06-03T19:57:21.000Z",
188
+ "identifier": "A001I"
189
+ }
A001I/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A001I", "accession": "A001I", "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 1MQ8", "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": ["1MQ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P05362", "P20701"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI", "QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQT"], "NUCLSEQ": [], "DOMAINS": ["Intercellular adhesion molecule 1", "Ig-like C2-type 1", "Ig-like C2-type 2", "Cell attachment site; atypical", "Integrin alpha-L", "VWFA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 5705, "SYSTRES": 361, "PROTATS": 5705, "PROTRES": 361, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.9032, "BOXSIZEY": 11.9032, "BOXSIZEZ": 8.40875, "mdName": "replica 1", "mdAtoms": 5705, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001I/files/topology.tpr", "length": 1959144, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001I/files/screenshot.jpg", "length": 18024, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001I/files/trajectory.bin", "length": 342368460, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 5001, "atoms": 5705}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_01.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_02.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_03.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_04.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_05.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_06.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_07.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_08.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001I/files/structure.pdb", "length": 462140, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001I/files/trajectory.xtc", "length": 108926208, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_00.jpg", "length": 18387, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_01.jpg", "length": 18738, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_02.jpg", "length": 17924, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_03.jpg", "length": 17643, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_04.jpg", "length": 17614, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_05.jpg", "length": 18064, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_06.jpg", "length": 18286, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_07.jpg", "length": 18583, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_08.jpg", "length": 17417, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_09.jpg", "length": 17457, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_10.jpg", "length": 16893, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_11.jpg", "length": 18311, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_12.jpg", "length": 17534, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_13.jpg", "length": 18359, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_14.jpg", "length": 16894, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_15.jpg", "length": 18600, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_16.jpg", "length": 16991, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_17.jpg", "length": 18179, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_18.jpg", "length": 17754, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_19.jpg", "length": 18254, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_20.jpg", "length": 17414, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_21.jpg", "length": 18315, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_00.jpg", "length": 18681, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_01.jpg", "length": 18523, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_02.jpg", "length": 18765, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_03.jpg", "length": 17071, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_04.jpg", "length": 18308, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_05.jpg", "length": 18003, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_06.jpg", "length": 18568, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_07.jpg", "length": 18259, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_08.jpg", "length": 17071, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_09.jpg", "length": 17296, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_10.jpg", "length": 16605, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_11.jpg", "length": 18273, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_12.jpg", "length": 18674, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_13.jpg", "length": 16866, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_14.jpg", "length": 17877, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_15.jpg", "length": 18006, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_16.jpg", "length": 18594, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_17.jpg", "length": 17893, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_18.jpg", "length": 18490, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_19.jpg", "length": 17756, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_20.jpg", "length": 18070, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001I/files/pocket_01.pdb", "length": 8442, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001I/files/pocket_02.pdb", "length": 3752, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}]}
2
+ {"project_identifier": "A001I", "accession": "A001I", "published": true, "md_index": 1, "md_name": "replica 2", "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 1MQ8", "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": ["1MQ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P05362", "P20701"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI", "QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQT"], "NUCLSEQ": [], "DOMAINS": ["Intercellular adhesion molecule 1", "Ig-like C2-type 1", "Ig-like C2-type 2", "Cell attachment site; atypical", "Integrin alpha-L", "VWFA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 5705, "SYSTRES": 361, "PROTATS": 5705, "PROTRES": 361, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.9032, "BOXSIZEY": 11.9032, "BOXSIZEZ": 8.40875, "mdName": "replica 1", "mdAtoms": 5705, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001I/files/topology.tpr", "length": 1959144, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001I/files/screenshot.jpg", "length": 18024, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001I/files/trajectory.bin", "length": 342368460, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 5001, "atoms": 5705}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_01.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_02.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_03.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_04.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_05.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_06.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_07.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_08.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001I/files/structure.pdb", "length": 462140, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001I/files/trajectory.xtc", "length": 108926208, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_00.jpg", "length": 18387, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_01.jpg", "length": 18738, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_02.jpg", "length": 17924, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_03.jpg", "length": 17643, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_04.jpg", "length": 17614, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_05.jpg", "length": 18064, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_06.jpg", "length": 18286, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_07.jpg", "length": 18583, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_08.jpg", "length": 17417, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_09.jpg", "length": 17457, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_10.jpg", "length": 16893, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_11.jpg", "length": 18311, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_12.jpg", "length": 17534, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_13.jpg", "length": 18359, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_14.jpg", "length": 16894, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_15.jpg", "length": 18600, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_16.jpg", "length": 16991, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_17.jpg", "length": 18179, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_18.jpg", "length": 17754, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_19.jpg", "length": 18254, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_20.jpg", "length": 17414, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_21.jpg", "length": 18315, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_00.jpg", "length": 18681, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_01.jpg", "length": 18523, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_02.jpg", "length": 18765, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_03.jpg", "length": 17071, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_04.jpg", "length": 18308, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_05.jpg", "length": 18003, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_06.jpg", "length": 18568, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_07.jpg", "length": 18259, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_08.jpg", "length": 17071, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_09.jpg", "length": 17296, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_10.jpg", "length": 16605, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_11.jpg", "length": 18273, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_12.jpg", "length": 18674, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_13.jpg", "length": 16866, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_14.jpg", "length": 17877, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_15.jpg", "length": 18006, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_16.jpg", "length": 18594, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_17.jpg", "length": 17893, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_18.jpg", "length": 18490, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_19.jpg", "length": 17756, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_20.jpg", "length": 18070, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001I/files/pocket_01.pdb", "length": 8442, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001I/files/pocket_02.pdb", "length": 3752, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}]}
3
+ {"project_identifier": "A001I", "accession": "A001I", "published": true, "md_index": 2, "md_name": "replica 3", "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 1MQ8", "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": ["1MQ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P05362", "P20701"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VDLVFLFDGSMSLQPDEFQKILDFMKDVMKKCSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLCTELQKKI", "QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQEDSQPMCYSNCPDGQSTAKTFLTVYWTPERVELAPLPSWQPVGKNLTLRCQVEGGAPRANLTVVLLRGEKELKREPAVGEPAEVTTTVLVRRDHHGANFSCRTELDLRPQGLELFENTSAPYQLQT"], "NUCLSEQ": [], "DOMAINS": ["Intercellular adhesion molecule 1", "Ig-like C2-type 1", "Ig-like C2-type 2", "Cell attachment site; atypical", "Integrin alpha-L", "VWFA"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 5705, "SYSTRES": 361, "PROTATS": 5705, "PROTRES": 361, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.9032, "BOXSIZEY": 11.9032, "BOXSIZEZ": 8.40875, "mdName": "replica 1", "mdAtoms": 5705, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001I/files/topology.tpr", "length": 1959144, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001I/files/screenshot.jpg", "length": 18024, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001I/files/trajectory.bin", "length": 342368460, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 5001, "atoms": 5705}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_01.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_02.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_03.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_04.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_05.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_06.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_07.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001I/files/pca_trajectory_08.bin", "length": 259920, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0, "frames": 20, "atoms": 1083}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001I/files/structure.pdb", "length": 462140, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001I/files/trajectory.xtc", "length": 108926208, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_00.jpg", "length": 18387, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_01.jpg", "length": 18738, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_02.jpg", "length": 17924, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_03.jpg", "length": 17643, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_04.jpg", "length": 17614, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_05.jpg", "length": 18064, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_06.jpg", "length": 18286, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_07.jpg", "length": 18583, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_08.jpg", "length": 17417, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_09.jpg", "length": 17457, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_10.jpg", "length": 16893, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_11.jpg", "length": 18311, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_12.jpg", "length": 17534, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_13.jpg", "length": 18359, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_14.jpg", "length": 16894, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_15.jpg", "length": 18600, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_16.jpg", "length": 16991, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_17.jpg", "length": 18179, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_18.jpg", "length": 17754, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_19.jpg", "length": 18254, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_20.jpg", "length": 17414, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A001I/files/clusters_00_screenshot_21.jpg", "length": 18315, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_00.jpg", "length": 18681, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_01.jpg", "length": 18523, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_02.jpg", "length": 18765, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_03.jpg", "length": 17071, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_04.jpg", "length": 18308, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_05.jpg", "length": 18003, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_06.jpg", "length": 18568, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_07.jpg", "length": 18259, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_08.jpg", "length": 17071, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_09.jpg", "length": 17296, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_10.jpg", "length": 16605, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_11.jpg", "length": 18273, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_12.jpg", "length": 18674, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_13.jpg", "length": 16866, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_14.jpg", "length": 17877, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_15.jpg", "length": 18006, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_16.jpg", "length": 18594, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_17.jpg", "length": 17893, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_18.jpg", "length": 18490, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_19.jpg", "length": 17756, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A001I/files/clusters_01_screenshot_20.jpg", "length": 18070, "contentType": "application/octet-stream", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001I/files/pocket_01.pdb", "length": 8442, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001I/files/pocket_02.pdb", "length": 3752, "contentType": "chemical/x-pdb", "metadata": {"project": "683f53a1b9e3119e941968bb", "md": 0}}]}
A001S/project.json ADDED
@@ -0,0 +1,555 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A001S",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1RLB",
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
+ "1RLB"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P02766",
31
+ "P02753"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "TGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEQFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE",
38
+ "ERDCRVSSFRVKENFDKARFAGTWYAMAKKDPEGLFLQDNIVAEFSVDENGHMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLNLDGTCADSYSFVFARDPSGFSPQVQKIVRQRQEELCLARQYRLIPHNGYC",
39
+ "SKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEQFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE"
40
+ ],
41
+ "NUCLSEQ": [],
42
+ "DOMAINS": [
43
+ "Transthyretin",
44
+ "Retinol-binding protein 4",
45
+ "Plasma retinol-binding protein(1-182)",
46
+ "Plasma retinol-binding protein(1-181)",
47
+ "Plasma retinol-binding protein(1-179)",
48
+ "Plasma retinol-binding protein(1-176)"
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": 12928,
60
+ "SYSTRES": 834,
61
+ "PROTATS": 12928,
62
+ "PROTRES": 834,
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
+ "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 A-chain D interaction",
93
+ "agent_1": "chain A",
94
+ "agent_2": "chain D",
95
+ "selection_1": "chain A",
96
+ "selection_2": "chain D",
97
+ "type": "protein-protein"
98
+ },
99
+ {
100
+ "name": "chain A-chain E interaction",
101
+ "agent_1": "chain A",
102
+ "agent_2": "chain E",
103
+ "selection_1": "chain A",
104
+ "selection_2": "chain E",
105
+ "type": "protein-protein"
106
+ },
107
+ {
108
+ "name": "chain A-chain F interaction",
109
+ "agent_1": "chain A",
110
+ "agent_2": "chain F",
111
+ "selection_1": "chain A",
112
+ "selection_2": "chain F",
113
+ "type": "protein-protein"
114
+ },
115
+ {
116
+ "name": "chain B-chain C interaction",
117
+ "agent_1": "chain B",
118
+ "agent_2": "chain C",
119
+ "selection_1": "chain B",
120
+ "selection_2": "chain C",
121
+ "type": "protein-protein"
122
+ },
123
+ {
124
+ "name": "chain B-chain D interaction",
125
+ "agent_1": "chain B",
126
+ "agent_2": "chain D",
127
+ "selection_1": "chain B",
128
+ "selection_2": "chain D",
129
+ "type": "protein-protein"
130
+ },
131
+ {
132
+ "name": "chain B-chain E interaction",
133
+ "agent_1": "chain B",
134
+ "agent_2": "chain E",
135
+ "selection_1": "chain B",
136
+ "selection_2": "chain E",
137
+ "type": "protein-protein"
138
+ },
139
+ {
140
+ "name": "chain B-chain F interaction",
141
+ "agent_1": "chain B",
142
+ "agent_2": "chain F",
143
+ "selection_1": "chain B",
144
+ "selection_2": "chain F",
145
+ "type": "protein-protein"
146
+ },
147
+ {
148
+ "name": "chain C-chain D interaction",
149
+ "agent_1": "chain C",
150
+ "agent_2": "chain D",
151
+ "selection_1": "chain C",
152
+ "selection_2": "chain D",
153
+ "type": "protein-protein"
154
+ },
155
+ {
156
+ "name": "chain C-chain E interaction",
157
+ "agent_1": "chain C",
158
+ "agent_2": "chain E",
159
+ "selection_1": "chain C",
160
+ "selection_2": "chain E",
161
+ "type": "protein-protein"
162
+ },
163
+ {
164
+ "name": "chain C-chain F interaction",
165
+ "agent_1": "chain C",
166
+ "agent_2": "chain F",
167
+ "selection_1": "chain C",
168
+ "selection_2": "chain F",
169
+ "type": "protein-protein"
170
+ },
171
+ {
172
+ "name": "chain D-chain F interaction",
173
+ "agent_1": "chain D",
174
+ "agent_2": "chain F",
175
+ "selection_1": "chain D",
176
+ "selection_2": "chain E",
177
+ "type": "protein-protein"
178
+ }
179
+ ],
180
+ "PBC_SELECTION": null,
181
+ "CHAINNAMES": null,
182
+ "MEMBRANES": null,
183
+ "CUSTOMS": null,
184
+ "ORIENTATION": null,
185
+ "PTM": [],
186
+ "MULTIMERIC": null,
187
+ "COLLECTIONS": "dynarepo",
188
+ "WARNINGS": [],
189
+ "BOXSIZEX": 14.5995,
190
+ "BOXSIZEY": 14.5995,
191
+ "BOXSIZEZ": 10.3657,
192
+ "mdName": "replica 1",
193
+ "mdAtoms": 12928,
194
+ "mdFrames": 5001
195
+ },
196
+ "mds": [
197
+ "replica 1",
198
+ "replica 2",
199
+ "replica 3"
200
+ ],
201
+ "mdref": 0,
202
+ "files": [
203
+ "topology.tpr",
204
+ "screenshot.jpg",
205
+ "trajectory.bin",
206
+ "pca_trajectory_01.bin",
207
+ "pca_trajectory_02.bin",
208
+ "pca_trajectory_03.bin",
209
+ "pca_trajectory_04.bin",
210
+ "pca_trajectory_05.bin",
211
+ "pca_trajectory_06.bin",
212
+ "pca_trajectory_07.bin",
213
+ "pca_trajectory_08.bin",
214
+ "pca_trajectory_09.bin",
215
+ "pca_trajectory_10.bin",
216
+ "structure.pdb",
217
+ "trajectory.xtc",
218
+ "clusters_00_screenshot_00.jpg",
219
+ "clusters_00_screenshot_01.jpg",
220
+ "clusters_00_screenshot_02.jpg",
221
+ "clusters_00_screenshot_03.jpg",
222
+ "clusters_00_screenshot_04.jpg",
223
+ "clusters_00_screenshot_05.jpg",
224
+ "clusters_00_screenshot_06.jpg",
225
+ "clusters_00_screenshot_07.jpg",
226
+ "clusters_00_screenshot_08.jpg",
227
+ "clusters_00_screenshot_09.jpg",
228
+ "clusters_00_screenshot_10.jpg",
229
+ "clusters_00_screenshot_11.jpg",
230
+ "clusters_00_screenshot_12.jpg",
231
+ "clusters_00_screenshot_13.jpg",
232
+ "clusters_00_screenshot_14.jpg",
233
+ "clusters_00_screenshot_15.jpg",
234
+ "clusters_00_screenshot_16.jpg",
235
+ "clusters_00_screenshot_17.jpg",
236
+ "clusters_00_screenshot_18.jpg",
237
+ "clusters_00_screenshot_19.jpg",
238
+ "clusters_00_screenshot_20.jpg",
239
+ "clusters_00_screenshot_21.jpg",
240
+ "clusters_01_screenshot_00.jpg",
241
+ "clusters_01_screenshot_01.jpg",
242
+ "clusters_01_screenshot_02.jpg",
243
+ "clusters_01_screenshot_03.jpg",
244
+ "clusters_01_screenshot_04.jpg",
245
+ "clusters_01_screenshot_05.jpg",
246
+ "clusters_01_screenshot_06.jpg",
247
+ "clusters_01_screenshot_07.jpg",
248
+ "clusters_01_screenshot_08.jpg",
249
+ "clusters_01_screenshot_09.jpg",
250
+ "clusters_01_screenshot_10.jpg",
251
+ "clusters_01_screenshot_11.jpg",
252
+ "clusters_01_screenshot_12.jpg",
253
+ "clusters_01_screenshot_13.jpg",
254
+ "clusters_01_screenshot_14.jpg",
255
+ "clusters_01_screenshot_15.jpg",
256
+ "clusters_01_screenshot_16.jpg",
257
+ "clusters_01_screenshot_17.jpg",
258
+ "clusters_01_screenshot_18.jpg",
259
+ "clusters_02_screenshot_00.jpg",
260
+ "clusters_02_screenshot_01.jpg",
261
+ "clusters_02_screenshot_02.jpg",
262
+ "clusters_02_screenshot_03.jpg",
263
+ "clusters_02_screenshot_04.jpg",
264
+ "clusters_02_screenshot_05.jpg",
265
+ "clusters_02_screenshot_06.jpg",
266
+ "clusters_02_screenshot_07.jpg",
267
+ "clusters_02_screenshot_08.jpg",
268
+ "clusters_02_screenshot_09.jpg",
269
+ "clusters_02_screenshot_10.jpg",
270
+ "clusters_02_screenshot_11.jpg",
271
+ "clusters_02_screenshot_12.jpg",
272
+ "clusters_02_screenshot_13.jpg",
273
+ "clusters_02_screenshot_14.jpg",
274
+ "clusters_02_screenshot_15.jpg",
275
+ "clusters_02_screenshot_16.jpg",
276
+ "clusters_02_screenshot_17.jpg",
277
+ "clusters_02_screenshot_18.jpg",
278
+ "clusters_02_screenshot_19.jpg",
279
+ "clusters_03_screenshot_00.jpg",
280
+ "clusters_03_screenshot_01.jpg",
281
+ "clusters_03_screenshot_02.jpg",
282
+ "clusters_03_screenshot_03.jpg",
283
+ "clusters_03_screenshot_04.jpg",
284
+ "clusters_03_screenshot_05.jpg",
285
+ "clusters_03_screenshot_06.jpg",
286
+ "clusters_03_screenshot_07.jpg",
287
+ "clusters_03_screenshot_08.jpg",
288
+ "clusters_03_screenshot_09.jpg",
289
+ "clusters_03_screenshot_10.jpg",
290
+ "clusters_03_screenshot_11.jpg",
291
+ "clusters_03_screenshot_12.jpg",
292
+ "clusters_03_screenshot_13.jpg",
293
+ "clusters_03_screenshot_14.jpg",
294
+ "clusters_03_screenshot_15.jpg",
295
+ "clusters_03_screenshot_16.jpg",
296
+ "clusters_03_screenshot_17.jpg",
297
+ "clusters_03_screenshot_18.jpg",
298
+ "clusters_03_screenshot_19.jpg",
299
+ "clusters_04_screenshot_00.jpg",
300
+ "clusters_04_screenshot_01.jpg",
301
+ "clusters_04_screenshot_02.jpg",
302
+ "clusters_04_screenshot_03.jpg",
303
+ "clusters_04_screenshot_04.jpg",
304
+ "clusters_04_screenshot_05.jpg",
305
+ "clusters_04_screenshot_06.jpg",
306
+ "clusters_04_screenshot_07.jpg",
307
+ "clusters_04_screenshot_08.jpg",
308
+ "clusters_04_screenshot_09.jpg",
309
+ "clusters_04_screenshot_10.jpg",
310
+ "clusters_04_screenshot_11.jpg",
311
+ "clusters_04_screenshot_12.jpg",
312
+ "clusters_04_screenshot_13.jpg",
313
+ "clusters_04_screenshot_14.jpg",
314
+ "clusters_04_screenshot_15.jpg",
315
+ "clusters_04_screenshot_16.jpg",
316
+ "clusters_04_screenshot_17.jpg",
317
+ "clusters_04_screenshot_18.jpg",
318
+ "clusters_04_screenshot_19.jpg",
319
+ "clusters_04_screenshot_20.jpg",
320
+ "clusters_05_screenshot_00.jpg",
321
+ "clusters_05_screenshot_01.jpg",
322
+ "clusters_05_screenshot_02.jpg",
323
+ "clusters_05_screenshot_03.jpg",
324
+ "clusters_05_screenshot_04.jpg",
325
+ "clusters_05_screenshot_05.jpg",
326
+ "clusters_05_screenshot_06.jpg",
327
+ "clusters_05_screenshot_07.jpg",
328
+ "clusters_05_screenshot_08.jpg",
329
+ "clusters_05_screenshot_09.jpg",
330
+ "clusters_05_screenshot_10.jpg",
331
+ "clusters_05_screenshot_11.jpg",
332
+ "clusters_05_screenshot_12.jpg",
333
+ "clusters_05_screenshot_13.jpg",
334
+ "clusters_05_screenshot_14.jpg",
335
+ "clusters_05_screenshot_15.jpg",
336
+ "clusters_05_screenshot_16.jpg",
337
+ "clusters_05_screenshot_17.jpg",
338
+ "clusters_05_screenshot_18.jpg",
339
+ "clusters_05_screenshot_19.jpg",
340
+ "clusters_05_screenshot_20.jpg",
341
+ "clusters_05_screenshot_21.jpg",
342
+ "clusters_06_screenshot_00.jpg",
343
+ "clusters_06_screenshot_01.jpg",
344
+ "clusters_06_screenshot_02.jpg",
345
+ "clusters_06_screenshot_03.jpg",
346
+ "clusters_06_screenshot_04.jpg",
347
+ "clusters_06_screenshot_05.jpg",
348
+ "clusters_06_screenshot_06.jpg",
349
+ "clusters_06_screenshot_07.jpg",
350
+ "clusters_06_screenshot_08.jpg",
351
+ "clusters_06_screenshot_09.jpg",
352
+ "clusters_06_screenshot_10.jpg",
353
+ "clusters_06_screenshot_11.jpg",
354
+ "clusters_06_screenshot_12.jpg",
355
+ "clusters_06_screenshot_13.jpg",
356
+ "clusters_06_screenshot_14.jpg",
357
+ "clusters_06_screenshot_15.jpg",
358
+ "clusters_06_screenshot_16.jpg",
359
+ "clusters_06_screenshot_17.jpg",
360
+ "clusters_06_screenshot_18.jpg",
361
+ "clusters_07_screenshot_00.jpg",
362
+ "clusters_07_screenshot_01.jpg",
363
+ "clusters_07_screenshot_02.jpg",
364
+ "clusters_07_screenshot_03.jpg",
365
+ "clusters_07_screenshot_04.jpg",
366
+ "clusters_07_screenshot_05.jpg",
367
+ "clusters_07_screenshot_06.jpg",
368
+ "clusters_07_screenshot_07.jpg",
369
+ "clusters_07_screenshot_08.jpg",
370
+ "clusters_07_screenshot_09.jpg",
371
+ "clusters_07_screenshot_10.jpg",
372
+ "clusters_07_screenshot_11.jpg",
373
+ "clusters_07_screenshot_12.jpg",
374
+ "clusters_07_screenshot_13.jpg",
375
+ "clusters_07_screenshot_14.jpg",
376
+ "clusters_07_screenshot_15.jpg",
377
+ "clusters_07_screenshot_16.jpg",
378
+ "clusters_07_screenshot_17.jpg",
379
+ "clusters_07_screenshot_18.jpg",
380
+ "clusters_08_screenshot_00.jpg",
381
+ "clusters_08_screenshot_01.jpg",
382
+ "clusters_08_screenshot_02.jpg",
383
+ "clusters_08_screenshot_03.jpg",
384
+ "clusters_08_screenshot_04.jpg",
385
+ "clusters_08_screenshot_05.jpg",
386
+ "clusters_08_screenshot_06.jpg",
387
+ "clusters_08_screenshot_07.jpg",
388
+ "clusters_08_screenshot_08.jpg",
389
+ "clusters_08_screenshot_09.jpg",
390
+ "clusters_08_screenshot_10.jpg",
391
+ "clusters_08_screenshot_11.jpg",
392
+ "clusters_08_screenshot_12.jpg",
393
+ "clusters_08_screenshot_13.jpg",
394
+ "clusters_08_screenshot_14.jpg",
395
+ "clusters_08_screenshot_15.jpg",
396
+ "clusters_08_screenshot_16.jpg",
397
+ "clusters_08_screenshot_17.jpg",
398
+ "clusters_08_screenshot_18.jpg",
399
+ "clusters_08_screenshot_19.jpg",
400
+ "clusters_08_screenshot_20.jpg",
401
+ "clusters_08_screenshot_21.jpg",
402
+ "clusters_09_screenshot_00.jpg",
403
+ "clusters_09_screenshot_01.jpg",
404
+ "clusters_09_screenshot_02.jpg",
405
+ "clusters_09_screenshot_03.jpg",
406
+ "clusters_09_screenshot_04.jpg",
407
+ "clusters_09_screenshot_05.jpg",
408
+ "clusters_09_screenshot_06.jpg",
409
+ "clusters_09_screenshot_07.jpg",
410
+ "clusters_09_screenshot_08.jpg",
411
+ "clusters_09_screenshot_09.jpg",
412
+ "clusters_09_screenshot_10.jpg",
413
+ "clusters_09_screenshot_11.jpg",
414
+ "clusters_09_screenshot_12.jpg",
415
+ "clusters_09_screenshot_13.jpg",
416
+ "clusters_09_screenshot_14.jpg",
417
+ "clusters_09_screenshot_15.jpg",
418
+ "clusters_09_screenshot_16.jpg",
419
+ "clusters_09_screenshot_17.jpg",
420
+ "clusters_09_screenshot_18.jpg",
421
+ "clusters_09_screenshot_19.jpg",
422
+ "clusters_10_screenshot_00.jpg",
423
+ "clusters_10_screenshot_01.jpg",
424
+ "clusters_10_screenshot_02.jpg",
425
+ "clusters_10_screenshot_03.jpg",
426
+ "clusters_10_screenshot_04.jpg",
427
+ "clusters_10_screenshot_05.jpg",
428
+ "clusters_10_screenshot_06.jpg",
429
+ "clusters_10_screenshot_07.jpg",
430
+ "clusters_10_screenshot_08.jpg",
431
+ "clusters_10_screenshot_09.jpg",
432
+ "clusters_10_screenshot_10.jpg",
433
+ "clusters_10_screenshot_11.jpg",
434
+ "clusters_10_screenshot_12.jpg",
435
+ "clusters_10_screenshot_13.jpg",
436
+ "clusters_10_screenshot_14.jpg",
437
+ "clusters_10_screenshot_15.jpg",
438
+ "clusters_10_screenshot_16.jpg",
439
+ "clusters_10_screenshot_17.jpg",
440
+ "clusters_10_screenshot_18.jpg",
441
+ "clusters_10_screenshot_19.jpg",
442
+ "clusters_10_screenshot_20.jpg",
443
+ "clusters_11_screenshot_00.jpg",
444
+ "clusters_11_screenshot_01.jpg",
445
+ "clusters_11_screenshot_02.jpg",
446
+ "clusters_11_screenshot_03.jpg",
447
+ "clusters_11_screenshot_04.jpg",
448
+ "clusters_11_screenshot_05.jpg",
449
+ "clusters_11_screenshot_06.jpg",
450
+ "clusters_11_screenshot_07.jpg",
451
+ "clusters_11_screenshot_08.jpg",
452
+ "clusters_11_screenshot_09.jpg",
453
+ "clusters_11_screenshot_10.jpg",
454
+ "clusters_11_screenshot_11.jpg",
455
+ "clusters_11_screenshot_12.jpg",
456
+ "clusters_11_screenshot_13.jpg",
457
+ "clusters_11_screenshot_14.jpg",
458
+ "clusters_11_screenshot_15.jpg",
459
+ "clusters_11_screenshot_16.jpg",
460
+ "clusters_11_screenshot_17.jpg",
461
+ "clusters_11_screenshot_18.jpg",
462
+ "clusters_11_screenshot_19.jpg",
463
+ "clusters_12_screenshot_00.jpg",
464
+ "clusters_12_screenshot_01.jpg",
465
+ "clusters_12_screenshot_02.jpg",
466
+ "clusters_12_screenshot_03.jpg",
467
+ "clusters_12_screenshot_04.jpg",
468
+ "clusters_12_screenshot_05.jpg",
469
+ "clusters_12_screenshot_06.jpg",
470
+ "clusters_12_screenshot_07.jpg",
471
+ "clusters_12_screenshot_08.jpg",
472
+ "clusters_12_screenshot_09.jpg",
473
+ "clusters_12_screenshot_10.jpg",
474
+ "clusters_12_screenshot_11.jpg",
475
+ "clusters_12_screenshot_12.jpg",
476
+ "clusters_12_screenshot_13.jpg",
477
+ "clusters_12_screenshot_14.jpg",
478
+ "clusters_12_screenshot_15.jpg",
479
+ "clusters_12_screenshot_16.jpg",
480
+ "clusters_12_screenshot_17.jpg",
481
+ "clusters_12_screenshot_18.jpg",
482
+ "clusters_12_screenshot_19.jpg",
483
+ "clusters_13_screenshot_00.jpg",
484
+ "clusters_13_screenshot_01.jpg",
485
+ "clusters_13_screenshot_02.jpg",
486
+ "clusters_13_screenshot_03.jpg",
487
+ "clusters_13_screenshot_04.jpg",
488
+ "clusters_13_screenshot_05.jpg",
489
+ "clusters_13_screenshot_06.jpg",
490
+ "clusters_13_screenshot_07.jpg",
491
+ "clusters_13_screenshot_08.jpg",
492
+ "clusters_13_screenshot_09.jpg",
493
+ "clusters_13_screenshot_10.jpg",
494
+ "clusters_13_screenshot_11.jpg",
495
+ "clusters_13_screenshot_12.jpg",
496
+ "clusters_13_screenshot_13.jpg",
497
+ "clusters_13_screenshot_14.jpg",
498
+ "clusters_13_screenshot_15.jpg",
499
+ "clusters_13_screenshot_16.jpg",
500
+ "clusters_13_screenshot_17.jpg",
501
+ "clusters_13_screenshot_18.jpg",
502
+ "clusters_13_screenshot_19.jpg",
503
+ "clusters_13_screenshot_20.jpg",
504
+ "clusters_13_screenshot_21.jpg",
505
+ "clusters_13_screenshot_22.jpg",
506
+ "clusters_13_screenshot_23.jpg",
507
+ "clusters_13_screenshot_24.jpg",
508
+ "pocket_01.pdb",
509
+ "pocket_02.pdb",
510
+ "pocket_03.pdb",
511
+ "pocket_04.pdb",
512
+ "pocket_05.pdb",
513
+ "pocket_06.pdb",
514
+ "pocket_07.pdb",
515
+ "pocket_08.pdb",
516
+ "pocket_09.pdb",
517
+ "pocket_10.pdb"
518
+ ],
519
+ "analyses": [
520
+ "clusters",
521
+ "clusters-00",
522
+ "clusters-01",
523
+ "clusters-02",
524
+ "clusters-03",
525
+ "clusters-04",
526
+ "clusters-05",
527
+ "clusters-06",
528
+ "clusters-07",
529
+ "clusters-08",
530
+ "clusters-09",
531
+ "clusters-10",
532
+ "clusters-11",
533
+ "clusters-12",
534
+ "clusters-13",
535
+ "dist-perres",
536
+ "energies",
537
+ "fluctuation",
538
+ "hbonds",
539
+ "interactions",
540
+ "pca",
541
+ "pockets",
542
+ "rgyr",
543
+ "rmsd-pairwise",
544
+ "rmsd-perres",
545
+ "rmsds",
546
+ "sasa",
547
+ "tmscores"
548
+ ],
549
+ "mdIndex": 0,
550
+ "mdNumber": 1,
551
+ "refframe": 0,
552
+ "internalId": "683f6396821889b377defe7a",
553
+ "creationDate": "2025-06-03T21:05:26.000Z",
554
+ "identifier": "A001S"
555
+ }
A001S/records.jsonl ADDED
The diff for this file is too large to render. See raw diff
 
A001V/project.json ADDED
@@ -0,0 +1,193 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A001V",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1S1Q",
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
+ "1S1Q"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "Q99816",
31
+ "P0CG48"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "VSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS",
38
+ "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Tumor susceptibility gene 101 protein",
43
+ "UEV",
44
+ "Ubiquitin",
45
+ "Ubiquitin-like 1",
46
+ "Interacts with activating enzyme",
47
+ "Essential for function"
48
+ ],
49
+ "FRAMESTEP": 0.1,
50
+ "TIMESTEP": 2,
51
+ "TEMP": 310,
52
+ "ENSEMBLE": "NPT",
53
+ "FF": [
54
+ "CHARMM36m"
55
+ ],
56
+ "WAT": "TIP3P",
57
+ "BOXTYPE": "Dodecahedron",
58
+ "SYSTATS": 3471,
59
+ "SYSTRES": 213,
60
+ "PROTATS": 3471,
61
+ "PROTRES": 213,
62
+ "NUCLATS": 0,
63
+ "NUCLRES": 0,
64
+ "LIPIATS": 0,
65
+ "LIPIRES": 0,
66
+ "CARBATS": 0,
67
+ "CARBRES": 0,
68
+ "SOLVATS": 0,
69
+ "SOLVRES": 0,
70
+ "COUNCAT": 0,
71
+ "COUNANI": 0,
72
+ "COUNION": 0,
73
+ "INTERACTIONS": [
74
+ {
75
+ "name": "chain A-chain B interaction",
76
+ "agent_1": "chain A",
77
+ "agent_2": "chain B",
78
+ "selection_1": "chain A",
79
+ "selection_2": "chain B",
80
+ "type": "protein-protein"
81
+ }
82
+ ],
83
+ "PBC_SELECTION": null,
84
+ "CHAINNAMES": null,
85
+ "MEMBRANES": null,
86
+ "CUSTOMS": null,
87
+ "ORIENTATION": null,
88
+ "PTM": [],
89
+ "MULTIMERIC": null,
90
+ "COLLECTIONS": "dynarepo",
91
+ "WARNINGS": [],
92
+ "BOXSIZEX": 8.11817,
93
+ "BOXSIZEY": 8.11817,
94
+ "BOXSIZEZ": 5.75796,
95
+ "mdName": "replica 1",
96
+ "mdAtoms": 3471,
97
+ "mdFrames": 5001
98
+ },
99
+ "mds": [
100
+ "replica 1",
101
+ "replica 2",
102
+ "replica 3"
103
+ ],
104
+ "mdref": 0,
105
+ "files": [
106
+ "topology.tpr",
107
+ "screenshot.jpg",
108
+ "trajectory.bin",
109
+ "pca_trajectory_01.bin",
110
+ "pca_trajectory_02.bin",
111
+ "pca_trajectory_03.bin",
112
+ "pca_trajectory_04.bin",
113
+ "pca_trajectory_05.bin",
114
+ "pca_trajectory_06.bin",
115
+ "pca_trajectory_07.bin",
116
+ "pca_trajectory_08.bin",
117
+ "pca_trajectory_09.bin",
118
+ "pca_trajectory_10.bin",
119
+ "pca_trajectory_11.bin",
120
+ "pca_trajectory_12.bin",
121
+ "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
+ "clusters_00_screenshot_04.jpg",
128
+ "clusters_00_screenshot_05.jpg",
129
+ "clusters_00_screenshot_06.jpg",
130
+ "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_01_screenshot_00.jpg",
145
+ "clusters_01_screenshot_01.jpg",
146
+ "clusters_01_screenshot_02.jpg",
147
+ "clusters_01_screenshot_03.jpg",
148
+ "clusters_01_screenshot_04.jpg",
149
+ "clusters_01_screenshot_05.jpg",
150
+ "clusters_01_screenshot_06.jpg",
151
+ "clusters_01_screenshot_07.jpg",
152
+ "clusters_01_screenshot_08.jpg",
153
+ "clusters_01_screenshot_09.jpg",
154
+ "clusters_01_screenshot_10.jpg",
155
+ "clusters_01_screenshot_11.jpg",
156
+ "clusters_01_screenshot_12.jpg",
157
+ "clusters_01_screenshot_13.jpg",
158
+ "clusters_01_screenshot_14.jpg",
159
+ "clusters_01_screenshot_15.jpg",
160
+ "clusters_01_screenshot_16.jpg",
161
+ "clusters_01_screenshot_17.jpg",
162
+ "clusters_01_screenshot_18.jpg",
163
+ "clusters_01_screenshot_19.jpg",
164
+ "pocket_01.pdb",
165
+ "pocket_02.pdb",
166
+ "pocket_03.pdb",
167
+ "pocket_04.pdb"
168
+ ],
169
+ "analyses": [
170
+ "clusters",
171
+ "clusters-00",
172
+ "clusters-01",
173
+ "dist-perres",
174
+ "energies",
175
+ "fluctuation",
176
+ "hbonds",
177
+ "interactions",
178
+ "pca",
179
+ "pockets",
180
+ "rgyr",
181
+ "rmsd-pairwise",
182
+ "rmsd-perres",
183
+ "rmsds",
184
+ "sasa",
185
+ "tmscores"
186
+ ],
187
+ "mdIndex": 0,
188
+ "mdNumber": 1,
189
+ "refframe": 0,
190
+ "internalId": "683f69e5c42215fa3dde639e",
191
+ "creationDate": "2025-06-03T21:32:21.000Z",
192
+ "identifier": "A001V"
193
+ }
A001V/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A001V", "accession": "A001V", "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 1S1Q", "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": ["1S1Q"], "FORCED_REFERENCES": null, "REFERENCES": ["Q99816", "P0CG48"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR"], "NUCLSEQ": [], "DOMAINS": ["Tumor susceptibility gene 101 protein", "UEV", "Ubiquitin", "Ubiquitin-like 1", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3471, "SYSTRES": 213, "PROTATS": 3471, "PROTRES": 213, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.11817, "BOXSIZEY": 8.11817, "BOXSIZEZ": 5.75796, "mdName": "replica 1", "mdAtoms": 3471, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001V/files/topology.tpr", "length": 1228936, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001V/files/screenshot.jpg", "length": 22403, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001V/files/trajectory.bin", "length": 208301652, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 5001, "atoms": 3471}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_01.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_02.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_03.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_04.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_05.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_06.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_07.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_08.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_09.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_10.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_11.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_12.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001V/files/structure.pdb", "length": 281186, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001V/files/trajectory.xtc", "length": 66084124, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_00.jpg", "length": 21024, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_01.jpg", "length": 20907, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_02.jpg", "length": 20294, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_03.jpg", "length": 20457, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_04.jpg", "length": 20490, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_05.jpg", "length": 20880, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_06.jpg", "length": 21098, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_07.jpg", "length": 20912, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_08.jpg", "length": 21043, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_09.jpg", "length": 20702, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_10.jpg", "length": 21108, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_11.jpg", "length": 21055, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_12.jpg", "length": 20639, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_13.jpg", "length": 21539, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_14.jpg", "length": 21044, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_15.jpg", "length": 21209, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_16.jpg", "length": 21015, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_17.jpg", "length": 20832, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_18.jpg", "length": 20416, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_19.jpg", "length": 20396, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_20.jpg", "length": 21497, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_00.jpg", "length": 22280, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_01.jpg", "length": 21250, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_02.jpg", "length": 20970, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_03.jpg", "length": 22198, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_04.jpg", "length": 21829, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_05.jpg", "length": 22140, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_06.jpg", "length": 22114, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_07.jpg", "length": 22410, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_08.jpg", "length": 22375, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_09.jpg", "length": 21494, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_10.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_11.jpg", "length": 21473, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_12.jpg", "length": 21386, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_13.jpg", "length": 20990, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_14.jpg", "length": 21540, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_15.jpg", "length": 20901, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_16.jpg", "length": 22037, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_17.jpg", "length": 21710, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_18.jpg", "length": 20863, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_19.jpg", "length": 21176, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001V/files/pocket_01.pdb", "length": 10653, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001V/files/pocket_02.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001V/files/pocket_03.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001V/files/pocket_04.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}]}
2
+ {"project_identifier": "A001V", "accession": "A001V", "published": true, "md_index": 1, "md_name": "replica 2", "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 1S1Q", "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": ["1S1Q"], "FORCED_REFERENCES": null, "REFERENCES": ["Q99816", "P0CG48"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR"], "NUCLSEQ": [], "DOMAINS": ["Tumor susceptibility gene 101 protein", "UEV", "Ubiquitin", "Ubiquitin-like 1", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3471, "SYSTRES": 213, "PROTATS": 3471, "PROTRES": 213, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.11817, "BOXSIZEY": 8.11817, "BOXSIZEZ": 5.75796, "mdName": "replica 1", "mdAtoms": 3471, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001V/files/topology.tpr", "length": 1228936, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001V/files/screenshot.jpg", "length": 22403, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001V/files/trajectory.bin", "length": 208301652, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 5001, "atoms": 3471}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_01.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_02.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_03.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_04.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_05.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_06.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_07.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_08.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_09.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_10.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_11.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_12.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001V/files/structure.pdb", "length": 281186, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001V/files/trajectory.xtc", "length": 66084124, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_00.jpg", "length": 21024, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_01.jpg", "length": 20907, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_02.jpg", "length": 20294, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_03.jpg", "length": 20457, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_04.jpg", "length": 20490, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_05.jpg", "length": 20880, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_06.jpg", "length": 21098, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_07.jpg", "length": 20912, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_08.jpg", "length": 21043, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_09.jpg", "length": 20702, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_10.jpg", "length": 21108, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_11.jpg", "length": 21055, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_12.jpg", "length": 20639, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_13.jpg", "length": 21539, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_14.jpg", "length": 21044, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_15.jpg", "length": 21209, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_16.jpg", "length": 21015, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_17.jpg", "length": 20832, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_18.jpg", "length": 20416, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_19.jpg", "length": 20396, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_20.jpg", "length": 21497, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_00.jpg", "length": 22280, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_01.jpg", "length": 21250, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_02.jpg", "length": 20970, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_03.jpg", "length": 22198, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_04.jpg", "length": 21829, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_05.jpg", "length": 22140, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_06.jpg", "length": 22114, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_07.jpg", "length": 22410, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_08.jpg", "length": 22375, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_09.jpg", "length": 21494, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_10.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_11.jpg", "length": 21473, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_12.jpg", "length": 21386, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_13.jpg", "length": 20990, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_14.jpg", "length": 21540, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_15.jpg", "length": 20901, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_16.jpg", "length": 22037, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_17.jpg", "length": 21710, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_18.jpg", "length": 20863, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_19.jpg", "length": 21176, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001V/files/pocket_01.pdb", "length": 10653, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001V/files/pocket_02.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001V/files/pocket_03.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001V/files/pocket_04.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}]}
3
+ {"project_identifier": "A001V", "accession": "A001V", "published": true, "md_index": 2, "md_name": "replica 3", "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 1S1Q", "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": ["1S1Q"], "FORCED_REFERENCES": null, "REFERENCES": ["Q99816", "P0CG48"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS", "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLR"], "NUCLSEQ": [], "DOMAINS": ["Tumor susceptibility gene 101 protein", "UEV", "Ubiquitin", "Ubiquitin-like 1", "Interacts with activating enzyme", "Essential for function"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3471, "SYSTRES": 213, "PROTATS": 3471, "PROTRES": 213, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.11817, "BOXSIZEY": 8.11817, "BOXSIZEZ": 5.75796, "mdName": "replica 1", "mdAtoms": 3471, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001V/files/topology.tpr", "length": 1228936, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001V/files/screenshot.jpg", "length": 22403, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001V/files/trajectory.bin", "length": 208301652, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 5001, "atoms": 3471}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_01.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_02.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_03.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_04.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_05.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_06.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_07.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_08.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_09.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_10.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_11.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001V/files/pca_trajectory_12.bin", "length": 153360, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0, "frames": 20, "atoms": 639}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001V/files/structure.pdb", "length": 281186, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001V/files/trajectory.xtc", "length": 66084124, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_00.jpg", "length": 21024, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_01.jpg", "length": 20907, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_02.jpg", "length": 20294, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_03.jpg", "length": 20457, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_04.jpg", "length": 20490, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_05.jpg", "length": 20880, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_06.jpg", "length": 21098, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_07.jpg", "length": 20912, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_08.jpg", "length": 21043, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_09.jpg", "length": 20702, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_10.jpg", "length": 21108, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_11.jpg", "length": 21055, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_12.jpg", "length": 20639, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_13.jpg", "length": 21539, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_14.jpg", "length": 21044, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_15.jpg", "length": 21209, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_16.jpg", "length": 21015, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_17.jpg", "length": 20832, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_18.jpg", "length": 20416, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_19.jpg", "length": 20396, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001V/files/clusters_00_screenshot_20.jpg", "length": 21497, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_00.jpg", "length": 22280, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_01.jpg", "length": 21250, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_02.jpg", "length": 20970, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_03.jpg", "length": 22198, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_04.jpg", "length": 21829, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_05.jpg", "length": 22140, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_06.jpg", "length": 22114, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_07.jpg", "length": 22410, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_08.jpg", "length": 22375, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_09.jpg", "length": 21494, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_10.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_11.jpg", "length": 21473, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_12.jpg", "length": 21386, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_13.jpg", "length": 20990, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_14.jpg", "length": 21540, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_15.jpg", "length": 20901, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_16.jpg", "length": 22037, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_17.jpg", "length": 21710, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_18.jpg", "length": 20863, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001V/files/clusters_01_screenshot_19.jpg", "length": 21176, "contentType": "application/octet-stream", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001V/files/pocket_01.pdb", "length": 10653, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001V/files/pocket_02.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001V/files/pocket_03.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001V/files/pocket_04.pdb", "length": 4020, "contentType": "chemical/x-pdb", "metadata": {"project": "683f69e5c42215fa3dde639e", "md": 0}}]}
A001X/project.json ADDED
@@ -0,0 +1,195 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A001X",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1SYQ",
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
+ "1SYQ"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P18206",
31
+ "Q9Y490"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "PLLQAAKGLAGAVSELLRSAQPASA",
38
+ "HMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Vinculin",
43
+ "N-terminal globular head",
44
+ "Talin-interaction",
45
+ "3 X 112 AA tandem repeats",
46
+ "Talin-1",
47
+ "Helical bundle R1"
48
+ ],
49
+ "FRAMESTEP": 0.1,
50
+ "TIMESTEP": 2,
51
+ "TEMP": 310,
52
+ "ENSEMBLE": "NPT",
53
+ "FF": [
54
+ "CHARMM36m"
55
+ ],
56
+ "WAT": "TIP3P",
57
+ "BOXTYPE": "Dodecahedron",
58
+ "SYSTATS": 4466,
59
+ "SYSTRES": 284,
60
+ "PROTATS": 4466,
61
+ "PROTRES": 284,
62
+ "NUCLATS": 0,
63
+ "NUCLRES": 0,
64
+ "LIPIATS": 0,
65
+ "LIPIRES": 0,
66
+ "CARBATS": 0,
67
+ "CARBRES": 0,
68
+ "SOLVATS": 0,
69
+ "SOLVRES": 0,
70
+ "COUNCAT": 0,
71
+ "COUNANI": 0,
72
+ "COUNION": 0,
73
+ "INTERACTIONS": [
74
+ {
75
+ "name": "chain A-chain B interaction",
76
+ "agent_1": "chain A",
77
+ "agent_2": "chain B",
78
+ "selection_1": "chain A",
79
+ "selection_2": "chain B",
80
+ "type": "protein-protein"
81
+ }
82
+ ],
83
+ "PBC_SELECTION": null,
84
+ "CHAINNAMES": null,
85
+ "MEMBRANES": null,
86
+ "CUSTOMS": null,
87
+ "ORIENTATION": null,
88
+ "PTM": [],
89
+ "MULTIMERIC": null,
90
+ "COLLECTIONS": "dynarepo",
91
+ "WARNINGS": [],
92
+ "BOXSIZEX": 12.5935,
93
+ "BOXSIZEY": 12.5935,
94
+ "BOXSIZEZ": 8.89058,
95
+ "mdName": "replica 1",
96
+ "mdAtoms": 4466,
97
+ "mdFrames": 5001
98
+ },
99
+ "mds": [
100
+ "replica 1",
101
+ "replica 2",
102
+ "replica 3"
103
+ ],
104
+ "mdref": 0,
105
+ "files": [
106
+ "topology.tpr",
107
+ "screenshot.jpg",
108
+ "trajectory.bin",
109
+ "pca_trajectory_01.bin",
110
+ "pca_trajectory_02.bin",
111
+ "pca_trajectory_03.bin",
112
+ "pca_trajectory_04.bin",
113
+ "pca_trajectory_05.bin",
114
+ "pca_trajectory_06.bin",
115
+ "pca_trajectory_07.bin",
116
+ "pca_trajectory_08.bin",
117
+ "pca_trajectory_09.bin",
118
+ "pca_trajectory_10.bin",
119
+ "pca_trajectory_11.bin",
120
+ "pca_trajectory_12.bin",
121
+ "pca_trajectory_13.bin",
122
+ "structure.pdb",
123
+ "trajectory.xtc",
124
+ "clusters_00_screenshot_00.jpg",
125
+ "clusters_00_screenshot_01.jpg",
126
+ "clusters_00_screenshot_02.jpg",
127
+ "clusters_00_screenshot_03.jpg",
128
+ "clusters_00_screenshot_04.jpg",
129
+ "clusters_00_screenshot_05.jpg",
130
+ "clusters_00_screenshot_06.jpg",
131
+ "clusters_00_screenshot_07.jpg",
132
+ "clusters_00_screenshot_08.jpg",
133
+ "clusters_00_screenshot_09.jpg",
134
+ "clusters_00_screenshot_10.jpg",
135
+ "clusters_00_screenshot_11.jpg",
136
+ "clusters_00_screenshot_12.jpg",
137
+ "clusters_00_screenshot_13.jpg",
138
+ "clusters_00_screenshot_14.jpg",
139
+ "clusters_00_screenshot_15.jpg",
140
+ "clusters_00_screenshot_16.jpg",
141
+ "clusters_00_screenshot_17.jpg",
142
+ "clusters_00_screenshot_18.jpg",
143
+ "clusters_00_screenshot_19.jpg",
144
+ "clusters_00_screenshot_20.jpg",
145
+ "clusters_01_screenshot_00.jpg",
146
+ "clusters_01_screenshot_01.jpg",
147
+ "clusters_01_screenshot_02.jpg",
148
+ "clusters_01_screenshot_03.jpg",
149
+ "clusters_01_screenshot_04.jpg",
150
+ "clusters_01_screenshot_05.jpg",
151
+ "clusters_01_screenshot_06.jpg",
152
+ "clusters_01_screenshot_07.jpg",
153
+ "clusters_01_screenshot_08.jpg",
154
+ "clusters_01_screenshot_09.jpg",
155
+ "clusters_01_screenshot_10.jpg",
156
+ "clusters_01_screenshot_11.jpg",
157
+ "clusters_01_screenshot_12.jpg",
158
+ "clusters_01_screenshot_13.jpg",
159
+ "clusters_01_screenshot_14.jpg",
160
+ "clusters_01_screenshot_15.jpg",
161
+ "clusters_01_screenshot_16.jpg",
162
+ "clusters_01_screenshot_17.jpg",
163
+ "clusters_01_screenshot_18.jpg",
164
+ "clusters_01_screenshot_19.jpg",
165
+ "pocket_01.pdb",
166
+ "pocket_02.pdb",
167
+ "pocket_03.pdb",
168
+ "pocket_04.pdb",
169
+ "pocket_05.pdb"
170
+ ],
171
+ "analyses": [
172
+ "clusters",
173
+ "clusters-00",
174
+ "clusters-01",
175
+ "dist-perres",
176
+ "energies",
177
+ "fluctuation",
178
+ "hbonds",
179
+ "interactions",
180
+ "pca",
181
+ "pockets",
182
+ "rgyr",
183
+ "rmsd-pairwise",
184
+ "rmsd-perres",
185
+ "rmsds",
186
+ "sasa",
187
+ "tmscores"
188
+ ],
189
+ "mdIndex": 0,
190
+ "mdNumber": 1,
191
+ "refframe": 0,
192
+ "internalId": "683f6be396ae352bdf893b46",
193
+ "creationDate": "2025-06-03T21:40:51.000Z",
194
+ "identifier": "A001X"
195
+ }
A001X/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A001X", "accession": "A001X", "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 1SYQ", "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": ["1SYQ"], "FORCED_REFERENCES": null, "REFERENCES": ["P18206", "Q9Y490"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PLLQAAKGLAGAVSELLRSAQPASA", "HMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW"], "NUCLSEQ": [], "DOMAINS": ["Vinculin", "N-terminal globular head", "Talin-interaction", "3 X 112 AA tandem repeats", "Talin-1", "Helical bundle R1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4466, "SYSTRES": 284, "PROTATS": 4466, "PROTRES": 284, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.5935, "BOXSIZEY": 12.5935, "BOXSIZEZ": 8.89058, "mdName": "replica 1", "mdAtoms": 4466, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001X/files/topology.tpr", "length": 1676740, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001X/files/screenshot.jpg", "length": 16708, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001X/files/trajectory.bin", "length": 268013592, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 5001, "atoms": 4466}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_01.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_02.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_03.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_04.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_05.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_06.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_07.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_08.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_09.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_10.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_11.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_12.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_13.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001X/files/structure.pdb", "length": 361781, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001X/files/trajectory.xtc", "length": 85664860, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_00.jpg", "length": 17011, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_01.jpg", "length": 16742, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_02.jpg", "length": 16647, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_03.jpg", "length": 16756, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_04.jpg", "length": 16332, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_05.jpg", "length": 16457, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_06.jpg", "length": 15969, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_07.jpg", "length": 16296, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_08.jpg", "length": 16668, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_09.jpg", "length": 16546, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_10.jpg", "length": 16424, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_11.jpg", "length": 16779, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_12.jpg", "length": 16513, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_13.jpg", "length": 16439, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_14.jpg", "length": 16927, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_15.jpg", "length": 16533, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_16.jpg", "length": 16752, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_17.jpg", "length": 16836, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_18.jpg", "length": 16227, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_19.jpg", "length": 17091, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_20.jpg", "length": 16474, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_00.jpg", "length": 16727, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_01.jpg", "length": 16884, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_02.jpg", "length": 16746, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_03.jpg", "length": 16337, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_04.jpg", "length": 16733, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_05.jpg", "length": 15996, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_06.jpg", "length": 16265, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_07.jpg", "length": 15895, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_08.jpg", "length": 16241, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_09.jpg", "length": 16312, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_10.jpg", "length": 15889, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_11.jpg", "length": 15969, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_12.jpg", "length": 16113, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_13.jpg", "length": 16044, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_14.jpg", "length": 15756, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_15.jpg", "length": 16179, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_16.jpg", "length": 16667, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_17.jpg", "length": 16495, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_18.jpg", "length": 16053, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_19.jpg", "length": 16630, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001X/files/pocket_01.pdb", "length": 7571, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001X/files/pocket_02.pdb", "length": 6499, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001X/files/pocket_03.pdb", "length": 5963, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001X/files/pocket_04.pdb", "length": 4489, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A001X/files/pocket_05.pdb", "length": 3819, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}]}
2
+ {"project_identifier": "A001X", "accession": "A001X", "published": true, "md_index": 1, "md_name": "replica 2", "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 1SYQ", "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": ["1SYQ"], "FORCED_REFERENCES": null, "REFERENCES": ["P18206", "Q9Y490"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PLLQAAKGLAGAVSELLRSAQPASA", "HMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW"], "NUCLSEQ": [], "DOMAINS": ["Vinculin", "N-terminal globular head", "Talin-interaction", "3 X 112 AA tandem repeats", "Talin-1", "Helical bundle R1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4466, "SYSTRES": 284, "PROTATS": 4466, "PROTRES": 284, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.5935, "BOXSIZEY": 12.5935, "BOXSIZEZ": 8.89058, "mdName": "replica 1", "mdAtoms": 4466, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001X/files/topology.tpr", "length": 1676740, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001X/files/screenshot.jpg", "length": 16708, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001X/files/trajectory.bin", "length": 268013592, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 5001, "atoms": 4466}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_01.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_02.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_03.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_04.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_05.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_06.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_07.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_08.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_09.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_10.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_11.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_12.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_13.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001X/files/structure.pdb", "length": 361781, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001X/files/trajectory.xtc", "length": 85664860, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_00.jpg", "length": 17011, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_01.jpg", "length": 16742, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_02.jpg", "length": 16647, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_03.jpg", "length": 16756, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_04.jpg", "length": 16332, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_05.jpg", "length": 16457, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_06.jpg", "length": 15969, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_07.jpg", "length": 16296, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_08.jpg", "length": 16668, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_09.jpg", "length": 16546, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_10.jpg", "length": 16424, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_11.jpg", "length": 16779, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_12.jpg", "length": 16513, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_13.jpg", "length": 16439, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_14.jpg", "length": 16927, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_15.jpg", "length": 16533, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_16.jpg", "length": 16752, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_17.jpg", "length": 16836, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_18.jpg", "length": 16227, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_19.jpg", "length": 17091, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_20.jpg", "length": 16474, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_00.jpg", "length": 16727, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_01.jpg", "length": 16884, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_02.jpg", "length": 16746, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_03.jpg", "length": 16337, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_04.jpg", "length": 16733, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_05.jpg", "length": 15996, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_06.jpg", "length": 16265, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_07.jpg", "length": 15895, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_08.jpg", "length": 16241, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_09.jpg", "length": 16312, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_10.jpg", "length": 15889, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_11.jpg", "length": 15969, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_12.jpg", "length": 16113, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_13.jpg", "length": 16044, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_14.jpg", "length": 15756, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_15.jpg", "length": 16179, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_16.jpg", "length": 16667, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_17.jpg", "length": 16495, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_18.jpg", "length": 16053, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_19.jpg", "length": 16630, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001X/files/pocket_01.pdb", "length": 7571, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001X/files/pocket_02.pdb", "length": 6499, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001X/files/pocket_03.pdb", "length": 5963, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001X/files/pocket_04.pdb", "length": 4489, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A001X/files/pocket_05.pdb", "length": 3819, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}]}
3
+ {"project_identifier": "A001X", "accession": "A001X", "published": true, "md_index": 2, "md_name": "replica 3", "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 1SYQ", "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": ["1SYQ"], "FORCED_REFERENCES": null, "REFERENCES": ["P18206", "Q9Y490"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["PLLQAAKGLAGAVSELLRSAQPASA", "HMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAW"], "NUCLSEQ": [], "DOMAINS": ["Vinculin", "N-terminal globular head", "Talin-interaction", "3 X 112 AA tandem repeats", "Talin-1", "Helical bundle R1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4466, "SYSTRES": 284, "PROTATS": 4466, "PROTRES": 284, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 12.5935, "BOXSIZEY": 12.5935, "BOXSIZEZ": 8.89058, "mdName": "replica 1", "mdAtoms": 4466, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A001X/files/topology.tpr", "length": 1676740, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A001X/files/screenshot.jpg", "length": 16708, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A001X/files/trajectory.bin", "length": 268013592, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 5001, "atoms": 4466}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_01.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_02.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_03.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_04.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_05.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_06.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_07.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_08.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_09.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_10.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_11.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_12.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A001X/files/pca_trajectory_13.bin", "length": 204480, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0, "frames": 20, "atoms": 852}}, {"name": "structure.pdb", "downloadUrl": "/projects/A001X/files/structure.pdb", "length": 361781, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A001X/files/trajectory.xtc", "length": 85664860, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_00.jpg", "length": 17011, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_01.jpg", "length": 16742, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_02.jpg", "length": 16647, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_03.jpg", "length": 16756, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_04.jpg", "length": 16332, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_05.jpg", "length": 16457, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_06.jpg", "length": 15969, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_07.jpg", "length": 16296, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_08.jpg", "length": 16668, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_09.jpg", "length": 16546, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_10.jpg", "length": 16424, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_11.jpg", "length": 16779, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_12.jpg", "length": 16513, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_13.jpg", "length": 16439, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_14.jpg", "length": 16927, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_15.jpg", "length": 16533, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_16.jpg", "length": 16752, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_17.jpg", "length": 16836, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_18.jpg", "length": 16227, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_19.jpg", "length": 17091, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A001X/files/clusters_00_screenshot_20.jpg", "length": 16474, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_00.jpg", "length": 16727, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_01.jpg", "length": 16884, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_02.jpg", "length": 16746, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_03.jpg", "length": 16337, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_04.jpg", "length": 16733, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_05.jpg", "length": 15996, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_06.jpg", "length": 16265, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_07.jpg", "length": 15895, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_08.jpg", "length": 16241, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_09.jpg", "length": 16312, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_10.jpg", "length": 15889, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_11.jpg", "length": 15969, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_12.jpg", "length": 16113, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_13.jpg", "length": 16044, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_14.jpg", "length": 15756, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_15.jpg", "length": 16179, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_16.jpg", "length": 16667, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_17.jpg", "length": 16495, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_18.jpg", "length": 16053, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A001X/files/clusters_01_screenshot_19.jpg", "length": 16630, "contentType": "application/octet-stream", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A001X/files/pocket_01.pdb", "length": 7571, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A001X/files/pocket_02.pdb", "length": 6499, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A001X/files/pocket_03.pdb", "length": 5963, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A001X/files/pocket_04.pdb", "length": 4489, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A001X/files/pocket_05.pdb", "length": 3819, "contentType": "chemical/x-pdb", "metadata": {"project": "683f6be396ae352bdf893b46", "md": 0}}]}
A0024/project.json ADDED
@@ -0,0 +1,197 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0024",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1UGH",
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
+ "1UGH"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P13051",
31
+ "P14739"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL",
38
+ "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Uracil-DNA glycosylase",
43
+ "Uracil-DNA glycosylase inhibitor"
44
+ ],
45
+ "FRAMESTEP": 0.1,
46
+ "TIMESTEP": 2,
47
+ "TEMP": 310,
48
+ "ENSEMBLE": "NPT",
49
+ "FF": [
50
+ "CHARMM36m"
51
+ ],
52
+ "WAT": "TIP3P",
53
+ "BOXTYPE": "Dodecahedron",
54
+ "SYSTATS": 4863,
55
+ "SYSTRES": 305,
56
+ "PROTATS": 4863,
57
+ "PROTRES": 305,
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": 8.47508,
89
+ "BOXSIZEY": 8.47508,
90
+ "BOXSIZEZ": 6.00649,
91
+ "mdName": "replica 1",
92
+ "mdAtoms": 4863,
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
+ "pca_trajectory_13.bin",
118
+ "pca_trajectory_14.bin",
119
+ "pca_trajectory_15.bin",
120
+ "structure.pdb",
121
+ "trajectory.xtc",
122
+ "clusters_00_screenshot_00.jpg",
123
+ "clusters_00_screenshot_01.jpg",
124
+ "clusters_00_screenshot_02.jpg",
125
+ "clusters_00_screenshot_03.jpg",
126
+ "clusters_00_screenshot_04.jpg",
127
+ "clusters_00_screenshot_05.jpg",
128
+ "clusters_00_screenshot_06.jpg",
129
+ "clusters_00_screenshot_07.jpg",
130
+ "clusters_00_screenshot_08.jpg",
131
+ "clusters_00_screenshot_09.jpg",
132
+ "clusters_00_screenshot_10.jpg",
133
+ "clusters_00_screenshot_11.jpg",
134
+ "clusters_00_screenshot_12.jpg",
135
+ "clusters_00_screenshot_13.jpg",
136
+ "clusters_00_screenshot_14.jpg",
137
+ "clusters_00_screenshot_15.jpg",
138
+ "clusters_00_screenshot_16.jpg",
139
+ "clusters_00_screenshot_17.jpg",
140
+ "clusters_00_screenshot_18.jpg",
141
+ "clusters_01_screenshot_00.jpg",
142
+ "clusters_01_screenshot_01.jpg",
143
+ "clusters_01_screenshot_02.jpg",
144
+ "clusters_01_screenshot_03.jpg",
145
+ "clusters_01_screenshot_04.jpg",
146
+ "clusters_01_screenshot_05.jpg",
147
+ "clusters_01_screenshot_06.jpg",
148
+ "clusters_01_screenshot_07.jpg",
149
+ "clusters_01_screenshot_08.jpg",
150
+ "clusters_01_screenshot_09.jpg",
151
+ "clusters_01_screenshot_10.jpg",
152
+ "clusters_01_screenshot_11.jpg",
153
+ "clusters_01_screenshot_12.jpg",
154
+ "clusters_01_screenshot_13.jpg",
155
+ "clusters_01_screenshot_14.jpg",
156
+ "clusters_01_screenshot_15.jpg",
157
+ "clusters_01_screenshot_16.jpg",
158
+ "clusters_01_screenshot_17.jpg",
159
+ "clusters_01_screenshot_18.jpg",
160
+ "clusters_01_screenshot_19.jpg",
161
+ "pocket_01.pdb",
162
+ "pocket_02.pdb",
163
+ "pocket_03.pdb",
164
+ "pocket_04.pdb",
165
+ "pocket_05.pdb",
166
+ "pocket_06.pdb",
167
+ "pocket_07.pdb",
168
+ "pocket_08.pdb",
169
+ "pocket_09.pdb",
170
+ "pocket_10.pdb"
171
+ ],
172
+ "analyses": [
173
+ "mem-map",
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": 1,
194
+ "internalId": "683f76bea396e03843709f82",
195
+ "creationDate": "2025-06-03T22:27:10.000Z",
196
+ "identifier": "A0024"
197
+ }
A0024/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A0024", "accession": "A0024", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "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 1UGH", "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": ["1UGH"], "FORCED_REFERENCES": null, "REFERENCES": ["P13051", "P14739"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL", "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"], "NUCLSEQ": [], "DOMAINS": ["Uracil-DNA glycosylase", "Uracil-DNA glycosylase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4863, "SYSTRES": 305, "PROTATS": 4863, "PROTRES": 305, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.47508, "BOXSIZEY": 8.47508, "BOXSIZEZ": 6.00649, "mdName": "replica 1", "mdAtoms": 4863, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0024/files/topology.tpr", "length": 1592244, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0024/files/screenshot.jpg", "length": 24851, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0024/files/trajectory.bin", "length": 291838356, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 5001, "atoms": 4863}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_01.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_02.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_03.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_04.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_05.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_06.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_07.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_08.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_09.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_10.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_11.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_12.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_13.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_14.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_15.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0024/files/structure.pdb", "length": 393938, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0024/files/trajectory.xtc", "length": 92564956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_00.jpg", "length": 25369, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_01.jpg", "length": 25994, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_02.jpg", "length": 25049, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_03.jpg", "length": 25589, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_04.jpg", "length": 25246, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_05.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_06.jpg", "length": 25258, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_07.jpg", "length": 25523, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_08.jpg", "length": 25475, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_09.jpg", "length": 25529, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_10.jpg", "length": 25187, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_11.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_12.jpg", "length": 25178, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_13.jpg", "length": 25329, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_14.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_15.jpg", "length": 25140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_16.jpg", "length": 25850, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_17.jpg", "length": 25854, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_18.jpg", "length": 25028, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_00.jpg", "length": 23093, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_01.jpg", "length": 23318, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_02.jpg", "length": 22575, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_03.jpg", "length": 22433, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_04.jpg", "length": 22957, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_05.jpg", "length": 22640, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_06.jpg", "length": 22337, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_07.jpg", "length": 22797, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_08.jpg", "length": 22783, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_09.jpg", "length": 22490, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_10.jpg", "length": 22710, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_11.jpg", "length": 23255, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_12.jpg", "length": 22654, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_13.jpg", "length": 22417, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_14.jpg", "length": 22794, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_15.jpg", "length": 22619, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_16.jpg", "length": 23140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_17.jpg", "length": 22549, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_18.jpg", "length": 23263, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_19.jpg", "length": 22721, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0024/files/pocket_01.pdb", "length": 22043, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0024/files/pocket_02.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0024/files/pocket_03.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0024/files/pocket_04.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0024/files/pocket_05.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0024/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0024/files/pocket_07.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0024/files/pocket_08.pdb", "length": 5226, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0024/files/pocket_09.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0024/files/pocket_10.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}]}
2
+ {"project_identifier": "A0024", "accession": "A0024", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["mem-map", "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 1UGH", "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": ["1UGH"], "FORCED_REFERENCES": null, "REFERENCES": ["P13051", "P14739"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL", "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"], "NUCLSEQ": [], "DOMAINS": ["Uracil-DNA glycosylase", "Uracil-DNA glycosylase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4863, "SYSTRES": 305, "PROTATS": 4863, "PROTRES": 305, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.47508, "BOXSIZEY": 8.47508, "BOXSIZEZ": 6.00649, "mdName": "replica 1", "mdAtoms": 4863, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0024/files/topology.tpr", "length": 1592244, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0024/files/screenshot.jpg", "length": 24851, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0024/files/trajectory.bin", "length": 291838356, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 5001, "atoms": 4863}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_01.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_02.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_03.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_04.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_05.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_06.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_07.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_08.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_09.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_10.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_11.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_12.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_13.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_14.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_15.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0024/files/structure.pdb", "length": 393938, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0024/files/trajectory.xtc", "length": 92564956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_00.jpg", "length": 25369, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_01.jpg", "length": 25994, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_02.jpg", "length": 25049, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_03.jpg", "length": 25589, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_04.jpg", "length": 25246, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_05.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_06.jpg", "length": 25258, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_07.jpg", "length": 25523, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_08.jpg", "length": 25475, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_09.jpg", "length": 25529, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_10.jpg", "length": 25187, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_11.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_12.jpg", "length": 25178, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_13.jpg", "length": 25329, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_14.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_15.jpg", "length": 25140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_16.jpg", "length": 25850, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_17.jpg", "length": 25854, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_18.jpg", "length": 25028, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_00.jpg", "length": 23093, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_01.jpg", "length": 23318, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_02.jpg", "length": 22575, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_03.jpg", "length": 22433, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_04.jpg", "length": 22957, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_05.jpg", "length": 22640, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_06.jpg", "length": 22337, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_07.jpg", "length": 22797, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_08.jpg", "length": 22783, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_09.jpg", "length": 22490, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_10.jpg", "length": 22710, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_11.jpg", "length": 23255, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_12.jpg", "length": 22654, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_13.jpg", "length": 22417, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_14.jpg", "length": 22794, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_15.jpg", "length": 22619, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_16.jpg", "length": 23140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_17.jpg", "length": 22549, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_18.jpg", "length": 23263, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_19.jpg", "length": 22721, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0024/files/pocket_01.pdb", "length": 22043, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0024/files/pocket_02.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0024/files/pocket_03.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0024/files/pocket_04.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0024/files/pocket_05.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0024/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0024/files/pocket_07.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0024/files/pocket_08.pdb", "length": 5226, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0024/files/pocket_09.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0024/files/pocket_10.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}]}
3
+ {"project_identifier": "A0024", "accession": "A0024", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["mem-map", "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 1UGH", "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": ["1UGH"], "FORCED_REFERENCES": null, "REFERENCES": ["P13051", "P14739"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MEFFGESWKKHLSGEFGKPYFIKLMGFVAEERKHYTVYPPPHQVFTWTQMCDIKDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEDFVHPGHGDLSGWAKQGVLLLNAVLTVRAHQANSHKERGWEQFTDAVVSWLNQNSNGLVFLLWGSYAQKKGSAIDRKRHHVLQTAHPSPLSVYRGFFGCRHFSKTNELLQKSGKKPIDWKEL", "NLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTSDAPEYKPWALVIQDSNGENKIKML"], "NUCLSEQ": [], "DOMAINS": ["Uracil-DNA glycosylase", "Uracil-DNA glycosylase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4863, "SYSTRES": 305, "PROTATS": 4863, "PROTRES": 305, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.47508, "BOXSIZEY": 8.47508, "BOXSIZEZ": 6.00649, "mdName": "replica 1", "mdAtoms": 4863, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0024/files/topology.tpr", "length": 1592244, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0024/files/screenshot.jpg", "length": 24851, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0024/files/trajectory.bin", "length": 291838356, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 5001, "atoms": 4863}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_01.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_02.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_03.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_04.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_05.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_06.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_07.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_08.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_09.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_10.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_11.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_12.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_13.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_14.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A0024/files/pca_trajectory_15.bin", "length": 219600, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0, "frames": 20, "atoms": 915}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0024/files/structure.pdb", "length": 393938, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0024/files/trajectory.xtc", "length": 92564956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_00.jpg", "length": 25369, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_01.jpg", "length": 25994, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_02.jpg", "length": 25049, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_03.jpg", "length": 25589, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_04.jpg", "length": 25246, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_05.jpg", "length": 24956, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_06.jpg", "length": 25258, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_07.jpg", "length": 25523, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_08.jpg", "length": 25475, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_09.jpg", "length": 25529, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_10.jpg", "length": 25187, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_11.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_12.jpg", "length": 25178, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_13.jpg", "length": 25329, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_14.jpg", "length": 25676, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_15.jpg", "length": 25140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_16.jpg", "length": 25850, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_17.jpg", "length": 25854, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_00_screenshot_18.jpg", "length": 25028, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_00.jpg", "length": 23093, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_01.jpg", "length": 23318, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_02.jpg", "length": 22575, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_03.jpg", "length": 22433, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_04.jpg", "length": 22957, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_05.jpg", "length": 22640, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_06.jpg", "length": 22337, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_07.jpg", "length": 22797, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_08.jpg", "length": 22783, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_09.jpg", "length": 22490, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_10.jpg", "length": 22710, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_11.jpg", "length": 23255, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_12.jpg", "length": 22654, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_13.jpg", "length": 22417, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_14.jpg", "length": 22794, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_15.jpg", "length": 22619, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_16.jpg", "length": 23140, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_17.jpg", "length": 22549, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_18.jpg", "length": 23263, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0024/files/clusters_01_screenshot_19.jpg", "length": 22721, "contentType": "application/octet-stream", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0024/files/pocket_01.pdb", "length": 22043, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0024/files/pocket_02.pdb", "length": 13936, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0024/files/pocket_03.pdb", "length": 8710, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0024/files/pocket_04.pdb", "length": 7973, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0024/files/pocket_05.pdb", "length": 7504, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0024/files/pocket_06.pdb", "length": 6633, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0024/files/pocket_07.pdb", "length": 6298, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0024/files/pocket_08.pdb", "length": 5226, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0024/files/pocket_09.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0024/files/pocket_10.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "683f76bea396e03843709f82", "md": 0}}]}
A002A/project.json ADDED
@@ -0,0 +1,191 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A002A",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 1WRD",
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
+ "1WRD"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "O60784",
31
+ "P0CH28"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
38
+ "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Target of Myb1 membrane trafficking protein",
43
+ "GAT",
44
+ "Disordered",
45
+ "Ubiquitin",
46
+ "Ubiquitin-like 2"
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": 2816,
58
+ "SYSTRES": 174,
59
+ "PROTATS": 2816,
60
+ "PROTRES": 174,
61
+ "NUCLATS": 0,
62
+ "NUCLRES": 0,
63
+ "LIPIATS": 0,
64
+ "LIPIRES": 0,
65
+ "CARBATS": 0,
66
+ "CARBRES": 0,
67
+ "SOLVATS": 0,
68
+ "SOLVRES": 0,
69
+ "COUNCAT": 0,
70
+ "COUNANI": 0,
71
+ "COUNION": 0,
72
+ "INTERACTIONS": [
73
+ {
74
+ "name": "chain A-chain B interaction",
75
+ "agent_1": "chain A",
76
+ "agent_2": "chain B",
77
+ "selection_1": "chain A",
78
+ "selection_2": "chain B",
79
+ "type": "protein-protein"
80
+ }
81
+ ],
82
+ "PBC_SELECTION": null,
83
+ "CHAINNAMES": null,
84
+ "MEMBRANES": null,
85
+ "CUSTOMS": null,
86
+ "ORIENTATION": null,
87
+ "PTM": [],
88
+ "MULTIMERIC": null,
89
+ "COLLECTIONS": "dynarepo",
90
+ "WARNINGS": [],
91
+ "BOXSIZEX": 8.13965,
92
+ "BOXSIZEY": 8.13965,
93
+ "BOXSIZEZ": 5.73787,
94
+ "mdName": "replica 1",
95
+ "mdAtoms": 2816,
96
+ "mdFrames": 5001
97
+ },
98
+ "mds": [
99
+ "replica 1",
100
+ "replica 2",
101
+ "replica 3"
102
+ ],
103
+ "mdref": 0,
104
+ "files": [
105
+ "topology.tpr",
106
+ "screenshot.jpg",
107
+ "trajectory.bin",
108
+ "pca_trajectory_01.bin",
109
+ "pca_trajectory_02.bin",
110
+ "pca_trajectory_03.bin",
111
+ "pca_trajectory_04.bin",
112
+ "pca_trajectory_05.bin",
113
+ "pca_trajectory_06.bin",
114
+ "pca_trajectory_07.bin",
115
+ "pca_trajectory_08.bin",
116
+ "pca_trajectory_09.bin",
117
+ "pca_trajectory_10.bin",
118
+ "pca_trajectory_11.bin",
119
+ "pca_trajectory_12.bin",
120
+ "pca_trajectory_13.bin",
121
+ "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
+ "clusters_00_screenshot_04.jpg",
128
+ "clusters_00_screenshot_05.jpg",
129
+ "clusters_00_screenshot_06.jpg",
130
+ "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_01_screenshot_00.jpg",
144
+ "clusters_01_screenshot_01.jpg",
145
+ "clusters_01_screenshot_02.jpg",
146
+ "clusters_01_screenshot_03.jpg",
147
+ "clusters_01_screenshot_04.jpg",
148
+ "clusters_01_screenshot_05.jpg",
149
+ "clusters_01_screenshot_06.jpg",
150
+ "clusters_01_screenshot_07.jpg",
151
+ "clusters_01_screenshot_08.jpg",
152
+ "clusters_01_screenshot_09.jpg",
153
+ "clusters_01_screenshot_10.jpg",
154
+ "clusters_01_screenshot_11.jpg",
155
+ "clusters_01_screenshot_12.jpg",
156
+ "clusters_01_screenshot_13.jpg",
157
+ "clusters_01_screenshot_14.jpg",
158
+ "clusters_01_screenshot_15.jpg",
159
+ "clusters_01_screenshot_16.jpg",
160
+ "clusters_01_screenshot_17.jpg",
161
+ "clusters_01_screenshot_18.jpg",
162
+ "clusters_01_screenshot_19.jpg",
163
+ "clusters_01_screenshot_20.jpg",
164
+ "pocket_01.pdb",
165
+ "pocket_02.pdb"
166
+ ],
167
+ "analyses": [
168
+ "clusters",
169
+ "clusters-00",
170
+ "clusters-01",
171
+ "dist-perres",
172
+ "energies",
173
+ "fluctuation",
174
+ "hbonds",
175
+ "interactions",
176
+ "pca",
177
+ "pockets",
178
+ "rgyr",
179
+ "rmsd-pairwise",
180
+ "rmsd-perres",
181
+ "rmsds",
182
+ "sasa",
183
+ "tmscores"
184
+ ],
185
+ "mdIndex": 0,
186
+ "mdNumber": 1,
187
+ "refframe": 0,
188
+ "internalId": "683f7e53033ad70f2bcb1da1",
189
+ "creationDate": "2025-06-03T22:59:31.000Z",
190
+ "identifier": "A002A"
191
+ }
A002A/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A002A", "accession": "A002A", "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 1WRD", "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": ["1WRD"], "FORCED_REFERENCES": null, "REFERENCES": ["O60784", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"], "NUCLSEQ": [], "DOMAINS": ["Target of Myb1 membrane trafficking protein", "GAT", "Disordered", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 174, "PROTATS": 2816, "PROTRES": 174, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.13965, "BOXSIZEY": 8.13965, "BOXSIZEZ": 5.73787, "mdName": "replica 1", "mdAtoms": 2816, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002A/files/topology.tpr", "length": 1048380, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002A/files/screenshot.jpg", "length": 19440, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002A/files/trajectory.bin", "length": 168993792, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 5001, "atoms": 2816}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_01.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_02.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_03.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_04.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_05.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_06.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_07.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_08.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_09.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_10.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_11.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_12.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_13.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002A/files/structure.pdb", "length": 228131, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002A/files/trajectory.xtc", "length": 53825612, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_00.jpg", "length": 19805, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_01.jpg", "length": 19505, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_02.jpg", "length": 19848, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_03.jpg", "length": 19407, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_04.jpg", "length": 19623, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_05.jpg", "length": 19060, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_06.jpg", "length": 20155, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_07.jpg", "length": 19354, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_08.jpg", "length": 18817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_09.jpg", "length": 19701, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_10.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_11.jpg", "length": 20265, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_12.jpg", "length": 19672, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_13.jpg", "length": 19500, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_14.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_15.jpg", "length": 19541, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_16.jpg", "length": 19730, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_17.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_18.jpg", "length": 20102, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_19.jpg", "length": 19629, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_00.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_01.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_02.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_03.jpg", "length": 21314, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_04.jpg", "length": 20980, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_05.jpg", "length": 20540, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_06.jpg", "length": 20162, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_07.jpg", "length": 20831, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_08.jpg", "length": 21204, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_09.jpg", "length": 21403, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_10.jpg", "length": 20775, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_11.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_12.jpg", "length": 20717, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_13.jpg", "length": 21232, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_14.jpg", "length": 21114, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_15.jpg", "length": 20099, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_16.jpg", "length": 19885, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_17.jpg", "length": 20853, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_18.jpg", "length": 20655, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_19.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_20.jpg", "length": 21297, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002A/files/pocket_01.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002A/files/pocket_02.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}]}
2
+ {"project_identifier": "A002A", "accession": "A002A", "published": true, "md_index": 1, "md_name": "replica 2", "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 1WRD", "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": ["1WRD"], "FORCED_REFERENCES": null, "REFERENCES": ["O60784", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"], "NUCLSEQ": [], "DOMAINS": ["Target of Myb1 membrane trafficking protein", "GAT", "Disordered", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 174, "PROTATS": 2816, "PROTRES": 174, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.13965, "BOXSIZEY": 8.13965, "BOXSIZEZ": 5.73787, "mdName": "replica 1", "mdAtoms": 2816, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002A/files/topology.tpr", "length": 1048380, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002A/files/screenshot.jpg", "length": 19440, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002A/files/trajectory.bin", "length": 168993792, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 5001, "atoms": 2816}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_01.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_02.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_03.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_04.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_05.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_06.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_07.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_08.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_09.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_10.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_11.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_12.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_13.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002A/files/structure.pdb", "length": 228131, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002A/files/trajectory.xtc", "length": 53825612, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_00.jpg", "length": 19805, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_01.jpg", "length": 19505, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_02.jpg", "length": 19848, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_03.jpg", "length": 19407, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_04.jpg", "length": 19623, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_05.jpg", "length": 19060, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_06.jpg", "length": 20155, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_07.jpg", "length": 19354, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_08.jpg", "length": 18817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_09.jpg", "length": 19701, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_10.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_11.jpg", "length": 20265, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_12.jpg", "length": 19672, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_13.jpg", "length": 19500, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_14.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_15.jpg", "length": 19541, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_16.jpg", "length": 19730, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_17.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_18.jpg", "length": 20102, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_19.jpg", "length": 19629, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_00.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_01.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_02.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_03.jpg", "length": 21314, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_04.jpg", "length": 20980, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_05.jpg", "length": 20540, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_06.jpg", "length": 20162, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_07.jpg", "length": 20831, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_08.jpg", "length": 21204, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_09.jpg", "length": 21403, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_10.jpg", "length": 20775, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_11.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_12.jpg", "length": 20717, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_13.jpg", "length": 21232, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_14.jpg", "length": 21114, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_15.jpg", "length": 20099, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_16.jpg", "length": 19885, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_17.jpg", "length": 20853, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_18.jpg", "length": 20655, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_19.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_20.jpg", "length": 21297, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002A/files/pocket_01.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002A/files/pocket_02.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}]}
3
+ {"project_identifier": "A002A", "accession": "A002A", "published": true, "md_index": 2, "md_name": "replica 3", "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 1WRD", "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": ["1WRD"], "FORCED_REFERENCES": null, "REFERENCES": ["O60784", "P0CH28"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG", "GPLGSEQIGKLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIANEQLTEELLIVNDNLNNVFLRHERFERFRTG"], "NUCLSEQ": [], "DOMAINS": ["Target of Myb1 membrane trafficking protein", "GAT", "Disordered", "Ubiquitin", "Ubiquitin-like 2"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2816, "SYSTRES": 174, "PROTATS": 2816, "PROTRES": 174, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.13965, "BOXSIZEY": 8.13965, "BOXSIZEZ": 5.73787, "mdName": "replica 1", "mdAtoms": 2816, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A002A/files/topology.tpr", "length": 1048380, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A002A/files/screenshot.jpg", "length": 19440, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A002A/files/trajectory.bin", "length": 168993792, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 5001, "atoms": 2816}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_01.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_02.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_03.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_04.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_05.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_06.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_07.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_08.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_09.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_10.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_11.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_12.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A002A/files/pca_trajectory_13.bin", "length": 125280, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0, "frames": 20, "atoms": 522}}, {"name": "structure.pdb", "downloadUrl": "/projects/A002A/files/structure.pdb", "length": 228131, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A002A/files/trajectory.xtc", "length": 53825612, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_00.jpg", "length": 19805, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_01.jpg", "length": 19505, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_02.jpg", "length": 19848, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_03.jpg", "length": 19407, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_04.jpg", "length": 19623, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_05.jpg", "length": 19060, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_06.jpg", "length": 20155, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_07.jpg", "length": 19354, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_08.jpg", "length": 18817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_09.jpg", "length": 19701, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_10.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_11.jpg", "length": 20265, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_12.jpg", "length": 19672, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_13.jpg", "length": 19500, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_14.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_15.jpg", "length": 19541, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_16.jpg", "length": 19730, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_17.jpg", "length": 19584, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_18.jpg", "length": 20102, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_00_screenshot_19.jpg", "length": 19629, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_00.jpg", "length": 20817, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_01.jpg", "length": 21311, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_02.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_03.jpg", "length": 21314, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_04.jpg", "length": 20980, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_05.jpg", "length": 20540, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_06.jpg", "length": 20162, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_07.jpg", "length": 20831, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_08.jpg", "length": 21204, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_09.jpg", "length": 21403, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_10.jpg", "length": 20775, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_11.jpg", "length": 20961, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_12.jpg", "length": 20717, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_13.jpg", "length": 21232, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_14.jpg", "length": 21114, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_15.jpg", "length": 20099, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_16.jpg", "length": 19885, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_17.jpg", "length": 20853, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_18.jpg", "length": 20655, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_19.jpg", "length": 21596, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A002A/files/clusters_01_screenshot_20.jpg", "length": 21297, "contentType": "application/octet-stream", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A002A/files/pocket_01.pdb", "length": 5628, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A002A/files/pocket_02.pdb", "length": 4087, "contentType": "chemical/x-pdb", "metadata": {"project": "683f7e53033ad70f2bcb1da1", "md": 0}}]}
A0039/project.json ADDED
@@ -0,0 +1,363 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0039",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2J8S",
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
+ "2J8S"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P31224",
31
+ "Q00420"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDI",
38
+ "GSDLGKKLLEAARAGRDDEVRILMANGADVNAADVVGWTPLHLAAYWGHLEIVEVLLKNGADVNAYDTLGSTPLHLAAHFGHLEIVEVLLKNGADVNAKDDNGITPLHLAANRGHLEIVEVLLKYGADVNAQDKFGKTAFDISINNGNEDLAEILQ",
39
+ "LGKKLLEAARAGRDDEVRILMANGADVNAADVVGWTPLHLAAYWGHLEIVEVLLKNGADVNAYDTLGSTPLHLAAHFGHLEIVEVLLKNGADVNAKDDNGITPLHLAANRGHLEIVEVLLKYGADVNAQDKFGKTAFDISINNGNEDLAEILQ",
40
+ "MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSH",
41
+ "MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRF"
42
+ ],
43
+ "NUCLSEQ": [],
44
+ "DOMAINS": [
45
+ "Multidrug efflux pump subunit AcrB",
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": 52497,
58
+ "SYSTRES": 3426,
59
+ "PROTATS": 52497,
60
+ "PROTRES": 3426,
61
+ "NUCLATS": 0,
62
+ "NUCLRES": 0,
63
+ "LIPIATS": 0,
64
+ "LIPIRES": 0,
65
+ "CARBATS": 0,
66
+ "CARBRES": 0,
67
+ "SOLVATS": 0,
68
+ "SOLVRES": 0,
69
+ "COUNCAT": 0,
70
+ "COUNANI": 0,
71
+ "COUNION": 0,
72
+ "INTERACTIONS": [
73
+ {
74
+ "name": "chain A-chain B interaction",
75
+ "agent_1": "chain A",
76
+ "agent_2": "chain B",
77
+ "selection_1": "chain A",
78
+ "selection_2": "chain B",
79
+ "type": "protein-protein"
80
+ },
81
+ {
82
+ "name": "chain A-chain C interaction",
83
+ "agent_1": "chain A",
84
+ "agent_2": "chain C",
85
+ "selection_1": "chain A",
86
+ "selection_2": "chain C",
87
+ "type": "protein-protein"
88
+ },
89
+ {
90
+ "name": "chain A-chain D interaction",
91
+ "agent_1": "chain A",
92
+ "agent_2": "chain D",
93
+ "selection_1": "chain A",
94
+ "selection_2": "chain D",
95
+ "type": "protein-protein"
96
+ },
97
+ {
98
+ "name": "chain A-chain E interaction",
99
+ "agent_1": "chain A",
100
+ "agent_2": "chain E",
101
+ "selection_1": "chain A",
102
+ "selection_2": "chain E",
103
+ "type": "protein-protein"
104
+ },
105
+ {
106
+ "name": "chain B-chain C interaction",
107
+ "agent_1": "chain B",
108
+ "agent_2": "chain C",
109
+ "selection_1": "chain B",
110
+ "selection_2": "chain C",
111
+ "type": "protein-protein"
112
+ },
113
+ {
114
+ "name": "chain B-chain D interaction",
115
+ "agent_1": "chain B",
116
+ "agent_2": "chain D",
117
+ "selection_1": "chain B",
118
+ "selection_2": "chain D",
119
+ "type": "protein-protein"
120
+ },
121
+ {
122
+ "name": "chain C-chain E interaction",
123
+ "agent_1": "chain C",
124
+ "agent_2": "chain E",
125
+ "selection_1": "chain B",
126
+ "selection_2": "chain E",
127
+ "type": "protein-protein"
128
+ }
129
+ ],
130
+ "PBC_SELECTION": null,
131
+ "CHAINNAMES": null,
132
+ "MEMBRANES": null,
133
+ "CUSTOMS": null,
134
+ "ORIENTATION": null,
135
+ "PTM": [],
136
+ "MULTIMERIC": null,
137
+ "COLLECTIONS": "dynarepo",
138
+ "WARNINGS": [],
139
+ "BOXSIZEX": 17.4064,
140
+ "BOXSIZEY": 17.4064,
141
+ "BOXSIZEZ": 12.3243,
142
+ "mdName": "replica 1",
143
+ "mdAtoms": 52497,
144
+ "mdFrames": 5001
145
+ },
146
+ "mds": [
147
+ "replica 1",
148
+ "replica 2",
149
+ "replica 3"
150
+ ],
151
+ "mdref": 0,
152
+ "files": [
153
+ "topology.tpr",
154
+ "screenshot.jpg",
155
+ "trajectory.bin",
156
+ "pca_trajectory_01.bin",
157
+ "pca_trajectory_02.bin",
158
+ "pca_trajectory_03.bin",
159
+ "pca_trajectory_04.bin",
160
+ "pca_trajectory_05.bin",
161
+ "pca_trajectory_06.bin",
162
+ "pca_trajectory_07.bin",
163
+ "pca_trajectory_08.bin",
164
+ "pca_trajectory_09.bin",
165
+ "structure.pdb",
166
+ "trajectory.xtc",
167
+ "clusters_00_screenshot_00.jpg",
168
+ "clusters_00_screenshot_01.jpg",
169
+ "clusters_00_screenshot_02.jpg",
170
+ "clusters_00_screenshot_03.jpg",
171
+ "clusters_00_screenshot_04.jpg",
172
+ "clusters_00_screenshot_05.jpg",
173
+ "clusters_00_screenshot_06.jpg",
174
+ "clusters_00_screenshot_07.jpg",
175
+ "clusters_00_screenshot_08.jpg",
176
+ "clusters_00_screenshot_09.jpg",
177
+ "clusters_00_screenshot_10.jpg",
178
+ "clusters_00_screenshot_11.jpg",
179
+ "clusters_00_screenshot_12.jpg",
180
+ "clusters_00_screenshot_13.jpg",
181
+ "clusters_00_screenshot_14.jpg",
182
+ "clusters_00_screenshot_15.jpg",
183
+ "clusters_00_screenshot_16.jpg",
184
+ "clusters_00_screenshot_17.jpg",
185
+ "clusters_00_screenshot_18.jpg",
186
+ "clusters_00_screenshot_19.jpg",
187
+ "clusters_00_screenshot_20.jpg",
188
+ "clusters_01_screenshot_00.jpg",
189
+ "clusters_01_screenshot_01.jpg",
190
+ "clusters_01_screenshot_02.jpg",
191
+ "clusters_01_screenshot_03.jpg",
192
+ "clusters_01_screenshot_04.jpg",
193
+ "clusters_01_screenshot_05.jpg",
194
+ "clusters_01_screenshot_06.jpg",
195
+ "clusters_01_screenshot_07.jpg",
196
+ "clusters_01_screenshot_08.jpg",
197
+ "clusters_01_screenshot_09.jpg",
198
+ "clusters_01_screenshot_10.jpg",
199
+ "clusters_01_screenshot_11.jpg",
200
+ "clusters_01_screenshot_12.jpg",
201
+ "clusters_01_screenshot_13.jpg",
202
+ "clusters_01_screenshot_14.jpg",
203
+ "clusters_01_screenshot_15.jpg",
204
+ "clusters_01_screenshot_16.jpg",
205
+ "clusters_01_screenshot_17.jpg",
206
+ "clusters_01_screenshot_18.jpg",
207
+ "clusters_01_screenshot_19.jpg",
208
+ "clusters_02_screenshot_00.jpg",
209
+ "clusters_02_screenshot_01.jpg",
210
+ "clusters_02_screenshot_02.jpg",
211
+ "clusters_02_screenshot_03.jpg",
212
+ "clusters_02_screenshot_04.jpg",
213
+ "clusters_02_screenshot_05.jpg",
214
+ "clusters_02_screenshot_06.jpg",
215
+ "clusters_02_screenshot_07.jpg",
216
+ "clusters_02_screenshot_08.jpg",
217
+ "clusters_02_screenshot_09.jpg",
218
+ "clusters_02_screenshot_10.jpg",
219
+ "clusters_02_screenshot_11.jpg",
220
+ "clusters_02_screenshot_12.jpg",
221
+ "clusters_02_screenshot_13.jpg",
222
+ "clusters_02_screenshot_14.jpg",
223
+ "clusters_02_screenshot_15.jpg",
224
+ "clusters_02_screenshot_16.jpg",
225
+ "clusters_02_screenshot_17.jpg",
226
+ "clusters_02_screenshot_18.jpg",
227
+ "clusters_02_screenshot_19.jpg",
228
+ "clusters_02_screenshot_20.jpg",
229
+ "clusters_03_screenshot_00.jpg",
230
+ "clusters_03_screenshot_01.jpg",
231
+ "clusters_03_screenshot_02.jpg",
232
+ "clusters_03_screenshot_03.jpg",
233
+ "clusters_03_screenshot_04.jpg",
234
+ "clusters_03_screenshot_05.jpg",
235
+ "clusters_03_screenshot_06.jpg",
236
+ "clusters_03_screenshot_07.jpg",
237
+ "clusters_03_screenshot_08.jpg",
238
+ "clusters_03_screenshot_09.jpg",
239
+ "clusters_03_screenshot_10.jpg",
240
+ "clusters_03_screenshot_11.jpg",
241
+ "clusters_03_screenshot_12.jpg",
242
+ "clusters_03_screenshot_13.jpg",
243
+ "clusters_03_screenshot_14.jpg",
244
+ "clusters_03_screenshot_15.jpg",
245
+ "clusters_03_screenshot_16.jpg",
246
+ "clusters_03_screenshot_17.jpg",
247
+ "clusters_03_screenshot_18.jpg",
248
+ "clusters_03_screenshot_19.jpg",
249
+ "clusters_04_screenshot_00.jpg",
250
+ "clusters_04_screenshot_01.jpg",
251
+ "clusters_04_screenshot_02.jpg",
252
+ "clusters_04_screenshot_03.jpg",
253
+ "clusters_04_screenshot_04.jpg",
254
+ "clusters_04_screenshot_05.jpg",
255
+ "clusters_04_screenshot_06.jpg",
256
+ "clusters_04_screenshot_07.jpg",
257
+ "clusters_04_screenshot_08.jpg",
258
+ "clusters_04_screenshot_09.jpg",
259
+ "clusters_04_screenshot_10.jpg",
260
+ "clusters_04_screenshot_11.jpg",
261
+ "clusters_04_screenshot_12.jpg",
262
+ "clusters_04_screenshot_13.jpg",
263
+ "clusters_04_screenshot_14.jpg",
264
+ "clusters_04_screenshot_15.jpg",
265
+ "clusters_04_screenshot_16.jpg",
266
+ "clusters_05_screenshot_00.jpg",
267
+ "clusters_05_screenshot_01.jpg",
268
+ "clusters_05_screenshot_02.jpg",
269
+ "clusters_05_screenshot_03.jpg",
270
+ "clusters_05_screenshot_04.jpg",
271
+ "clusters_05_screenshot_05.jpg",
272
+ "clusters_05_screenshot_06.jpg",
273
+ "clusters_05_screenshot_07.jpg",
274
+ "clusters_05_screenshot_08.jpg",
275
+ "clusters_05_screenshot_09.jpg",
276
+ "clusters_05_screenshot_10.jpg",
277
+ "clusters_05_screenshot_11.jpg",
278
+ "clusters_05_screenshot_12.jpg",
279
+ "clusters_05_screenshot_13.jpg",
280
+ "clusters_05_screenshot_14.jpg",
281
+ "clusters_05_screenshot_15.jpg",
282
+ "clusters_05_screenshot_16.jpg",
283
+ "clusters_05_screenshot_17.jpg",
284
+ "clusters_06_screenshot_00.jpg",
285
+ "clusters_06_screenshot_01.jpg",
286
+ "clusters_06_screenshot_02.jpg",
287
+ "clusters_06_screenshot_03.jpg",
288
+ "clusters_06_screenshot_04.jpg",
289
+ "clusters_06_screenshot_05.jpg",
290
+ "clusters_06_screenshot_06.jpg",
291
+ "clusters_06_screenshot_07.jpg",
292
+ "clusters_06_screenshot_08.jpg",
293
+ "clusters_06_screenshot_09.jpg",
294
+ "clusters_06_screenshot_10.jpg",
295
+ "clusters_06_screenshot_11.jpg",
296
+ "clusters_06_screenshot_12.jpg",
297
+ "clusters_06_screenshot_13.jpg",
298
+ "clusters_06_screenshot_14.jpg",
299
+ "clusters_06_screenshot_15.jpg",
300
+ "clusters_06_screenshot_16.jpg",
301
+ "clusters_06_screenshot_17.jpg",
302
+ "clusters_06_screenshot_18.jpg",
303
+ "clusters_06_screenshot_19.jpg",
304
+ "clusters_07_screenshot_00.jpg",
305
+ "clusters_07_screenshot_01.jpg",
306
+ "clusters_07_screenshot_02.jpg",
307
+ "clusters_07_screenshot_03.jpg",
308
+ "clusters_07_screenshot_04.jpg",
309
+ "clusters_07_screenshot_05.jpg",
310
+ "clusters_07_screenshot_06.jpg",
311
+ "clusters_07_screenshot_07.jpg",
312
+ "clusters_07_screenshot_08.jpg",
313
+ "clusters_07_screenshot_09.jpg",
314
+ "clusters_07_screenshot_10.jpg",
315
+ "clusters_07_screenshot_11.jpg",
316
+ "clusters_07_screenshot_12.jpg",
317
+ "clusters_07_screenshot_13.jpg",
318
+ "clusters_07_screenshot_14.jpg",
319
+ "clusters_07_screenshot_15.jpg",
320
+ "clusters_07_screenshot_16.jpg",
321
+ "clusters_07_screenshot_17.jpg",
322
+ "pocket_01.pdb",
323
+ "pocket_02.pdb",
324
+ "pocket_03.pdb",
325
+ "pocket_04.pdb",
326
+ "pocket_05.pdb",
327
+ "pocket_06.pdb",
328
+ "pocket_07.pdb",
329
+ "pocket_08.pdb",
330
+ "pocket_09.pdb",
331
+ "pocket_10.pdb"
332
+ ],
333
+ "analyses": [
334
+ "clusters",
335
+ "clusters-00",
336
+ "clusters-01",
337
+ "clusters-02",
338
+ "clusters-03",
339
+ "clusters-04",
340
+ "clusters-05",
341
+ "clusters-06",
342
+ "clusters-07",
343
+ "dist-perres",
344
+ "energies",
345
+ "fluctuation",
346
+ "hbonds",
347
+ "interactions",
348
+ "pca",
349
+ "pockets",
350
+ "rgyr",
351
+ "rmsd-pairwise",
352
+ "rmsd-perres",
353
+ "rmsds",
354
+ "sasa",
355
+ "tmscores"
356
+ ],
357
+ "mdIndex": 0,
358
+ "mdNumber": 1,
359
+ "refframe": 2,
360
+ "internalId": "6840518f52ff4a1c32039c0a",
361
+ "creationDate": "2025-06-04T14:00:47.000Z",
362
+ "identifier": "A0039"
363
+ }
A0039/records.jsonl ADDED
The diff for this file is too large to render. See raw diff
 
A003E/project.json ADDED
@@ -0,0 +1,200 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A003E",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2NQD",
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
+ "2NQD"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "Q966X9",
31
+ "P07711"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "EAPRSVDWREKGYVTPVKNQGQCGSAWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV",
38
+ "SHKVTKAHNGATLTVAVGELVEIQLPSNPTTGFAWYFEGGTKESPNESMFTVENKYFPPDSKLLGAGGTEHFHVTVKAAGTHAVNLTYMRPWTGPSHDSERFTVYLKAN"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Chagasin",
43
+ "BC loop",
44
+ "DE loop",
45
+ "FG loop",
46
+ "Cathepsin L",
47
+ "Cathepsin L heavy chain",
48
+ "Cathepsin L light chain",
49
+ "Cleavage; by autolysis"
50
+ ],
51
+ "FRAMESTEP": 0.1,
52
+ "TIMESTEP": 2,
53
+ "TEMP": 310,
54
+ "ENSEMBLE": "NPT",
55
+ "FF": [
56
+ "CHARMM36m"
57
+ ],
58
+ "WAT": "TIP3P",
59
+ "BOXTYPE": "Dodecahedron",
60
+ "SYSTATS": 4933,
61
+ "SYSTRES": 330,
62
+ "PROTATS": 4933,
63
+ "PROTRES": 330,
64
+ "NUCLATS": 0,
65
+ "NUCLRES": 0,
66
+ "LIPIATS": 0,
67
+ "LIPIRES": 0,
68
+ "CARBATS": 0,
69
+ "CARBRES": 0,
70
+ "SOLVATS": 0,
71
+ "SOLVRES": 0,
72
+ "COUNCAT": 0,
73
+ "COUNANI": 0,
74
+ "COUNION": 0,
75
+ "INTERACTIONS": [
76
+ {
77
+ "name": "chain A-chain B interaction",
78
+ "agent_1": "chain A",
79
+ "agent_2": "chain B",
80
+ "selection_1": "chain A",
81
+ "selection_2": "chain B",
82
+ "type": "protein-protein"
83
+ }
84
+ ],
85
+ "PBC_SELECTION": null,
86
+ "CHAINNAMES": null,
87
+ "MEMBRANES": null,
88
+ "CUSTOMS": null,
89
+ "ORIENTATION": null,
90
+ "PTM": [],
91
+ "MULTIMERIC": null,
92
+ "COLLECTIONS": "dynarepo",
93
+ "WARNINGS": [],
94
+ "BOXSIZEX": 9.95686,
95
+ "BOXSIZEY": 9.95686,
96
+ "BOXSIZEZ": 7.07656,
97
+ "mdName": "replica 1",
98
+ "mdAtoms": 4933,
99
+ "mdFrames": 5001
100
+ },
101
+ "mds": [
102
+ "replica 1",
103
+ "replica 2",
104
+ "replica 3"
105
+ ],
106
+ "mdref": 0,
107
+ "files": [
108
+ "topology.tpr",
109
+ "screenshot.jpg",
110
+ "trajectory.bin",
111
+ "pca_trajectory_01.bin",
112
+ "pca_trajectory_02.bin",
113
+ "pca_trajectory_03.bin",
114
+ "pca_trajectory_04.bin",
115
+ "pca_trajectory_05.bin",
116
+ "pca_trajectory_06.bin",
117
+ "pca_trajectory_07.bin",
118
+ "pca_trajectory_08.bin",
119
+ "pca_trajectory_09.bin",
120
+ "pca_trajectory_10.bin",
121
+ "pca_trajectory_11.bin",
122
+ "pca_trajectory_12.bin",
123
+ "pca_trajectory_13.bin",
124
+ "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_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
+ "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": "6840630af49fd4972b4ea47e",
198
+ "creationDate": "2025-06-04T15:15:22.000Z",
199
+ "identifier": "A003E"
200
+ }
A003E/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A003E", "accession": "A003E", "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 2NQD", "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": ["2NQD"], "FORCED_REFERENCES": null, "REFERENCES": ["Q966X9", "P07711"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EAPRSVDWREKGYVTPVKNQGQCGSAWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV", "SHKVTKAHNGATLTVAVGELVEIQLPSNPTTGFAWYFEGGTKESPNESMFTVENKYFPPDSKLLGAGGTEHFHVTVKAAGTHAVNLTYMRPWTGPSHDSERFTVYLKAN"], "NUCLSEQ": [], "DOMAINS": ["Chagasin", "BC loop", "DE loop", "FG loop", "Cathepsin L", "Cathepsin L heavy chain", "Cathepsin L light chain", "Cleavage; by autolysis"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4933, "SYSTRES": 330, "PROTATS": 4933, "PROTRES": 330, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.95686, "BOXSIZEY": 9.95686, "BOXSIZEZ": 7.07656, "mdName": "replica 1", "mdAtoms": 4933, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003E/files/topology.tpr", "length": 1653476, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003E/files/screenshot.jpg", "length": 21351, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003E/files/trajectory.bin", "length": 296039196, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 5001, "atoms": 4933}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_01.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_02.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_03.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_04.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_05.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_06.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_07.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_08.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_09.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_10.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_11.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_12.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_13.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003E/files/structure.pdb", "length": 399608, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003E/files/trajectory.xtc", "length": 93726548, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_00.jpg", "length": 21746, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_01.jpg", "length": 21926, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_02.jpg", "length": 22645, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_03.jpg", "length": 21982, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_04.jpg", "length": 21807, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_05.jpg", "length": 21581, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_06.jpg", "length": 21374, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_07.jpg", "length": 21648, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_08.jpg", "length": 22069, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_09.jpg", "length": 21950, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_10.jpg", "length": 21617, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_11.jpg", "length": 21984, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_12.jpg", "length": 21741, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_13.jpg", "length": 21883, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_14.jpg", "length": 22264, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_15.jpg", "length": 22018, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_16.jpg", "length": 21621, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_17.jpg", "length": 21421, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_18.jpg", "length": 22217, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_19.jpg", "length": 22040, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_00.jpg", "length": 21962, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_01.jpg", "length": 21868, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_02.jpg", "length": 22002, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_03.jpg", "length": 22097, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_04.jpg", "length": 21468, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_05.jpg", "length": 22288, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_06.jpg", "length": 22256, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_07.jpg", "length": 22063, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_08.jpg", "length": 22186, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_09.jpg", "length": 22074, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_10.jpg", "length": 22235, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_11.jpg", "length": 22693, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_12.jpg", "length": 22180, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_13.jpg", "length": 22099, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_14.jpg", "length": 22435, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_15.jpg", "length": 21816, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_16.jpg", "length": 21977, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_17.jpg", "length": 21843, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_18.jpg", "length": 22379, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003E/files/pocket_01.pdb", "length": 13467, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003E/files/pocket_02.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003E/files/pocket_03.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003E/files/pocket_04.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003E/files/pocket_05.pdb", "length": 10385, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003E/files/pocket_06.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003E/files/pocket_07.pdb", "length": 7705, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A003E/files/pocket_08.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A003E/files/pocket_09.pdb", "length": 4958, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A003E/files/pocket_10.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}]}
2
+ {"project_identifier": "A003E", "accession": "A003E", "published": true, "md_index": 1, "md_name": "replica 2", "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 2NQD", "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": ["2NQD"], "FORCED_REFERENCES": null, "REFERENCES": ["Q966X9", "P07711"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EAPRSVDWREKGYVTPVKNQGQCGSAWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV", "SHKVTKAHNGATLTVAVGELVEIQLPSNPTTGFAWYFEGGTKESPNESMFTVENKYFPPDSKLLGAGGTEHFHVTVKAAGTHAVNLTYMRPWTGPSHDSERFTVYLKAN"], "NUCLSEQ": [], "DOMAINS": ["Chagasin", "BC loop", "DE loop", "FG loop", "Cathepsin L", "Cathepsin L heavy chain", "Cathepsin L light chain", "Cleavage; by autolysis"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4933, "SYSTRES": 330, "PROTATS": 4933, "PROTRES": 330, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.95686, "BOXSIZEY": 9.95686, "BOXSIZEZ": 7.07656, "mdName": "replica 1", "mdAtoms": 4933, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003E/files/topology.tpr", "length": 1653476, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003E/files/screenshot.jpg", "length": 21351, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003E/files/trajectory.bin", "length": 296039196, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 5001, "atoms": 4933}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_01.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_02.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_03.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_04.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_05.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_06.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_07.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_08.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_09.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_10.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_11.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_12.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_13.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003E/files/structure.pdb", "length": 399608, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003E/files/trajectory.xtc", "length": 93726548, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_00.jpg", "length": 21746, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_01.jpg", "length": 21926, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_02.jpg", "length": 22645, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_03.jpg", "length": 21982, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_04.jpg", "length": 21807, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_05.jpg", "length": 21581, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_06.jpg", "length": 21374, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_07.jpg", "length": 21648, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_08.jpg", "length": 22069, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_09.jpg", "length": 21950, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_10.jpg", "length": 21617, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_11.jpg", "length": 21984, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_12.jpg", "length": 21741, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_13.jpg", "length": 21883, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_14.jpg", "length": 22264, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_15.jpg", "length": 22018, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_16.jpg", "length": 21621, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_17.jpg", "length": 21421, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_18.jpg", "length": 22217, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_19.jpg", "length": 22040, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_00.jpg", "length": 21962, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_01.jpg", "length": 21868, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_02.jpg", "length": 22002, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_03.jpg", "length": 22097, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_04.jpg", "length": 21468, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_05.jpg", "length": 22288, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_06.jpg", "length": 22256, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_07.jpg", "length": 22063, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_08.jpg", "length": 22186, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_09.jpg", "length": 22074, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_10.jpg", "length": 22235, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_11.jpg", "length": 22693, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_12.jpg", "length": 22180, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_13.jpg", "length": 22099, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_14.jpg", "length": 22435, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_15.jpg", "length": 21816, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_16.jpg", "length": 21977, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_17.jpg", "length": 21843, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_18.jpg", "length": 22379, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003E/files/pocket_01.pdb", "length": 13467, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003E/files/pocket_02.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003E/files/pocket_03.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003E/files/pocket_04.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003E/files/pocket_05.pdb", "length": 10385, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003E/files/pocket_06.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003E/files/pocket_07.pdb", "length": 7705, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A003E/files/pocket_08.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A003E/files/pocket_09.pdb", "length": 4958, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A003E/files/pocket_10.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}]}
3
+ {"project_identifier": "A003E", "accession": "A003E", "published": true, "md_index": 2, "md_name": "replica 3", "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 2NQD", "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": ["2NQD"], "FORCED_REFERENCES": null, "REFERENCES": ["Q966X9", "P07711"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EAPRSVDWREKGYVTPVKNQGQCGSAWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV", "SHKVTKAHNGATLTVAVGELVEIQLPSNPTTGFAWYFEGGTKESPNESMFTVENKYFPPDSKLLGAGGTEHFHVTVKAAGTHAVNLTYMRPWTGPSHDSERFTVYLKAN"], "NUCLSEQ": [], "DOMAINS": ["Chagasin", "BC loop", "DE loop", "FG loop", "Cathepsin L", "Cathepsin L heavy chain", "Cathepsin L light chain", "Cleavage; by autolysis"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4933, "SYSTRES": 330, "PROTATS": 4933, "PROTRES": 330, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.95686, "BOXSIZEY": 9.95686, "BOXSIZEZ": 7.07656, "mdName": "replica 1", "mdAtoms": 4933, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003E/files/topology.tpr", "length": 1653476, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003E/files/screenshot.jpg", "length": 21351, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003E/files/trajectory.bin", "length": 296039196, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 5001, "atoms": 4933}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_01.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_02.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_03.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_04.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_05.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_06.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_07.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_08.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_09.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_10.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_11.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_12.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003E/files/pca_trajectory_13.bin", "length": 237600, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0, "frames": 20, "atoms": 990}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003E/files/structure.pdb", "length": 399608, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003E/files/trajectory.xtc", "length": 93726548, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_00.jpg", "length": 21746, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_01.jpg", "length": 21926, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_02.jpg", "length": 22645, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_03.jpg", "length": 21982, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_04.jpg", "length": 21807, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_05.jpg", "length": 21581, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_06.jpg", "length": 21374, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_07.jpg", "length": 21648, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_08.jpg", "length": 22069, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_09.jpg", "length": 21950, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_10.jpg", "length": 21617, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_11.jpg", "length": 21984, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_12.jpg", "length": 21741, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_13.jpg", "length": 21883, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_14.jpg", "length": 22264, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_15.jpg", "length": 22018, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_16.jpg", "length": 21621, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_17.jpg", "length": 21421, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_18.jpg", "length": 22217, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003E/files/clusters_00_screenshot_19.jpg", "length": 22040, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_00.jpg", "length": 21962, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_01.jpg", "length": 21868, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_02.jpg", "length": 22002, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_03.jpg", "length": 22097, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_04.jpg", "length": 21468, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_05.jpg", "length": 22288, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_06.jpg", "length": 22256, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_07.jpg", "length": 22063, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_08.jpg", "length": 22186, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_09.jpg", "length": 22074, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_10.jpg", "length": 22235, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_11.jpg", "length": 22693, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_12.jpg", "length": 22180, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_13.jpg", "length": 22099, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_14.jpg", "length": 22435, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_15.jpg", "length": 21816, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_16.jpg", "length": 21977, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_17.jpg", "length": 21843, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003E/files/clusters_01_screenshot_18.jpg", "length": 22379, "contentType": "application/octet-stream", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003E/files/pocket_01.pdb", "length": 13467, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003E/files/pocket_02.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003E/files/pocket_03.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003E/files/pocket_04.pdb", "length": 11189, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003E/files/pocket_05.pdb", "length": 10385, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003E/files/pocket_06.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003E/files/pocket_07.pdb", "length": 7705, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A003E/files/pocket_08.pdb", "length": 5762, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A003E/files/pocket_09.pdb", "length": 4958, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A003E/files/pocket_10.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "6840630af49fd4972b4ea47e", "md": 0}}]}
A003L/project.json ADDED
@@ -0,0 +1,191 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A003L",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2PCB",
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
+ "2PCB"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P00431",
31
+ "P00004"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL",
38
+ "GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Cytochrome c peroxidase, mitochondrial",
43
+ "Transition state stabilizer",
44
+ "Cytochrome c"
45
+ ],
46
+ "FRAMESTEP": 0.1,
47
+ "TIMESTEP": 2,
48
+ "TEMP": 310,
49
+ "ENSEMBLE": "NPT",
50
+ "FF": [
51
+ "CHARMM36m"
52
+ ],
53
+ "WAT": "TIP3P",
54
+ "BOXTYPE": "Dodecahedron",
55
+ "SYSTATS": 6295,
56
+ "SYSTRES": 398,
57
+ "PROTATS": 6295,
58
+ "PROTRES": 398,
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": 10.2184,
90
+ "BOXSIZEY": 10.2184,
91
+ "BOXSIZEZ": 7.22271,
92
+ "mdName": "replica 1",
93
+ "mdAtoms": 6295,
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
+ "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
+ "pocket_01.pdb",
161
+ "pocket_02.pdb",
162
+ "pocket_03.pdb",
163
+ "pocket_04.pdb",
164
+ "pocket_05.pdb",
165
+ "pocket_06.pdb"
166
+ ],
167
+ "analyses": [
168
+ "clusters",
169
+ "clusters-00",
170
+ "clusters-01",
171
+ "dist-perres",
172
+ "energies",
173
+ "fluctuation",
174
+ "hbonds",
175
+ "interactions",
176
+ "pca",
177
+ "pockets",
178
+ "rgyr",
179
+ "rmsd-pairwise",
180
+ "rmsd-perres",
181
+ "rmsds",
182
+ "sasa",
183
+ "tmscores"
184
+ ],
185
+ "mdIndex": 0,
186
+ "mdNumber": 1,
187
+ "refframe": 0,
188
+ "internalId": "68407531c16de68ddf4d4a74",
189
+ "creationDate": "2025-06-04T16:32:49.000Z",
190
+ "identifier": "A003L"
191
+ }
A003L/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A003L", "accession": "A003L", "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 2PCB", "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": ["2PCB"], "FORCED_REFERENCES": null, "REFERENCES": ["P00431", "P00004"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL", "GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE"], "NUCLSEQ": [], "DOMAINS": ["Cytochrome c peroxidase, mitochondrial", "Transition state stabilizer", "Cytochrome c"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6295, "SYSTRES": 398, "PROTATS": 6295, "PROTRES": 398, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.2184, "BOXSIZEY": 10.2184, "BOXSIZEZ": 7.22271, "mdName": "replica 1", "mdAtoms": 6295, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003L/files/topology.tpr", "length": 2016772, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003L/files/screenshot.jpg", "length": 25912, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003L/files/trajectory.bin", "length": 377775540, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 5001, "atoms": 6295}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_01.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_02.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_03.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_04.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_05.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_06.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_07.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_08.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_09.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_10.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_11.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003L/files/structure.pdb", "length": 509930, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003L/files/trajectory.xtc", "length": 119867972, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_00.jpg", "length": 22855, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_01.jpg", "length": 23777, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_02.jpg", "length": 23499, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_03.jpg", "length": 22895, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_04.jpg", "length": 23001, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_05.jpg", "length": 23663, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_06.jpg", "length": 23201, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_07.jpg", "length": 23546, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_08.jpg", "length": 23352, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_09.jpg", "length": 24150, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_10.jpg", "length": 23839, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_11.jpg", "length": 23310, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_12.jpg", "length": 24036, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_13.jpg", "length": 23929, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_14.jpg", "length": 22733, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_15.jpg", "length": 24208, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_16.jpg", "length": 24110, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_17.jpg", "length": 23767, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_18.jpg", "length": 23799, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_19.jpg", "length": 23219, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_00.jpg", "length": 24774, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_01.jpg", "length": 23975, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_02.jpg", "length": 24115, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_03.jpg", "length": 24183, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_04.jpg", "length": 24581, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_05.jpg", "length": 24613, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_06.jpg", "length": 23988, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_07.jpg", "length": 24675, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_08.jpg", "length": 24940, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_09.jpg", "length": 24531, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_10.jpg", "length": 24879, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_11.jpg", "length": 24212, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_12.jpg", "length": 23830, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_13.jpg", "length": 24418, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_14.jpg", "length": 25023, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_15.jpg", "length": 24513, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_16.jpg", "length": 24429, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_17.jpg", "length": 24877, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_18.jpg", "length": 24430, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_19.jpg", "length": 24827, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_20.jpg", "length": 24517, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003L/files/pocket_01.pdb", "length": 61439, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003L/files/pocket_02.pdb", "length": 27269, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003L/files/pocket_03.pdb", "length": 8643, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003L/files/pocket_04.pdb", "length": 8375, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003L/files/pocket_05.pdb", "length": 3886, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003L/files/pocket_06.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}]}
2
+ {"project_identifier": "A003L", "accession": "A003L", "published": true, "md_index": 1, "md_name": "replica 2", "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 2PCB", "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": ["2PCB"], "FORCED_REFERENCES": null, "REFERENCES": ["P00431", "P00004"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL", "GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE"], "NUCLSEQ": [], "DOMAINS": ["Cytochrome c peroxidase, mitochondrial", "Transition state stabilizer", "Cytochrome c"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6295, "SYSTRES": 398, "PROTATS": 6295, "PROTRES": 398, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.2184, "BOXSIZEY": 10.2184, "BOXSIZEZ": 7.22271, "mdName": "replica 1", "mdAtoms": 6295, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003L/files/topology.tpr", "length": 2016772, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003L/files/screenshot.jpg", "length": 25912, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003L/files/trajectory.bin", "length": 377775540, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 5001, "atoms": 6295}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_01.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_02.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_03.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_04.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_05.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_06.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_07.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_08.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_09.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_10.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_11.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003L/files/structure.pdb", "length": 509930, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003L/files/trajectory.xtc", "length": 119867972, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_00.jpg", "length": 22855, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_01.jpg", "length": 23777, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_02.jpg", "length": 23499, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_03.jpg", "length": 22895, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_04.jpg", "length": 23001, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_05.jpg", "length": 23663, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_06.jpg", "length": 23201, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_07.jpg", "length": 23546, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_08.jpg", "length": 23352, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_09.jpg", "length": 24150, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_10.jpg", "length": 23839, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_11.jpg", "length": 23310, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_12.jpg", "length": 24036, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_13.jpg", "length": 23929, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_14.jpg", "length": 22733, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_15.jpg", "length": 24208, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_16.jpg", "length": 24110, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_17.jpg", "length": 23767, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_18.jpg", "length": 23799, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_19.jpg", "length": 23219, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_00.jpg", "length": 24774, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_01.jpg", "length": 23975, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_02.jpg", "length": 24115, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_03.jpg", "length": 24183, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_04.jpg", "length": 24581, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_05.jpg", "length": 24613, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_06.jpg", "length": 23988, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_07.jpg", "length": 24675, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_08.jpg", "length": 24940, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_09.jpg", "length": 24531, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_10.jpg", "length": 24879, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_11.jpg", "length": 24212, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_12.jpg", "length": 23830, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_13.jpg", "length": 24418, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_14.jpg", "length": 25023, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_15.jpg", "length": 24513, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_16.jpg", "length": 24429, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_17.jpg", "length": 24877, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_18.jpg", "length": 24430, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_19.jpg", "length": 24827, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_20.jpg", "length": 24517, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003L/files/pocket_01.pdb", "length": 61439, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003L/files/pocket_02.pdb", "length": 27269, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003L/files/pocket_03.pdb", "length": 8643, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003L/files/pocket_04.pdb", "length": 8375, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003L/files/pocket_05.pdb", "length": 3886, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003L/files/pocket_06.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}]}
3
+ {"project_identifier": "A003L", "accession": "A003L", "published": true, "md_index": 2, "md_name": "replica 3", "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 2PCB", "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": ["2PCB"], "FORCED_REFERENCES": null, "REFERENCES": ["P00431", "P00004"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHISGTWDKHDNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQGPKIPWRCGRVDTPEDTTPDNGRLPDADKDAGYVRTFFQRLNMNDREVVALMGAHALGKTHLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQDPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL", "GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE"], "NUCLSEQ": [], "DOMAINS": ["Cytochrome c peroxidase, mitochondrial", "Transition state stabilizer", "Cytochrome c"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6295, "SYSTRES": 398, "PROTATS": 6295, "PROTRES": 398, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 10.2184, "BOXSIZEY": 10.2184, "BOXSIZEZ": 7.22271, "mdName": "replica 1", "mdAtoms": 6295, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003L/files/topology.tpr", "length": 2016772, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003L/files/screenshot.jpg", "length": 25912, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003L/files/trajectory.bin", "length": 377775540, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 5001, "atoms": 6295}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_01.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_02.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_03.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_04.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_05.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_06.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_07.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_08.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_09.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_10.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003L/files/pca_trajectory_11.bin", "length": 286560, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0, "frames": 20, "atoms": 1194}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003L/files/structure.pdb", "length": 509930, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003L/files/trajectory.xtc", "length": 119867972, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_00.jpg", "length": 22855, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_01.jpg", "length": 23777, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_02.jpg", "length": 23499, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_03.jpg", "length": 22895, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_04.jpg", "length": 23001, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_05.jpg", "length": 23663, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_06.jpg", "length": 23201, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_07.jpg", "length": 23546, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_08.jpg", "length": 23352, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_09.jpg", "length": 24150, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_10.jpg", "length": 23839, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_11.jpg", "length": 23310, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_12.jpg", "length": 24036, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_13.jpg", "length": 23929, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_14.jpg", "length": 22733, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_15.jpg", "length": 24208, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_16.jpg", "length": 24110, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_17.jpg", "length": 23767, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_18.jpg", "length": 23799, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003L/files/clusters_00_screenshot_19.jpg", "length": 23219, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_00.jpg", "length": 24774, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_01.jpg", "length": 23975, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_02.jpg", "length": 24115, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_03.jpg", "length": 24183, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_04.jpg", "length": 24581, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_05.jpg", "length": 24613, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_06.jpg", "length": 23988, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_07.jpg", "length": 24675, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_08.jpg", "length": 24940, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_09.jpg", "length": 24531, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_10.jpg", "length": 24879, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_11.jpg", "length": 24212, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_12.jpg", "length": 23830, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_13.jpg", "length": 24418, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_14.jpg", "length": 25023, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_15.jpg", "length": 24513, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_16.jpg", "length": 24429, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_17.jpg", "length": 24877, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_18.jpg", "length": 24430, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_19.jpg", "length": 24827, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "clusters_01_screenshot_20.jpg", "downloadUrl": "/projects/A003L/files/clusters_01_screenshot_20.jpg", "length": 24517, "contentType": "application/octet-stream", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003L/files/pocket_01.pdb", "length": 61439, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003L/files/pocket_02.pdb", "length": 27269, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003L/files/pocket_03.pdb", "length": 8643, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003L/files/pocket_04.pdb", "length": 8375, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003L/files/pocket_05.pdb", "length": 3886, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003L/files/pocket_06.pdb", "length": 3685, "contentType": "chemical/x-pdb", "metadata": {"project": "68407531c16de68ddf4d4a74", "md": 0}}]}
A003M/project.json ADDED
@@ -0,0 +1,245 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A003M",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2PJY",
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
+ "2PJY"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P10600",
31
+ "P37173",
32
+ "P36897"
33
+ ],
34
+ "INPUT_LIGANDS": null,
35
+ "LIGANDS": [],
36
+ "LIGANDNAMES": null,
37
+ "PROTSEQ": [
38
+ "ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS",
39
+ "AGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIF",
40
+ "ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIEL"
41
+ ],
42
+ "NUCLSEQ": [],
43
+ "DOMAINS": [
44
+ "Transforming growth factor beta-3",
45
+ "TGF-beta receptor type-2",
46
+ "TGF-beta receptor type-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": 4573,
58
+ "SYSTRES": 299,
59
+ "PROTATS": 4573,
60
+ "PROTRES": 299,
61
+ "NUCLATS": 0,
62
+ "NUCLRES": 0,
63
+ "LIPIATS": 0,
64
+ "LIPIRES": 0,
65
+ "CARBATS": 0,
66
+ "CARBRES": 0,
67
+ "SOLVATS": 0,
68
+ "SOLVRES": 0,
69
+ "COUNCAT": 0,
70
+ "COUNANI": 0,
71
+ "COUNION": 0,
72
+ "INTERACTIONS": [
73
+ {
74
+ "name": "chain A-chain B interaction",
75
+ "agent_1": "chain A",
76
+ "agent_2": "chain B",
77
+ "selection_1": "chain A",
78
+ "selection_2": "chain B",
79
+ "type": "protein-protein"
80
+ },
81
+ {
82
+ "name": "chain A-chain C interaction",
83
+ "agent_1": "chain A",
84
+ "agent_2": "chain C",
85
+ "selection_1": "chain A",
86
+ "selection_2": "chain C",
87
+ "type": "protein-protein"
88
+ },
89
+ {
90
+ "name": "chain B-chain C interaction",
91
+ "agent_1": "chain B",
92
+ "agent_2": "chain C",
93
+ "selection_1": "chain B",
94
+ "selection_2": "chain C",
95
+ "type": "protein-protein"
96
+ }
97
+ ],
98
+ "PBC_SELECTION": null,
99
+ "CHAINNAMES": null,
100
+ "MEMBRANES": null,
101
+ "CUSTOMS": null,
102
+ "ORIENTATION": null,
103
+ "PTM": [],
104
+ "MULTIMERIC": null,
105
+ "COLLECTIONS": "dynarepo",
106
+ "WARNINGS": [],
107
+ "BOXSIZEX": 11.6362,
108
+ "BOXSIZEY": 11.6362,
109
+ "BOXSIZEZ": 8.22071,
110
+ "mdName": "replica 1",
111
+ "mdAtoms": 4573,
112
+ "mdFrames": 5001
113
+ },
114
+ "mds": [
115
+ "replica 1",
116
+ "replica 2",
117
+ "replica 3"
118
+ ],
119
+ "mdref": 0,
120
+ "files": [
121
+ "topology.tpr",
122
+ "screenshot.jpg",
123
+ "trajectory.bin",
124
+ "pca_trajectory_01.bin",
125
+ "pca_trajectory_02.bin",
126
+ "pca_trajectory_03.bin",
127
+ "pca_trajectory_04.bin",
128
+ "pca_trajectory_05.bin",
129
+ "pca_trajectory_06.bin",
130
+ "pca_trajectory_07.bin",
131
+ "pca_trajectory_08.bin",
132
+ "pca_trajectory_09.bin",
133
+ "pca_trajectory_10.bin",
134
+ "pca_trajectory_11.bin",
135
+ "pca_trajectory_12.bin",
136
+ "structure.pdb",
137
+ "trajectory.xtc",
138
+ "clusters_00_screenshot_00.jpg",
139
+ "clusters_00_screenshot_01.jpg",
140
+ "clusters_00_screenshot_02.jpg",
141
+ "clusters_00_screenshot_03.jpg",
142
+ "clusters_00_screenshot_04.jpg",
143
+ "clusters_00_screenshot_05.jpg",
144
+ "clusters_00_screenshot_06.jpg",
145
+ "clusters_00_screenshot_07.jpg",
146
+ "clusters_00_screenshot_08.jpg",
147
+ "clusters_00_screenshot_09.jpg",
148
+ "clusters_00_screenshot_10.jpg",
149
+ "clusters_00_screenshot_11.jpg",
150
+ "clusters_00_screenshot_12.jpg",
151
+ "clusters_00_screenshot_13.jpg",
152
+ "clusters_00_screenshot_14.jpg",
153
+ "clusters_00_screenshot_15.jpg",
154
+ "clusters_00_screenshot_16.jpg",
155
+ "clusters_00_screenshot_17.jpg",
156
+ "clusters_00_screenshot_18.jpg",
157
+ "clusters_00_screenshot_19.jpg",
158
+ "clusters_01_screenshot_00.jpg",
159
+ "clusters_01_screenshot_01.jpg",
160
+ "clusters_01_screenshot_02.jpg",
161
+ "clusters_01_screenshot_03.jpg",
162
+ "clusters_01_screenshot_04.jpg",
163
+ "clusters_01_screenshot_05.jpg",
164
+ "clusters_01_screenshot_06.jpg",
165
+ "clusters_01_screenshot_07.jpg",
166
+ "clusters_01_screenshot_08.jpg",
167
+ "clusters_01_screenshot_09.jpg",
168
+ "clusters_01_screenshot_10.jpg",
169
+ "clusters_01_screenshot_11.jpg",
170
+ "clusters_01_screenshot_12.jpg",
171
+ "clusters_01_screenshot_13.jpg",
172
+ "clusters_01_screenshot_14.jpg",
173
+ "clusters_01_screenshot_15.jpg",
174
+ "clusters_02_screenshot_00.jpg",
175
+ "clusters_02_screenshot_01.jpg",
176
+ "clusters_02_screenshot_02.jpg",
177
+ "clusters_02_screenshot_03.jpg",
178
+ "clusters_02_screenshot_04.jpg",
179
+ "clusters_02_screenshot_05.jpg",
180
+ "clusters_02_screenshot_06.jpg",
181
+ "clusters_02_screenshot_07.jpg",
182
+ "clusters_02_screenshot_08.jpg",
183
+ "clusters_02_screenshot_09.jpg",
184
+ "clusters_02_screenshot_10.jpg",
185
+ "clusters_02_screenshot_11.jpg",
186
+ "clusters_02_screenshot_12.jpg",
187
+ "clusters_02_screenshot_13.jpg",
188
+ "clusters_02_screenshot_14.jpg",
189
+ "clusters_02_screenshot_15.jpg",
190
+ "clusters_02_screenshot_16.jpg",
191
+ "clusters_02_screenshot_17.jpg",
192
+ "clusters_02_screenshot_18.jpg",
193
+ "clusters_02_screenshot_19.jpg",
194
+ "clusters_03_screenshot_00.jpg",
195
+ "clusters_03_screenshot_01.jpg",
196
+ "clusters_03_screenshot_02.jpg",
197
+ "clusters_03_screenshot_03.jpg",
198
+ "clusters_03_screenshot_04.jpg",
199
+ "clusters_03_screenshot_05.jpg",
200
+ "clusters_03_screenshot_06.jpg",
201
+ "clusters_03_screenshot_07.jpg",
202
+ "clusters_03_screenshot_08.jpg",
203
+ "clusters_03_screenshot_09.jpg",
204
+ "clusters_03_screenshot_10.jpg",
205
+ "clusters_03_screenshot_11.jpg",
206
+ "clusters_03_screenshot_12.jpg",
207
+ "clusters_03_screenshot_13.jpg",
208
+ "clusters_03_screenshot_14.jpg",
209
+ "clusters_03_screenshot_15.jpg",
210
+ "clusters_03_screenshot_16.jpg",
211
+ "clusters_03_screenshot_17.jpg",
212
+ "clusters_03_screenshot_18.jpg",
213
+ "clusters_03_screenshot_19.jpg",
214
+ "clusters_03_screenshot_20.jpg",
215
+ "pocket_01.pdb",
216
+ "pocket_02.pdb",
217
+ "pocket_03.pdb"
218
+ ],
219
+ "analyses": [
220
+ "clusters",
221
+ "clusters-00",
222
+ "clusters-01",
223
+ "clusters-02",
224
+ "clusters-03",
225
+ "dist-perres",
226
+ "energies",
227
+ "fluctuation",
228
+ "hbonds",
229
+ "interactions",
230
+ "pca",
231
+ "pockets",
232
+ "rgyr",
233
+ "rmsd-pairwise",
234
+ "rmsd-perres",
235
+ "rmsds",
236
+ "sasa",
237
+ "tmscores"
238
+ ],
239
+ "mdIndex": 0,
240
+ "mdNumber": 1,
241
+ "refframe": 0,
242
+ "internalId": "684077693a7982f1ea8aa72e",
243
+ "creationDate": "2025-06-04T16:42:17.000Z",
244
+ "identifier": "A003M"
245
+ }
A003M/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A003M", "accession": "A003M", "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 2PJY", "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": ["2PJY"], "FORCED_REFERENCES": null, "REFERENCES": ["P10600", "P37173", "P36897"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS", "AGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIF", "ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIEL"], "NUCLSEQ": [], "DOMAINS": ["Transforming growth factor beta-3", "TGF-beta receptor type-2", "TGF-beta receptor type-1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4573, "SYSTRES": 299, "PROTATS": 4573, "PROTRES": 299, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.6362, "BOXSIZEY": 11.6362, "BOXSIZEZ": 8.22071, "mdName": "replica 1", "mdAtoms": 4573, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003M/files/topology.tpr", "length": 1666480, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003M/files/screenshot.jpg", "length": 19636, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003M/files/trajectory.bin", "length": 274434876, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 5001, "atoms": 4573}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_01.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_02.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_03.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_04.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_05.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_06.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_07.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_08.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_09.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_10.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_11.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_12.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003M/files/structure.pdb", "length": 370448, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003M/files/trajectory.xtc", "length": 87287692, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_00.jpg", "length": 18033, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_01.jpg", "length": 18008, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_02.jpg", "length": 18724, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_03.jpg", "length": 18152, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_04.jpg", "length": 17669, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_05.jpg", "length": 19381, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_06.jpg", "length": 19907, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_07.jpg", "length": 18791, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_08.jpg", "length": 18917, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_09.jpg", "length": 18513, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_10.jpg", "length": 18986, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_11.jpg", "length": 18570, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_12.jpg", "length": 18546, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_13.jpg", "length": 18540, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_14.jpg", "length": 18287, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_15.jpg", "length": 17857, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_16.jpg", "length": 17543, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_17.jpg", "length": 17724, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_18.jpg", "length": 17834, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_19.jpg", "length": 18694, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_00.jpg", "length": 17759, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_01.jpg", "length": 18103, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_02.jpg", "length": 18407, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_03.jpg", "length": 18095, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_04.jpg", "length": 18451, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_05.jpg", "length": 18170, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_06.jpg", "length": 18583, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_07.jpg", "length": 18002, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_08.jpg", "length": 17946, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_09.jpg", "length": 17743, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_10.jpg", "length": 17988, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_11.jpg", "length": 17381, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_12.jpg", "length": 17918, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_13.jpg", "length": 17821, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_14.jpg", "length": 18177, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_15.jpg", "length": 18430, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_00.jpg", "length": 17998, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_01.jpg", "length": 18558, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_02.jpg", "length": 18285, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_03.jpg", "length": 19037, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_04.jpg", "length": 18955, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_05.jpg", "length": 18681, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_06.jpg", "length": 18056, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_07.jpg", "length": 18318, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_08.jpg", "length": 18651, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_09.jpg", "length": 17743, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_10.jpg", "length": 19164, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_11.jpg", "length": 19253, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_12.jpg", "length": 18916, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_13.jpg", "length": 18996, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_14.jpg", "length": 19303, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_15.jpg", "length": 18240, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_16.jpg", "length": 17872, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_17.jpg", "length": 17995, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_18.jpg", "length": 17749, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_19.jpg", "length": 18744, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_00.jpg", "length": 18884, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_01.jpg", "length": 19478, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_02.jpg", "length": 19555, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_03.jpg", "length": 20238, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_04.jpg", "length": 20882, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_05.jpg", "length": 20018, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_06.jpg", "length": 19733, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_07.jpg", "length": 20247, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_08.jpg", "length": 19376, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_09.jpg", "length": 19298, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_10.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_11.jpg", "length": 20191, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_12.jpg", "length": 20014, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_13.jpg", "length": 19461, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_14.jpg", "length": 18826, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_15.jpg", "length": 19644, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_16.jpg", "length": 20182, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_17.jpg", "length": 19874, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_18.jpg", "length": 19675, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_19.jpg", "length": 20361, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_20.jpg", "length": 19383, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003M/files/pocket_01.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003M/files/pocket_02.pdb", "length": 5829, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003M/files/pocket_03.pdb", "length": 4154, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}]}
2
+ {"project_identifier": "A003M", "accession": "A003M", "published": true, "md_index": 1, "md_name": "replica 2", "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 2PJY", "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": ["2PJY"], "FORCED_REFERENCES": null, "REFERENCES": ["P10600", "P37173", "P36897"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS", "AGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIF", "ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIEL"], "NUCLSEQ": [], "DOMAINS": ["Transforming growth factor beta-3", "TGF-beta receptor type-2", "TGF-beta receptor type-1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4573, "SYSTRES": 299, "PROTATS": 4573, "PROTRES": 299, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.6362, "BOXSIZEY": 11.6362, "BOXSIZEZ": 8.22071, "mdName": "replica 1", "mdAtoms": 4573, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003M/files/topology.tpr", "length": 1666480, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003M/files/screenshot.jpg", "length": 19636, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003M/files/trajectory.bin", "length": 274434876, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 5001, "atoms": 4573}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_01.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_02.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_03.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_04.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_05.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_06.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_07.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_08.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_09.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_10.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_11.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_12.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003M/files/structure.pdb", "length": 370448, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003M/files/trajectory.xtc", "length": 87287692, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_00.jpg", "length": 18033, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_01.jpg", "length": 18008, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_02.jpg", "length": 18724, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_03.jpg", "length": 18152, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_04.jpg", "length": 17669, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_05.jpg", "length": 19381, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_06.jpg", "length": 19907, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_07.jpg", "length": 18791, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_08.jpg", "length": 18917, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_09.jpg", "length": 18513, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_10.jpg", "length": 18986, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_11.jpg", "length": 18570, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_12.jpg", "length": 18546, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_13.jpg", "length": 18540, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_14.jpg", "length": 18287, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_15.jpg", "length": 17857, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_16.jpg", "length": 17543, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_17.jpg", "length": 17724, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_18.jpg", "length": 17834, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_19.jpg", "length": 18694, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_00.jpg", "length": 17759, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_01.jpg", "length": 18103, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_02.jpg", "length": 18407, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_03.jpg", "length": 18095, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_04.jpg", "length": 18451, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_05.jpg", "length": 18170, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_06.jpg", "length": 18583, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_07.jpg", "length": 18002, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_08.jpg", "length": 17946, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_09.jpg", "length": 17743, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_10.jpg", "length": 17988, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_11.jpg", "length": 17381, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_12.jpg", "length": 17918, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_13.jpg", "length": 17821, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_14.jpg", "length": 18177, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_15.jpg", "length": 18430, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_00.jpg", "length": 17998, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_01.jpg", "length": 18558, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_02.jpg", "length": 18285, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_03.jpg", "length": 19037, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_04.jpg", "length": 18955, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_05.jpg", "length": 18681, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_06.jpg", "length": 18056, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_07.jpg", "length": 18318, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_08.jpg", "length": 18651, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_09.jpg", "length": 17743, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_10.jpg", "length": 19164, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_11.jpg", "length": 19253, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_12.jpg", "length": 18916, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_13.jpg", "length": 18996, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_14.jpg", "length": 19303, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_15.jpg", "length": 18240, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_16.jpg", "length": 17872, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_17.jpg", "length": 17995, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_18.jpg", "length": 17749, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_19.jpg", "length": 18744, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_00.jpg", "length": 18884, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_01.jpg", "length": 19478, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_02.jpg", "length": 19555, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_03.jpg", "length": 20238, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_04.jpg", "length": 20882, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_05.jpg", "length": 20018, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_06.jpg", "length": 19733, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_07.jpg", "length": 20247, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_08.jpg", "length": 19376, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_09.jpg", "length": 19298, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_10.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_11.jpg", "length": 20191, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_12.jpg", "length": 20014, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_13.jpg", "length": 19461, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_14.jpg", "length": 18826, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_15.jpg", "length": 19644, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_16.jpg", "length": 20182, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_17.jpg", "length": 19874, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_18.jpg", "length": 19675, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_19.jpg", "length": 20361, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_20.jpg", "length": 19383, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003M/files/pocket_01.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003M/files/pocket_02.pdb", "length": 5829, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003M/files/pocket_03.pdb", "length": 4154, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}]}
3
+ {"project_identifier": "A003M", "accession": "A003M", "published": true, "md_index": 2, "md_name": "replica 3", "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 2PJY", "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": ["2PJY"], "FORCED_REFERENCES": null, "REFERENCES": ["P10600", "P37173", "P36897"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["ALDTNYCFRNLEENCCVRPLYIDFRQDLGWKWVHEPKGYYANFCSGPCPYLRSADTTHSTVLGLYNTLNPEASASPCCVPQDLEPLTILYYVGRTPKVEQLSNMVVKSCKCS", "AGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIF", "ALQCFCHLCTKDNFTCVTDGLCFVSVTETTDKVIHNSSCIAEIDLIPRDRPFVCAPSSKTGSVTTTYCCNQDHCNKIEL"], "NUCLSEQ": [], "DOMAINS": ["Transforming growth factor beta-3", "TGF-beta receptor type-2", "TGF-beta receptor type-1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4573, "SYSTRES": 299, "PROTATS": 4573, "PROTRES": 299, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}, {"name": "chain A-chain C interaction", "agent_1": "chain A", "agent_2": "chain C", "selection_1": "chain A", "selection_2": "chain C", "type": "protein-protein"}, {"name": "chain B-chain C interaction", "agent_1": "chain B", "agent_2": "chain C", "selection_1": "chain B", "selection_2": "chain C", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.6362, "BOXSIZEY": 11.6362, "BOXSIZEZ": 8.22071, "mdName": "replica 1", "mdAtoms": 4573, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003M/files/topology.tpr", "length": 1666480, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003M/files/screenshot.jpg", "length": 19636, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003M/files/trajectory.bin", "length": 274434876, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 5001, "atoms": 4573}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_01.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_02.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_03.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_04.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_05.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_06.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_07.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_08.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_09.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_10.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_11.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003M/files/pca_trajectory_12.bin", "length": 215280, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0, "frames": 20, "atoms": 897}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003M/files/structure.pdb", "length": 370448, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003M/files/trajectory.xtc", "length": 87287692, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_00.jpg", "length": 18033, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_01.jpg", "length": 18008, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_02.jpg", "length": 18724, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_03.jpg", "length": 18152, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_04.jpg", "length": 17669, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_05.jpg", "length": 19381, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_06.jpg", "length": 19907, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_07.jpg", "length": 18791, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_08.jpg", "length": 18917, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_09.jpg", "length": 18513, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_10.jpg", "length": 18986, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_11.jpg", "length": 18570, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_12.jpg", "length": 18546, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_13.jpg", "length": 18540, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_14.jpg", "length": 18287, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_15.jpg", "length": 17857, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_16.jpg", "length": 17543, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_17.jpg", "length": 17724, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_18.jpg", "length": 17834, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_00_screenshot_19.jpg", "length": 18694, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_00.jpg", "length": 17759, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_01.jpg", "length": 18103, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_02.jpg", "length": 18407, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_03.jpg", "length": 18095, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_04.jpg", "length": 18451, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_05.jpg", "length": 18170, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_06.jpg", "length": 18583, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_07.jpg", "length": 18002, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_08.jpg", "length": 17946, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_09.jpg", "length": 17743, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_10.jpg", "length": 17988, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_11.jpg", "length": 17381, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_12.jpg", "length": 17918, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_13.jpg", "length": 17821, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_14.jpg", "length": 18177, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_01_screenshot_15.jpg", "length": 18430, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_00.jpg", "length": 17998, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_01.jpg", "length": 18558, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_02.jpg", "length": 18285, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_03.jpg", "length": 19037, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_04.jpg", "length": 18955, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_05.jpg", "length": 18681, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_06.jpg", "length": 18056, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_07.jpg", "length": 18318, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_08.jpg", "length": 18651, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_09.jpg", "length": 17743, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_10.jpg", "length": 19164, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_11.jpg", "length": 19253, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_12.jpg", "length": 18916, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_13.jpg", "length": 18996, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_14.jpg", "length": 19303, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_15.jpg", "length": 18240, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_16.jpg", "length": 17872, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_17.jpg", "length": 17995, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_18.jpg", "length": 17749, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_02_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_02_screenshot_19.jpg", "length": 18744, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_00.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_00.jpg", "length": 18884, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_01.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_01.jpg", "length": 19478, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_02.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_02.jpg", "length": 19555, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_03.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_03.jpg", "length": 20238, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_04.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_04.jpg", "length": 20882, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_05.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_05.jpg", "length": 20018, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_06.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_06.jpg", "length": 19733, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_07.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_07.jpg", "length": 20247, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_08.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_08.jpg", "length": 19376, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_09.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_09.jpg", "length": 19298, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_10.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_10.jpg", "length": 19811, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_11.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_11.jpg", "length": 20191, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_12.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_12.jpg", "length": 20014, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_13.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_13.jpg", "length": 19461, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_14.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_14.jpg", "length": 18826, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_15.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_15.jpg", "length": 19644, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_16.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_16.jpg", "length": 20182, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_17.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_17.jpg", "length": 19874, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_18.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_18.jpg", "length": 19675, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_19.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_19.jpg", "length": 20361, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "clusters_03_screenshot_20.jpg", "downloadUrl": "/projects/A003M/files/clusters_03_screenshot_20.jpg", "length": 19383, "contentType": "application/octet-stream", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003M/files/pocket_01.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003M/files/pocket_02.pdb", "length": 5829, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003M/files/pocket_03.pdb", "length": 4154, "contentType": "chemical/x-pdb", "metadata": {"project": "684077693a7982f1ea8aa72e", "md": 0}}]}
A003O/project.json ADDED
@@ -0,0 +1,196 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A003O",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2PTT",
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
+ "2PTT"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P18181",
31
+ "Q07763"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "DCPDSSEEVVGVSGKPVQLRPSNIQTKDVSVQWKKTEQGSHRKIEILNWYNDGPSWSNVSFSDIYGFDYGDFALSIKSAKLQDSGHYLLEITNTGGKVCNKNFQLLIL",
38
+ "GSIPDINAYTGSNVTLKIHKDPLGPYRRITWLHTKNQKILEYNYNSTKTIFESEFKGRVYLEENNGALHISNVRKEDKGTYYMRVLRETENELKITLEVFDPV"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "CD48 antigen",
43
+ "Ig-like C2-type 1",
44
+ "Natural killer cell receptor 2B4",
45
+ "Ig-like 1"
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": 3383,
57
+ "SYSTRES": 211,
58
+ "PROTATS": 3383,
59
+ "PROTRES": 211,
60
+ "NUCLATS": 0,
61
+ "NUCLRES": 0,
62
+ "LIPIATS": 0,
63
+ "LIPIRES": 0,
64
+ "CARBATS": 0,
65
+ "CARBRES": 0,
66
+ "SOLVATS": 0,
67
+ "SOLVRES": 0,
68
+ "COUNCAT": 0,
69
+ "COUNANI": 0,
70
+ "COUNION": 0,
71
+ "INTERACTIONS": [
72
+ {
73
+ "name": "chain A-chain B interaction",
74
+ "agent_1": "chain A",
75
+ "agent_2": "chain B",
76
+ "selection_1": "chain A",
77
+ "selection_2": "chain B",
78
+ "type": "protein-protein"
79
+ }
80
+ ],
81
+ "PBC_SELECTION": null,
82
+ "CHAINNAMES": null,
83
+ "MEMBRANES": null,
84
+ "CUSTOMS": null,
85
+ "ORIENTATION": null,
86
+ "PTM": [],
87
+ "MULTIMERIC": null,
88
+ "COLLECTIONS": "dynarepo",
89
+ "WARNINGS": [],
90
+ "BOXSIZEX": 9.60575,
91
+ "BOXSIZEY": 9.60575,
92
+ "BOXSIZEZ": 6.82951,
93
+ "mdName": "replica 1",
94
+ "mdAtoms": 3383,
95
+ "mdFrames": 5001
96
+ },
97
+ "mds": [
98
+ "replica 1",
99
+ "replica 2",
100
+ "replica 3"
101
+ ],
102
+ "mdref": 0,
103
+ "files": [
104
+ "topology.tpr",
105
+ "screenshot.jpg",
106
+ "trajectory.bin",
107
+ "pca_trajectory_01.bin",
108
+ "pca_trajectory_02.bin",
109
+ "pca_trajectory_03.bin",
110
+ "pca_trajectory_04.bin",
111
+ "pca_trajectory_05.bin",
112
+ "pca_trajectory_06.bin",
113
+ "pca_trajectory_07.bin",
114
+ "pca_trajectory_08.bin",
115
+ "pca_trajectory_09.bin",
116
+ "pca_trajectory_10.bin",
117
+ "pca_trajectory_11.bin",
118
+ "pca_trajectory_12.bin",
119
+ "pca_trajectory_13.bin",
120
+ "pca_trajectory_14.bin",
121
+ "pca_trajectory_15.bin",
122
+ "pca_trajectory_16.bin",
123
+ "pca_trajectory_17.bin",
124
+ "pca_trajectory_18.bin",
125
+ "structure.pdb",
126
+ "trajectory.xtc",
127
+ "clusters_00_screenshot_00.jpg",
128
+ "clusters_00_screenshot_01.jpg",
129
+ "clusters_00_screenshot_02.jpg",
130
+ "clusters_00_screenshot_03.jpg",
131
+ "clusters_00_screenshot_04.jpg",
132
+ "clusters_00_screenshot_05.jpg",
133
+ "clusters_00_screenshot_06.jpg",
134
+ "clusters_00_screenshot_07.jpg",
135
+ "clusters_00_screenshot_08.jpg",
136
+ "clusters_00_screenshot_09.jpg",
137
+ "clusters_00_screenshot_10.jpg",
138
+ "clusters_00_screenshot_11.jpg",
139
+ "clusters_00_screenshot_12.jpg",
140
+ "clusters_00_screenshot_13.jpg",
141
+ "clusters_00_screenshot_14.jpg",
142
+ "clusters_00_screenshot_15.jpg",
143
+ "clusters_00_screenshot_16.jpg",
144
+ "clusters_00_screenshot_17.jpg",
145
+ "clusters_01_screenshot_00.jpg",
146
+ "clusters_01_screenshot_01.jpg",
147
+ "clusters_01_screenshot_02.jpg",
148
+ "clusters_01_screenshot_03.jpg",
149
+ "clusters_01_screenshot_04.jpg",
150
+ "clusters_01_screenshot_05.jpg",
151
+ "clusters_01_screenshot_06.jpg",
152
+ "clusters_01_screenshot_07.jpg",
153
+ "clusters_01_screenshot_08.jpg",
154
+ "clusters_01_screenshot_09.jpg",
155
+ "clusters_01_screenshot_10.jpg",
156
+ "clusters_01_screenshot_11.jpg",
157
+ "clusters_01_screenshot_12.jpg",
158
+ "clusters_01_screenshot_13.jpg",
159
+ "clusters_01_screenshot_14.jpg",
160
+ "clusters_01_screenshot_15.jpg",
161
+ "clusters_01_screenshot_16.jpg",
162
+ "clusters_01_screenshot_17.jpg",
163
+ "clusters_01_screenshot_18.jpg",
164
+ "pocket_01.pdb",
165
+ "pocket_02.pdb",
166
+ "pocket_03.pdb",
167
+ "pocket_04.pdb",
168
+ "pocket_05.pdb",
169
+ "pocket_06.pdb",
170
+ "pocket_07.pdb"
171
+ ],
172
+ "analyses": [
173
+ "clusters",
174
+ "clusters-00",
175
+ "clusters-01",
176
+ "dist-perres",
177
+ "energies",
178
+ "fluctuation",
179
+ "hbonds",
180
+ "interactions",
181
+ "pca",
182
+ "pockets",
183
+ "rgyr",
184
+ "rmsd-pairwise",
185
+ "rmsd-perres",
186
+ "rmsds",
187
+ "sasa",
188
+ "tmscores"
189
+ ],
190
+ "mdIndex": 0,
191
+ "mdNumber": 1,
192
+ "refframe": 0,
193
+ "internalId": "68407a6eb314550fea852822",
194
+ "creationDate": "2025-06-04T16:55:10.000Z",
195
+ "identifier": "A003O"
196
+ }
A003O/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A003O", "accession": "A003O", "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 2PTT", "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": ["2PTT"], "FORCED_REFERENCES": null, "REFERENCES": ["P18181", "Q07763"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DCPDSSEEVVGVSGKPVQLRPSNIQTKDVSVQWKKTEQGSHRKIEILNWYNDGPSWSNVSFSDIYGFDYGDFALSIKSAKLQDSGHYLLEITNTGGKVCNKNFQLLIL", "GSIPDINAYTGSNVTLKIHKDPLGPYRRITWLHTKNQKILEYNYNSTKTIFESEFKGRVYLEENNGALHISNVRKEDKGTYYMRVLRETENELKITLEVFDPV"], "NUCLSEQ": [], "DOMAINS": ["CD48 antigen", "Ig-like C2-type 1", "Natural killer cell receptor 2B4", "Ig-like 1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3383, "SYSTRES": 211, "PROTATS": 3383, "PROTRES": 211, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.60575, "BOXSIZEY": 9.60575, "BOXSIZEZ": 6.82951, "mdName": "replica 1", "mdAtoms": 3383, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003O/files/topology.tpr", "length": 1250564, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003O/files/screenshot.jpg", "length": 19095, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003O/files/trajectory.bin", "length": 203020596, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 5001, "atoms": 3383}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_01.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_02.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_03.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_04.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_05.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_06.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_07.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_08.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_09.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_10.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_11.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_12.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_13.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_14.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_15.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_16.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_17.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_18.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003O/files/structure.pdb", "length": 274058, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003O/files/trajectory.xtc", "length": 64301336, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_00.jpg", "length": 19796, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_01.jpg", "length": 18557, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_02.jpg", "length": 19372, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_03.jpg", "length": 18928, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_04.jpg", "length": 18771, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_05.jpg", "length": 19622, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_06.jpg", "length": 19203, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_07.jpg", "length": 19509, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_08.jpg", "length": 18565, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_09.jpg", "length": 19195, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_10.jpg", "length": 19108, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_11.jpg", "length": 18702, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_12.jpg", "length": 18964, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_13.jpg", "length": 19655, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_14.jpg", "length": 18533, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_15.jpg", "length": 19120, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_16.jpg", "length": 19391, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_17.jpg", "length": 18900, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_00.jpg", "length": 19570, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_01.jpg", "length": 19456, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_02.jpg", "length": 19536, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_03.jpg", "length": 19342, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_04.jpg", "length": 19587, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_05.jpg", "length": 18811, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_06.jpg", "length": 19078, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_07.jpg", "length": 19074, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_08.jpg", "length": 19983, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_09.jpg", "length": 19517, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_10.jpg", "length": 19785, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_11.jpg", "length": 18983, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_12.jpg", "length": 19821, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_13.jpg", "length": 19220, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_14.jpg", "length": 19226, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_15.jpg", "length": 19134, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_16.jpg", "length": 18721, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_17.jpg", "length": 19356, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_18.jpg", "length": 19091, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003O/files/pocket_01.pdb", "length": 16013, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003O/files/pocket_02.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003O/files/pocket_03.pdb", "length": 11524, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003O/files/pocket_04.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003O/files/pocket_05.pdb", "length": 7169, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003O/files/pocket_06.pdb", "length": 3417, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003O/files/pocket_07.pdb", "length": 3216, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}]}
2
+ {"project_identifier": "A003O", "accession": "A003O", "published": true, "md_index": 1, "md_name": "replica 2", "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 2PTT", "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": ["2PTT"], "FORCED_REFERENCES": null, "REFERENCES": ["P18181", "Q07763"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DCPDSSEEVVGVSGKPVQLRPSNIQTKDVSVQWKKTEQGSHRKIEILNWYNDGPSWSNVSFSDIYGFDYGDFALSIKSAKLQDSGHYLLEITNTGGKVCNKNFQLLIL", "GSIPDINAYTGSNVTLKIHKDPLGPYRRITWLHTKNQKILEYNYNSTKTIFESEFKGRVYLEENNGALHISNVRKEDKGTYYMRVLRETENELKITLEVFDPV"], "NUCLSEQ": [], "DOMAINS": ["CD48 antigen", "Ig-like C2-type 1", "Natural killer cell receptor 2B4", "Ig-like 1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3383, "SYSTRES": 211, "PROTATS": 3383, "PROTRES": 211, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.60575, "BOXSIZEY": 9.60575, "BOXSIZEZ": 6.82951, "mdName": "replica 1", "mdAtoms": 3383, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003O/files/topology.tpr", "length": 1250564, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003O/files/screenshot.jpg", "length": 19095, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003O/files/trajectory.bin", "length": 203020596, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 5001, "atoms": 3383}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_01.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_02.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_03.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_04.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_05.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_06.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_07.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_08.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_09.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_10.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_11.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_12.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_13.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_14.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_15.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_16.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_17.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_18.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003O/files/structure.pdb", "length": 274058, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003O/files/trajectory.xtc", "length": 64301336, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_00.jpg", "length": 19796, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_01.jpg", "length": 18557, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_02.jpg", "length": 19372, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_03.jpg", "length": 18928, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_04.jpg", "length": 18771, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_05.jpg", "length": 19622, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_06.jpg", "length": 19203, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_07.jpg", "length": 19509, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_08.jpg", "length": 18565, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_09.jpg", "length": 19195, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_10.jpg", "length": 19108, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_11.jpg", "length": 18702, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_12.jpg", "length": 18964, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_13.jpg", "length": 19655, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_14.jpg", "length": 18533, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_15.jpg", "length": 19120, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_16.jpg", "length": 19391, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_17.jpg", "length": 18900, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_00.jpg", "length": 19570, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_01.jpg", "length": 19456, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_02.jpg", "length": 19536, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_03.jpg", "length": 19342, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_04.jpg", "length": 19587, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_05.jpg", "length": 18811, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_06.jpg", "length": 19078, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_07.jpg", "length": 19074, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_08.jpg", "length": 19983, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_09.jpg", "length": 19517, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_10.jpg", "length": 19785, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_11.jpg", "length": 18983, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_12.jpg", "length": 19821, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_13.jpg", "length": 19220, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_14.jpg", "length": 19226, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_15.jpg", "length": 19134, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_16.jpg", "length": 18721, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_17.jpg", "length": 19356, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_18.jpg", "length": 19091, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003O/files/pocket_01.pdb", "length": 16013, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003O/files/pocket_02.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003O/files/pocket_03.pdb", "length": 11524, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003O/files/pocket_04.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003O/files/pocket_05.pdb", "length": 7169, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003O/files/pocket_06.pdb", "length": 3417, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003O/files/pocket_07.pdb", "length": 3216, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}]}
3
+ {"project_identifier": "A003O", "accession": "A003O", "published": true, "md_index": 2, "md_name": "replica 3", "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 2PTT", "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": ["2PTT"], "FORCED_REFERENCES": null, "REFERENCES": ["P18181", "Q07763"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DCPDSSEEVVGVSGKPVQLRPSNIQTKDVSVQWKKTEQGSHRKIEILNWYNDGPSWSNVSFSDIYGFDYGDFALSIKSAKLQDSGHYLLEITNTGGKVCNKNFQLLIL", "GSIPDINAYTGSNVTLKIHKDPLGPYRRITWLHTKNQKILEYNYNSTKTIFESEFKGRVYLEENNGALHISNVRKEDKGTYYMRVLRETENELKITLEVFDPV"], "NUCLSEQ": [], "DOMAINS": ["CD48 antigen", "Ig-like C2-type 1", "Natural killer cell receptor 2B4", "Ig-like 1"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3383, "SYSTRES": 211, "PROTATS": 3383, "PROTRES": 211, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.60575, "BOXSIZEY": 9.60575, "BOXSIZEZ": 6.82951, "mdName": "replica 1", "mdAtoms": 3383, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003O/files/topology.tpr", "length": 1250564, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003O/files/screenshot.jpg", "length": 19095, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003O/files/trajectory.bin", "length": 203020596, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 5001, "atoms": 3383}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_01.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_02.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_03.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_04.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_05.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_06.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_07.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_08.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_09.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_10.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_11.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_12.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_13.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_14.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_15.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_16.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_17.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A003O/files/pca_trajectory_18.bin", "length": 151920, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0, "frames": 20, "atoms": 633}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003O/files/structure.pdb", "length": 274058, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003O/files/trajectory.xtc", "length": 64301336, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_00.jpg", "length": 19796, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_01.jpg", "length": 18557, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_02.jpg", "length": 19372, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_03.jpg", "length": 18928, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_04.jpg", "length": 18771, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_05.jpg", "length": 19622, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_06.jpg", "length": 19203, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_07.jpg", "length": 19509, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_08.jpg", "length": 18565, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_09.jpg", "length": 19195, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_10.jpg", "length": 19108, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_11.jpg", "length": 18702, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_12.jpg", "length": 18964, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_13.jpg", "length": 19655, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_14.jpg", "length": 18533, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_15.jpg", "length": 19120, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_16.jpg", "length": 19391, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003O/files/clusters_00_screenshot_17.jpg", "length": 18900, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_00.jpg", "length": 19570, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_01.jpg", "length": 19456, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_02.jpg", "length": 19536, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_03.jpg", "length": 19342, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_04.jpg", "length": 19587, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_05.jpg", "length": 18811, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_06.jpg", "length": 19078, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_07.jpg", "length": 19074, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_08.jpg", "length": 19983, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_09.jpg", "length": 19517, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_10.jpg", "length": 19785, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_11.jpg", "length": 18983, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_12.jpg", "length": 19821, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_13.jpg", "length": 19220, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_14.jpg", "length": 19226, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_15.jpg", "length": 19134, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_16.jpg", "length": 18721, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_17.jpg", "length": 19356, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003O/files/clusters_01_screenshot_18.jpg", "length": 19091, "contentType": "application/octet-stream", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003O/files/pocket_01.pdb", "length": 16013, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003O/files/pocket_02.pdb", "length": 12663, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003O/files/pocket_03.pdb", "length": 11524, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003O/files/pocket_04.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003O/files/pocket_05.pdb", "length": 7169, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003O/files/pocket_06.pdb", "length": 3417, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003O/files/pocket_07.pdb", "length": 3216, "contentType": "chemical/x-pdb", "metadata": {"project": "68407a6eb314550fea852822", "md": 0}}]}
A003S/project.json ADDED
@@ -0,0 +1,202 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A003S",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2QXV",
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
+ "2QXV"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "Q921E6",
31
+ "Q61188"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "TMFSSNRQKILERTETLNQEWKQRRIQPV",
38
+ "FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Polycomb protein EED",
43
+ "Interaction with EZH2",
44
+ "Histone-lysine N-methyltransferase EZH2",
45
+ "Interaction with DNMT1, DNMT3A and DNMT3B",
46
+ "Interaction with EED"
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": 6132,
58
+ "SYSTRES": 381,
59
+ "PROTATS": 6132,
60
+ "PROTRES": 381,
61
+ "NUCLATS": 0,
62
+ "NUCLRES": 0,
63
+ "LIPIATS": 0,
64
+ "LIPIRES": 0,
65
+ "CARBATS": 0,
66
+ "CARBRES": 0,
67
+ "SOLVATS": 0,
68
+ "SOLVRES": 0,
69
+ "COUNCAT": 0,
70
+ "COUNANI": 0,
71
+ "COUNION": 0,
72
+ "INTERACTIONS": [
73
+ {
74
+ "name": "chain A-chain B interaction",
75
+ "agent_1": "chain A",
76
+ "agent_2": "chain B",
77
+ "selection_1": "chain A",
78
+ "selection_2": "chain B",
79
+ "type": "protein-protein"
80
+ }
81
+ ],
82
+ "PBC_SELECTION": null,
83
+ "CHAINNAMES": null,
84
+ "MEMBRANES": null,
85
+ "CUSTOMS": null,
86
+ "ORIENTATION": null,
87
+ "PTM": [],
88
+ "MULTIMERIC": null,
89
+ "COLLECTIONS": "dynarepo",
90
+ "WARNINGS": [],
91
+ "BOXSIZEX": 8.49332,
92
+ "BOXSIZEY": 8.49332,
93
+ "BOXSIZEZ": 6.0081,
94
+ "mdName": "replica 1",
95
+ "mdAtoms": 6132,
96
+ "mdFrames": 5001
97
+ },
98
+ "mds": [
99
+ "replica 1",
100
+ "replica 2",
101
+ "replica 3"
102
+ ],
103
+ "mdref": 0,
104
+ "files": [
105
+ "topology.tpr",
106
+ "screenshot.jpg",
107
+ "trajectory.bin",
108
+ "pca_trajectory_01.bin",
109
+ "pca_trajectory_02.bin",
110
+ "pca_trajectory_03.bin",
111
+ "pca_trajectory_04.bin",
112
+ "pca_trajectory_05.bin",
113
+ "pca_trajectory_06.bin",
114
+ "pca_trajectory_07.bin",
115
+ "pca_trajectory_08.bin",
116
+ "pca_trajectory_09.bin",
117
+ "pca_trajectory_10.bin",
118
+ "pca_trajectory_11.bin",
119
+ "pca_trajectory_12.bin",
120
+ "pca_trajectory_13.bin",
121
+ "pca_trajectory_14.bin",
122
+ "pca_trajectory_15.bin",
123
+ "pca_trajectory_16.bin",
124
+ "pca_trajectory_17.bin",
125
+ "pca_trajectory_18.bin",
126
+ "pca_trajectory_19.bin",
127
+ "structure.pdb",
128
+ "trajectory.xtc",
129
+ "clusters_00_screenshot_00.jpg",
130
+ "clusters_00_screenshot_01.jpg",
131
+ "clusters_00_screenshot_02.jpg",
132
+ "clusters_00_screenshot_03.jpg",
133
+ "clusters_00_screenshot_04.jpg",
134
+ "clusters_00_screenshot_05.jpg",
135
+ "clusters_00_screenshot_06.jpg",
136
+ "clusters_00_screenshot_07.jpg",
137
+ "clusters_00_screenshot_08.jpg",
138
+ "clusters_00_screenshot_09.jpg",
139
+ "clusters_00_screenshot_10.jpg",
140
+ "clusters_00_screenshot_11.jpg",
141
+ "clusters_00_screenshot_12.jpg",
142
+ "clusters_00_screenshot_13.jpg",
143
+ "clusters_00_screenshot_14.jpg",
144
+ "clusters_00_screenshot_15.jpg",
145
+ "clusters_00_screenshot_16.jpg",
146
+ "clusters_00_screenshot_17.jpg",
147
+ "clusters_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
+ "clusters_01_screenshot_18.jpg",
168
+ "clusters_01_screenshot_19.jpg",
169
+ "pocket_01.pdb",
170
+ "pocket_02.pdb",
171
+ "pocket_03.pdb",
172
+ "pocket_04.pdb",
173
+ "pocket_05.pdb",
174
+ "pocket_06.pdb",
175
+ "pocket_07.pdb",
176
+ "pocket_08.pdb"
177
+ ],
178
+ "analyses": [
179
+ "clusters",
180
+ "clusters-00",
181
+ "clusters-01",
182
+ "dist-perres",
183
+ "energies",
184
+ "fluctuation",
185
+ "hbonds",
186
+ "interactions",
187
+ "pca",
188
+ "pockets",
189
+ "rgyr",
190
+ "rmsd-pairwise",
191
+ "rmsd-perres",
192
+ "rmsds",
193
+ "sasa",
194
+ "tmscores"
195
+ ],
196
+ "mdIndex": 0,
197
+ "mdNumber": 1,
198
+ "refframe": 0,
199
+ "internalId": "6840856ec90c3a181a98ed1a",
200
+ "creationDate": "2025-06-04T17:42:06.000Z",
201
+ "identifier": "A003S"
202
+ }
A003S/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A003S", "accession": "A003S", "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 2QXV", "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": ["2QXV"], "FORCED_REFERENCES": null, "REFERENCES": ["Q921E6", "Q61188"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TMFSSNRQKILERTETLNQEWKQRRIQPV", "FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"], "NUCLSEQ": [], "DOMAINS": ["Polycomb protein EED", "Interaction with EZH2", "Histone-lysine N-methyltransferase EZH2", "Interaction with DNMT1, DNMT3A and DNMT3B", "Interaction with EED"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6132, "SYSTRES": 381, "PROTATS": 6132, "PROTRES": 381, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.49332, "BOXSIZEY": 8.49332, "BOXSIZEZ": 6.0081, "mdName": "replica 1", "mdAtoms": 6132, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003S/files/topology.tpr", "length": 1904752, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003S/files/screenshot.jpg", "length": 25037, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003S/files/trajectory.bin", "length": 367993584, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 5001, "atoms": 6132}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_01.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_02.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_03.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_04.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_05.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_06.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_07.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_08.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_09.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_10.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_11.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_12.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_13.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_14.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_15.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_16.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_17.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_18.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_19.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_19.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003S/files/structure.pdb", "length": 496727, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003S/files/trajectory.xtc", "length": 116352264, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_00.jpg", "length": 25815, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_01.jpg", "length": 24893, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_02.jpg", "length": 25114, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_03.jpg", "length": 25379, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_04.jpg", "length": 25337, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_05.jpg", "length": 25448, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_06.jpg", "length": 25284, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_07.jpg", "length": 25347, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_08.jpg", "length": 25980, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_09.jpg", "length": 25563, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_10.jpg", "length": 25580, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_11.jpg", "length": 25700, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_12.jpg", "length": 25419, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_13.jpg", "length": 25673, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_14.jpg", "length": 25672, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_15.jpg", "length": 25553, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_16.jpg", "length": 26526, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_17.jpg", "length": 26084, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_18.jpg", "length": 25261, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_19.jpg", "length": 25898, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_00.jpg", "length": 26899, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_01.jpg", "length": 27423, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_02.jpg", "length": 27424, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_03.jpg", "length": 26854, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_04.jpg", "length": 27513, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_05.jpg", "length": 27170, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_06.jpg", "length": 27121, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_07.jpg", "length": 27525, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_08.jpg", "length": 27428, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_09.jpg", "length": 27207, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_10.jpg", "length": 27639, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_11.jpg", "length": 27202, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_12.jpg", "length": 27154, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_13.jpg", "length": 27262, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_14.jpg", "length": 27459, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_15.jpg", "length": 27216, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_16.jpg", "length": 27196, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_17.jpg", "length": 26823, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_18.jpg", "length": 27326, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_19.jpg", "length": 27502, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003S/files/pocket_01.pdb", "length": 73499, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003S/files/pocket_02.pdb", "length": 9045, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003S/files/pocket_03.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003S/files/pocket_04.pdb", "length": 8040, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003S/files/pocket_05.pdb", "length": 7303, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003S/files/pocket_06.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003S/files/pocket_07.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A003S/files/pocket_08.pdb", "length": 5561, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}]}
2
+ {"project_identifier": "A003S", "accession": "A003S", "published": true, "md_index": 1, "md_name": "replica 2", "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 2QXV", "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": ["2QXV"], "FORCED_REFERENCES": null, "REFERENCES": ["Q921E6", "Q61188"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TMFSSNRQKILERTETLNQEWKQRRIQPV", "FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"], "NUCLSEQ": [], "DOMAINS": ["Polycomb protein EED", "Interaction with EZH2", "Histone-lysine N-methyltransferase EZH2", "Interaction with DNMT1, DNMT3A and DNMT3B", "Interaction with EED"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6132, "SYSTRES": 381, "PROTATS": 6132, "PROTRES": 381, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.49332, "BOXSIZEY": 8.49332, "BOXSIZEZ": 6.0081, "mdName": "replica 1", "mdAtoms": 6132, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003S/files/topology.tpr", "length": 1904752, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003S/files/screenshot.jpg", "length": 25037, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003S/files/trajectory.bin", "length": 367993584, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 5001, "atoms": 6132}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_01.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_02.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_03.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_04.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_05.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_06.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_07.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_08.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_09.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_10.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_11.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_12.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_13.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_14.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_15.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_16.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_17.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_18.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_19.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_19.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003S/files/structure.pdb", "length": 496727, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003S/files/trajectory.xtc", "length": 116352264, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_00.jpg", "length": 25815, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_01.jpg", "length": 24893, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_02.jpg", "length": 25114, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_03.jpg", "length": 25379, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_04.jpg", "length": 25337, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_05.jpg", "length": 25448, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_06.jpg", "length": 25284, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_07.jpg", "length": 25347, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_08.jpg", "length": 25980, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_09.jpg", "length": 25563, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_10.jpg", "length": 25580, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_11.jpg", "length": 25700, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_12.jpg", "length": 25419, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_13.jpg", "length": 25673, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_14.jpg", "length": 25672, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_15.jpg", "length": 25553, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_16.jpg", "length": 26526, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_17.jpg", "length": 26084, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_18.jpg", "length": 25261, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_19.jpg", "length": 25898, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_00.jpg", "length": 26899, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_01.jpg", "length": 27423, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_02.jpg", "length": 27424, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_03.jpg", "length": 26854, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_04.jpg", "length": 27513, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_05.jpg", "length": 27170, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_06.jpg", "length": 27121, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_07.jpg", "length": 27525, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_08.jpg", "length": 27428, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_09.jpg", "length": 27207, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_10.jpg", "length": 27639, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_11.jpg", "length": 27202, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_12.jpg", "length": 27154, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_13.jpg", "length": 27262, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_14.jpg", "length": 27459, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_15.jpg", "length": 27216, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_16.jpg", "length": 27196, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_17.jpg", "length": 26823, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_18.jpg", "length": 27326, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_19.jpg", "length": 27502, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003S/files/pocket_01.pdb", "length": 73499, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003S/files/pocket_02.pdb", "length": 9045, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003S/files/pocket_03.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003S/files/pocket_04.pdb", "length": 8040, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003S/files/pocket_05.pdb", "length": 7303, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003S/files/pocket_06.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003S/files/pocket_07.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A003S/files/pocket_08.pdb", "length": 5561, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}]}
3
+ {"project_identifier": "A003S", "accession": "A003S", "published": true, "md_index": 2, "md_name": "replica 3", "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 2QXV", "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": ["2QXV"], "FORCED_REFERENCES": null, "REFERENCES": ["Q921E6", "Q61188"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["TMFSSNRQKILERTETLNQEWKQRRIQPV", "FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL"], "NUCLSEQ": [], "DOMAINS": ["Polycomb protein EED", "Interaction with EZH2", "Histone-lysine N-methyltransferase EZH2", "Interaction with DNMT1, DNMT3A and DNMT3B", "Interaction with EED"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 6132, "SYSTRES": 381, "PROTATS": 6132, "PROTRES": 381, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.49332, "BOXSIZEY": 8.49332, "BOXSIZEZ": 6.0081, "mdName": "replica 1", "mdAtoms": 6132, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003S/files/topology.tpr", "length": 1904752, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003S/files/screenshot.jpg", "length": 25037, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003S/files/trajectory.bin", "length": 367993584, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 5001, "atoms": 6132}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_01.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_02.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_03.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_04.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_05.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_06.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_07.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_08.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_09.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_10.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_11.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_12.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_13.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_14.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_15.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_16.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_17.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_18.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "pca_trajectory_19.bin", "downloadUrl": "/projects/A003S/files/pca_trajectory_19.bin", "length": 274320, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0, "frames": 20, "atoms": 1143}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003S/files/structure.pdb", "length": 496727, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003S/files/trajectory.xtc", "length": 116352264, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_00.jpg", "length": 25815, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_01.jpg", "length": 24893, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_02.jpg", "length": 25114, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_03.jpg", "length": 25379, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_04.jpg", "length": 25337, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_05.jpg", "length": 25448, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_06.jpg", "length": 25284, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_07.jpg", "length": 25347, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_08.jpg", "length": 25980, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_09.jpg", "length": 25563, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_10.jpg", "length": 25580, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_11.jpg", "length": 25700, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_12.jpg", "length": 25419, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_13.jpg", "length": 25673, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_14.jpg", "length": 25672, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_15.jpg", "length": 25553, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_16.jpg", "length": 26526, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_17.jpg", "length": 26084, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_18.jpg", "length": 25261, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003S/files/clusters_00_screenshot_19.jpg", "length": 25898, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_00.jpg", "length": 26899, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_01.jpg", "length": 27423, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_02.jpg", "length": 27424, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_03.jpg", "length": 26854, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_04.jpg", "length": 27513, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_05.jpg", "length": 27170, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_06.jpg", "length": 27121, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_07.jpg", "length": 27525, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_08.jpg", "length": 27428, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_09.jpg", "length": 27207, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_10.jpg", "length": 27639, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_11.jpg", "length": 27202, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_12.jpg", "length": 27154, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_13.jpg", "length": 27262, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_14.jpg", "length": 27459, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_15.jpg", "length": 27216, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_16.jpg", "length": 27196, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_17.jpg", "length": 26823, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_18.jpg", "length": 27326, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003S/files/clusters_01_screenshot_19.jpg", "length": 27502, "contentType": "application/octet-stream", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003S/files/pocket_01.pdb", "length": 73499, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003S/files/pocket_02.pdb", "length": 9045, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003S/files/pocket_03.pdb", "length": 8174, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003S/files/pocket_04.pdb", "length": 8040, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003S/files/pocket_05.pdb", "length": 7303, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003S/files/pocket_06.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003S/files/pocket_07.pdb", "length": 6231, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A003S/files/pocket_08.pdb", "length": 5561, "contentType": "chemical/x-pdb", "metadata": {"project": "6840856ec90c3a181a98ed1a", "md": 0}}]}
A003T/project.json ADDED
@@ -0,0 +1,195 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A003T",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2SNI",
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
+ "2SNI"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P00782",
31
+ "P01053"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG",
38
+ "AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLQNTTTKLGDSFYYGKGLINVQAAAQ"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Subtilisin BPN'",
43
+ "Peptidase S8",
44
+ "Subtilisin-chymotrypsin inhibitor-2A",
45
+ "Disordered",
46
+ "Reactive bond"
47
+ ],
48
+ "FRAMESTEP": 0.1,
49
+ "TIMESTEP": 2,
50
+ "TEMP": 310,
51
+ "ENSEMBLE": "NPT",
52
+ "FF": [
53
+ "CHARMM36m"
54
+ ],
55
+ "WAT": "TIP3P",
56
+ "BOXTYPE": "Dodecahedron",
57
+ "SYSTATS": 4901,
58
+ "SYSTRES": 339,
59
+ "PROTATS": 4901,
60
+ "PROTRES": 339,
61
+ "NUCLATS": 0,
62
+ "NUCLRES": 0,
63
+ "LIPIATS": 0,
64
+ "LIPIRES": 0,
65
+ "CARBATS": 0,
66
+ "CARBRES": 0,
67
+ "SOLVATS": 0,
68
+ "SOLVRES": 0,
69
+ "COUNCAT": 0,
70
+ "COUNANI": 0,
71
+ "COUNION": 0,
72
+ "INTERACTIONS": [
73
+ {
74
+ "name": "chain A-chain B interaction",
75
+ "agent_1": "chain A",
76
+ "agent_2": "chain B",
77
+ "selection_1": "chain A",
78
+ "selection_2": "chain B",
79
+ "type": "protein-protein"
80
+ }
81
+ ],
82
+ "PBC_SELECTION": null,
83
+ "CHAINNAMES": null,
84
+ "MEMBRANES": null,
85
+ "CUSTOMS": null,
86
+ "ORIENTATION": null,
87
+ "PTM": [],
88
+ "MULTIMERIC": null,
89
+ "COLLECTIONS": "dynarepo",
90
+ "WARNINGS": [],
91
+ "BOXSIZEX": 8.76713,
92
+ "BOXSIZEY": 8.76713,
93
+ "BOXSIZEZ": 6.24666,
94
+ "mdName": "replica 1",
95
+ "mdAtoms": 4901,
96
+ "mdFrames": 5001
97
+ },
98
+ "mds": [
99
+ "replica 1",
100
+ "replica 2",
101
+ "replica 3"
102
+ ],
103
+ "mdref": 0,
104
+ "files": [
105
+ "topology.tpr",
106
+ "screenshot.jpg",
107
+ "trajectory.bin",
108
+ "pca_trajectory_01.bin",
109
+ "pca_trajectory_02.bin",
110
+ "pca_trajectory_03.bin",
111
+ "pca_trajectory_04.bin",
112
+ "pca_trajectory_05.bin",
113
+ "pca_trajectory_06.bin",
114
+ "pca_trajectory_07.bin",
115
+ "pca_trajectory_08.bin",
116
+ "pca_trajectory_09.bin",
117
+ "pca_trajectory_10.bin",
118
+ "pca_trajectory_11.bin",
119
+ "pca_trajectory_12.bin",
120
+ "pca_trajectory_13.bin",
121
+ "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
+ "clusters_00_screenshot_04.jpg",
128
+ "clusters_00_screenshot_05.jpg",
129
+ "clusters_00_screenshot_06.jpg",
130
+ "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_01_screenshot_00.jpg",
144
+ "clusters_01_screenshot_01.jpg",
145
+ "clusters_01_screenshot_02.jpg",
146
+ "clusters_01_screenshot_03.jpg",
147
+ "clusters_01_screenshot_04.jpg",
148
+ "clusters_01_screenshot_05.jpg",
149
+ "clusters_01_screenshot_06.jpg",
150
+ "clusters_01_screenshot_07.jpg",
151
+ "clusters_01_screenshot_08.jpg",
152
+ "clusters_01_screenshot_09.jpg",
153
+ "clusters_01_screenshot_10.jpg",
154
+ "clusters_01_screenshot_11.jpg",
155
+ "clusters_01_screenshot_12.jpg",
156
+ "clusters_01_screenshot_13.jpg",
157
+ "clusters_01_screenshot_14.jpg",
158
+ "clusters_01_screenshot_15.jpg",
159
+ "clusters_01_screenshot_16.jpg",
160
+ "clusters_01_screenshot_17.jpg",
161
+ "clusters_01_screenshot_18.jpg",
162
+ "clusters_01_screenshot_19.jpg",
163
+ "pocket_01.pdb",
164
+ "pocket_02.pdb",
165
+ "pocket_03.pdb",
166
+ "pocket_04.pdb",
167
+ "pocket_05.pdb",
168
+ "pocket_06.pdb",
169
+ "pocket_07.pdb"
170
+ ],
171
+ "analyses": [
172
+ "clusters",
173
+ "clusters-00",
174
+ "clusters-01",
175
+ "dist-perres",
176
+ "energies",
177
+ "fluctuation",
178
+ "hbonds",
179
+ "interactions",
180
+ "pca",
181
+ "pockets",
182
+ "rgyr",
183
+ "rmsd-pairwise",
184
+ "rmsd-perres",
185
+ "rmsds",
186
+ "sasa",
187
+ "tmscores"
188
+ ],
189
+ "mdIndex": 0,
190
+ "mdNumber": 1,
191
+ "refframe": 0,
192
+ "internalId": "6840878bcbe8a3cd5b0dede8",
193
+ "creationDate": "2025-06-04T17:51:07.000Z",
194
+ "identifier": "A003T"
195
+ }
A003T/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A003T", "accession": "A003T", "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 2SNI", "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": ["2SNI"], "FORCED_REFERENCES": null, "REFERENCES": ["P00782", "P01053"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG", "AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLQNTTTKLGDSFYYGKGLINVQAAAQ"], "NUCLSEQ": [], "DOMAINS": ["Subtilisin BPN'", "Peptidase S8", "Subtilisin-chymotrypsin inhibitor-2A", "Disordered", "Reactive bond"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4901, "SYSTRES": 339, "PROTATS": 4901, "PROTRES": 339, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.76713, "BOXSIZEY": 8.76713, "BOXSIZEZ": 6.24666, "mdName": "replica 1", "mdAtoms": 4901, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003T/files/topology.tpr", "length": 1600144, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003T/files/screenshot.jpg", "length": 24563, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003T/files/trajectory.bin", "length": 294118812, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 5001, "atoms": 4901}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_01.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_02.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_03.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_04.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_05.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_06.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_07.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_08.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_09.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_10.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_11.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_12.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_13.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003T/files/structure.pdb", "length": 397016, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003T/files/trajectory.xtc", "length": 93254072, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_00.jpg", "length": 24892, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_01.jpg", "length": 25056, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_02.jpg", "length": 25127, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_03.jpg", "length": 25310, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_04.jpg", "length": 25354, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_05.jpg", "length": 25494, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_06.jpg", "length": 25402, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_07.jpg", "length": 24777, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_08.jpg", "length": 24965, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_09.jpg", "length": 25344, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_10.jpg", "length": 24677, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_11.jpg", "length": 25286, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_12.jpg", "length": 24949, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_13.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_14.jpg", "length": 25394, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_15.jpg", "length": 24567, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_16.jpg", "length": 25181, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_17.jpg", "length": 25071, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_18.jpg", "length": 25446, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_19.jpg", "length": 25547, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_00.jpg", "length": 25492, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_01.jpg", "length": 25427, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_02.jpg", "length": 25818, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_03.jpg", "length": 25864, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_04.jpg", "length": 26055, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_05.jpg", "length": 25649, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_06.jpg", "length": 25531, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_07.jpg", "length": 26451, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_08.jpg", "length": 25699, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_09.jpg", "length": 25817, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_10.jpg", "length": 25795, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_11.jpg", "length": 25713, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_12.jpg", "length": 24952, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_13.jpg", "length": 26372, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_14.jpg", "length": 25897, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_15.jpg", "length": 26085, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_16.jpg", "length": 25581, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_17.jpg", "length": 25728, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_18.jpg", "length": 26009, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_19.jpg", "length": 25791, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003T/files/pocket_01.pdb", "length": 25661, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003T/files/pocket_02.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003T/files/pocket_03.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003T/files/pocket_04.pdb", "length": 6834, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003T/files/pocket_05.pdb", "length": 6164, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003T/files/pocket_06.pdb", "length": 3551, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003T/files/pocket_07.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}]}
2
+ {"project_identifier": "A003T", "accession": "A003T", "published": true, "md_index": 1, "md_name": "replica 2", "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 2SNI", "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": ["2SNI"], "FORCED_REFERENCES": null, "REFERENCES": ["P00782", "P01053"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG", "AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLQNTTTKLGDSFYYGKGLINVQAAAQ"], "NUCLSEQ": [], "DOMAINS": ["Subtilisin BPN'", "Peptidase S8", "Subtilisin-chymotrypsin inhibitor-2A", "Disordered", "Reactive bond"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4901, "SYSTRES": 339, "PROTATS": 4901, "PROTRES": 339, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.76713, "BOXSIZEY": 8.76713, "BOXSIZEZ": 6.24666, "mdName": "replica 1", "mdAtoms": 4901, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003T/files/topology.tpr", "length": 1600144, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003T/files/screenshot.jpg", "length": 24563, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003T/files/trajectory.bin", "length": 294118812, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 5001, "atoms": 4901}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_01.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_02.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_03.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_04.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_05.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_06.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_07.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_08.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_09.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_10.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_11.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_12.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_13.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003T/files/structure.pdb", "length": 397016, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003T/files/trajectory.xtc", "length": 93254072, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_00.jpg", "length": 24892, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_01.jpg", "length": 25056, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_02.jpg", "length": 25127, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_03.jpg", "length": 25310, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_04.jpg", "length": 25354, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_05.jpg", "length": 25494, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_06.jpg", "length": 25402, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_07.jpg", "length": 24777, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_08.jpg", "length": 24965, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_09.jpg", "length": 25344, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_10.jpg", "length": 24677, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_11.jpg", "length": 25286, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_12.jpg", "length": 24949, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_13.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_14.jpg", "length": 25394, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_15.jpg", "length": 24567, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_16.jpg", "length": 25181, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_17.jpg", "length": 25071, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_18.jpg", "length": 25446, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_19.jpg", "length": 25547, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_00.jpg", "length": 25492, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_01.jpg", "length": 25427, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_02.jpg", "length": 25818, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_03.jpg", "length": 25864, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_04.jpg", "length": 26055, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_05.jpg", "length": 25649, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_06.jpg", "length": 25531, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_07.jpg", "length": 26451, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_08.jpg", "length": 25699, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_09.jpg", "length": 25817, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_10.jpg", "length": 25795, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_11.jpg", "length": 25713, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_12.jpg", "length": 24952, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_13.jpg", "length": 26372, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_14.jpg", "length": 25897, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_15.jpg", "length": 26085, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_16.jpg", "length": 25581, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_17.jpg", "length": 25728, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_18.jpg", "length": 26009, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_19.jpg", "length": 25791, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003T/files/pocket_01.pdb", "length": 25661, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003T/files/pocket_02.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003T/files/pocket_03.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003T/files/pocket_04.pdb", "length": 6834, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003T/files/pocket_05.pdb", "length": 6164, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003T/files/pocket_06.pdb", "length": 3551, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003T/files/pocket_07.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}]}
3
+ {"project_identifier": "A003T", "accession": "A003T", "published": true, "md_index": 2, "md_name": "replica 3", "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 2SNI", "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": ["2SNI"], "FORCED_REFERENCES": null, "REFERENCES": ["P00782", "P01053"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG", "AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLQNTTTKLGDSFYYGKGLINVQAAAQ"], "NUCLSEQ": [], "DOMAINS": ["Subtilisin BPN'", "Peptidase S8", "Subtilisin-chymotrypsin inhibitor-2A", "Disordered", "Reactive bond"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 4901, "SYSTRES": 339, "PROTATS": 4901, "PROTRES": 339, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.76713, "BOXSIZEY": 8.76713, "BOXSIZEZ": 6.24666, "mdName": "replica 1", "mdAtoms": 4901, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A003T/files/topology.tpr", "length": 1600144, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A003T/files/screenshot.jpg", "length": 24563, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A003T/files/trajectory.bin", "length": 294118812, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 5001, "atoms": 4901}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_01.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_02.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_03.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_04.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_05.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_06.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_07.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_08.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_09.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_10.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_11.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_12.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A003T/files/pca_trajectory_13.bin", "length": 244080, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0, "frames": 20, "atoms": 1017}}, {"name": "structure.pdb", "downloadUrl": "/projects/A003T/files/structure.pdb", "length": 397016, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A003T/files/trajectory.xtc", "length": 93254072, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_00.jpg", "length": 24892, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_01.jpg", "length": 25056, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_02.jpg", "length": 25127, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_03.jpg", "length": 25310, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_04.jpg", "length": 25354, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_05.jpg", "length": 25494, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_06.jpg", "length": 25402, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_07.jpg", "length": 24777, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_08.jpg", "length": 24965, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_09.jpg", "length": 25344, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_10.jpg", "length": 24677, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_11.jpg", "length": 25286, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_12.jpg", "length": 24949, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_13.jpg", "length": 25306, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_14.jpg", "length": 25394, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_15.jpg", "length": 24567, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_16.jpg", "length": 25181, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_17.jpg", "length": 25071, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_18.jpg", "length": 25446, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A003T/files/clusters_00_screenshot_19.jpg", "length": 25547, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_00.jpg", "length": 25492, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_01.jpg", "length": 25427, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_02.jpg", "length": 25818, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_03.jpg", "length": 25864, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_04.jpg", "length": 26055, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_05.jpg", "length": 25649, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_06.jpg", "length": 25531, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_07.jpg", "length": 26451, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_08.jpg", "length": 25699, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_09.jpg", "length": 25817, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_10.jpg", "length": 25795, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_11.jpg", "length": 25713, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_12.jpg", "length": 24952, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_13.jpg", "length": 26372, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_14.jpg", "length": 25897, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_15.jpg", "length": 26085, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_16.jpg", "length": 25581, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_17.jpg", "length": 25728, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_18.jpg", "length": 26009, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A003T/files/clusters_01_screenshot_19.jpg", "length": 25791, "contentType": "application/octet-stream", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A003T/files/pocket_01.pdb", "length": 25661, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A003T/files/pocket_02.pdb", "length": 8107, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A003T/files/pocket_03.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A003T/files/pocket_04.pdb", "length": 6834, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A003T/files/pocket_05.pdb", "length": 6164, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A003T/files/pocket_06.pdb", "length": 3551, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A003T/files/pocket_07.pdb", "length": 3484, "contentType": "chemical/x-pdb", "metadata": {"project": "6840878bcbe8a3cd5b0dede8", "md": 0}}]}
A0046/project.json ADDED
@@ -0,0 +1,180 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0046",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2X89",
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
+ "2X89"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P61769"
31
+ ],
32
+ "INPUT_LIGANDS": null,
33
+ "LIGANDS": [],
34
+ "LIGANDNAMES": null,
35
+ "PROTSEQ": [
36
+ "MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD",
37
+ "MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR"
38
+ ],
39
+ "NUCLSEQ": [],
40
+ "DOMAINS": [
41
+ "Beta-2-microglobulin",
42
+ "Beta-2-microglobulin form pI 5.3",
43
+ "Ig-like C1-type"
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": 2978,
55
+ "SYSTRES": 183,
56
+ "PROTATS": 2978,
57
+ "PROTRES": 183,
58
+ "NUCLATS": 0,
59
+ "NUCLRES": 0,
60
+ "LIPIATS": 0,
61
+ "LIPIRES": 0,
62
+ "CARBATS": 0,
63
+ "CARBRES": 0,
64
+ "SOLVATS": 0,
65
+ "SOLVRES": 0,
66
+ "COUNCAT": 0,
67
+ "COUNANI": 0,
68
+ "COUNION": 0,
69
+ "INTERACTIONS": [
70
+ {
71
+ "name": "chain A-chain B interaction",
72
+ "agent_1": "chain A",
73
+ "agent_2": "chain B",
74
+ "selection_1": "chain A",
75
+ "selection_2": "chain B",
76
+ "type": "protein-protein"
77
+ }
78
+ ],
79
+ "PBC_SELECTION": null,
80
+ "CHAINNAMES": null,
81
+ "MEMBRANES": null,
82
+ "CUSTOMS": null,
83
+ "ORIENTATION": null,
84
+ "PTM": [],
85
+ "MULTIMERIC": null,
86
+ "COLLECTIONS": "dynarepo",
87
+ "WARNINGS": [],
88
+ "BOXSIZEX": 9.36749,
89
+ "BOXSIZEY": 9.36749,
90
+ "BOXSIZEZ": 6.57096,
91
+ "mdName": "replica 1",
92
+ "mdAtoms": 2978,
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
+ "structure.pdb",
113
+ "trajectory.xtc",
114
+ "clusters_00_screenshot_00.jpg",
115
+ "clusters_00_screenshot_01.jpg",
116
+ "clusters_00_screenshot_02.jpg",
117
+ "clusters_00_screenshot_03.jpg",
118
+ "clusters_00_screenshot_04.jpg",
119
+ "clusters_00_screenshot_05.jpg",
120
+ "clusters_00_screenshot_06.jpg",
121
+ "clusters_00_screenshot_07.jpg",
122
+ "clusters_00_screenshot_08.jpg",
123
+ "clusters_00_screenshot_09.jpg",
124
+ "clusters_00_screenshot_10.jpg",
125
+ "clusters_00_screenshot_11.jpg",
126
+ "clusters_00_screenshot_12.jpg",
127
+ "clusters_00_screenshot_13.jpg",
128
+ "clusters_00_screenshot_14.jpg",
129
+ "clusters_00_screenshot_15.jpg",
130
+ "clusters_00_screenshot_16.jpg",
131
+ "clusters_00_screenshot_17.jpg",
132
+ "clusters_00_screenshot_18.jpg",
133
+ "clusters_00_screenshot_19.jpg",
134
+ "clusters_00_screenshot_20.jpg",
135
+ "clusters_00_screenshot_21.jpg",
136
+ "clusters_01_screenshot_00.jpg",
137
+ "clusters_01_screenshot_01.jpg",
138
+ "clusters_01_screenshot_02.jpg",
139
+ "clusters_01_screenshot_03.jpg",
140
+ "clusters_01_screenshot_04.jpg",
141
+ "clusters_01_screenshot_05.jpg",
142
+ "clusters_01_screenshot_06.jpg",
143
+ "clusters_01_screenshot_07.jpg",
144
+ "clusters_01_screenshot_08.jpg",
145
+ "clusters_01_screenshot_09.jpg",
146
+ "clusters_01_screenshot_10.jpg",
147
+ "clusters_01_screenshot_11.jpg",
148
+ "clusters_01_screenshot_12.jpg",
149
+ "clusters_01_screenshot_13.jpg",
150
+ "clusters_01_screenshot_14.jpg",
151
+ "clusters_01_screenshot_15.jpg",
152
+ "clusters_01_screenshot_16.jpg",
153
+ "clusters_01_screenshot_17.jpg",
154
+ "clusters_01_screenshot_18.jpg",
155
+ "clusters_01_screenshot_19.jpg"
156
+ ],
157
+ "analyses": [
158
+ "clusters",
159
+ "clusters-00",
160
+ "clusters-01",
161
+ "dist-perres",
162
+ "energies",
163
+ "fluctuation",
164
+ "hbonds",
165
+ "interactions",
166
+ "pca",
167
+ "rgyr",
168
+ "rmsd-pairwise",
169
+ "rmsd-perres",
170
+ "rmsds",
171
+ "sasa",
172
+ "tmscores"
173
+ ],
174
+ "mdIndex": 0,
175
+ "mdNumber": 1,
176
+ "refframe": 0,
177
+ "internalId": "6840aadb3d674274ef7d6e1e",
178
+ "creationDate": "2025-06-04T20:21:47.000Z",
179
+ "identifier": "A0046"
180
+ }
A0046/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A0046", "accession": "A0046", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2X89", "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": ["2X89"], "FORCED_REFERENCES": null, "REFERENCES": ["P61769"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD", "MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR"], "NUCLSEQ": [], "DOMAINS": ["Beta-2-microglobulin", "Beta-2-microglobulin form pI 5.3", "Ig-like C1-type"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2978, "SYSTRES": 183, "PROTATS": 2978, "PROTRES": 183, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.36749, "BOXSIZEY": 9.36749, "BOXSIZEZ": 6.57096, "mdName": "replica 1", "mdAtoms": 2978, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0046/files/topology.tpr", "length": 1138116, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0046/files/screenshot.jpg", "length": 16711, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0046/files/trajectory.bin", "length": 178715736, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 5001, "atoms": 2978}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_01.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_02.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_03.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_04.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_05.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_06.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_07.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0046/files/structure.pdb", "length": 241253, "contentType": "chemical/x-pdb", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0046/files/trajectory.xtc", "length": 56908008, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_00.jpg", "length": 16145, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_01.jpg", "length": 15379, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_02.jpg", "length": 17033, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_03.jpg", "length": 14695, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_04.jpg", "length": 15350, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_05.jpg", "length": 15414, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_06.jpg", "length": 16247, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_07.jpg", "length": 16830, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_08.jpg", "length": 15561, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_09.jpg", "length": 16363, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_10.jpg", "length": 17266, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_11.jpg", "length": 13877, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_12.jpg", "length": 16908, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_13.jpg", "length": 16218, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_14.jpg", "length": 16099, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_15.jpg", "length": 16204, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_16.jpg", "length": 15198, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_17.jpg", "length": 16401, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_18.jpg", "length": 17057, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_19.jpg", "length": 16042, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_20.jpg", "length": 17026, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_21.jpg", "length": 16867, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_00.jpg", "length": 15382, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_01.jpg", "length": 14375, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_02.jpg", "length": 15517, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_03.jpg", "length": 13803, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_04.jpg", "length": 14712, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_05.jpg", "length": 14505, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_06.jpg", "length": 15045, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_07.jpg", "length": 16085, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_08.jpg", "length": 14541, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_09.jpg", "length": 14786, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_10.jpg", "length": 15941, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_11.jpg", "length": 12791, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_12.jpg", "length": 15739, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_13.jpg", "length": 14977, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_14.jpg", "length": 14902, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_15.jpg", "length": 15086, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_16.jpg", "length": 13629, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_17.jpg", "length": 15768, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_18.jpg", "length": 14628, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_19.jpg", "length": 15527, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}]}
2
+ {"project_identifier": "A0046", "accession": "A0046", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2X89", "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": ["2X89"], "FORCED_REFERENCES": null, "REFERENCES": ["P61769"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD", "MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR"], "NUCLSEQ": [], "DOMAINS": ["Beta-2-microglobulin", "Beta-2-microglobulin form pI 5.3", "Ig-like C1-type"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2978, "SYSTRES": 183, "PROTATS": 2978, "PROTRES": 183, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.36749, "BOXSIZEY": 9.36749, "BOXSIZEZ": 6.57096, "mdName": "replica 1", "mdAtoms": 2978, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0046/files/topology.tpr", "length": 1138116, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0046/files/screenshot.jpg", "length": 16711, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0046/files/trajectory.bin", "length": 178715736, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 5001, "atoms": 2978}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_01.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_02.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_03.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_04.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_05.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_06.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_07.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0046/files/structure.pdb", "length": 241253, "contentType": "chemical/x-pdb", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0046/files/trajectory.xtc", "length": 56908008, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_00.jpg", "length": 16145, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_01.jpg", "length": 15379, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_02.jpg", "length": 17033, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_03.jpg", "length": 14695, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_04.jpg", "length": 15350, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_05.jpg", "length": 15414, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_06.jpg", "length": 16247, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_07.jpg", "length": 16830, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_08.jpg", "length": 15561, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_09.jpg", "length": 16363, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_10.jpg", "length": 17266, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_11.jpg", "length": 13877, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_12.jpg", "length": 16908, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_13.jpg", "length": 16218, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_14.jpg", "length": 16099, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_15.jpg", "length": 16204, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_16.jpg", "length": 15198, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_17.jpg", "length": 16401, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_18.jpg", "length": 17057, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_19.jpg", "length": 16042, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_20.jpg", "length": 17026, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_21.jpg", "length": 16867, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_00.jpg", "length": 15382, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_01.jpg", "length": 14375, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_02.jpg", "length": 15517, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_03.jpg", "length": 13803, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_04.jpg", "length": 14712, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_05.jpg", "length": 14505, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_06.jpg", "length": 15045, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_07.jpg", "length": 16085, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_08.jpg", "length": 14541, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_09.jpg", "length": 14786, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_10.jpg", "length": 15941, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_11.jpg", "length": 12791, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_12.jpg", "length": 15739, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_13.jpg", "length": 14977, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_14.jpg", "length": 14902, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_15.jpg", "length": 15086, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_16.jpg", "length": 13629, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_17.jpg", "length": 15768, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_18.jpg", "length": 14628, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_19.jpg", "length": 15527, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}]}
3
+ {"project_identifier": "A0046", "accession": "A0046", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 2X89", "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": ["2X89"], "FORCED_REFERENCES": null, "REFERENCES": ["P61769"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD", "MIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR"], "NUCLSEQ": [], "DOMAINS": ["Beta-2-microglobulin", "Beta-2-microglobulin form pI 5.3", "Ig-like C1-type"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 2978, "SYSTRES": 183, "PROTATS": 2978, "PROTRES": 183, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 9.36749, "BOXSIZEY": 9.36749, "BOXSIZEZ": 6.57096, "mdName": "replica 1", "mdAtoms": 2978, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0046/files/topology.tpr", "length": 1138116, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0046/files/screenshot.jpg", "length": 16711, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0046/files/trajectory.bin", "length": 178715736, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 5001, "atoms": 2978}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_01.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_02.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_03.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_04.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_05.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_06.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0046/files/pca_trajectory_07.bin", "length": 131760, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0, "frames": 20, "atoms": 549}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0046/files/structure.pdb", "length": 241253, "contentType": "chemical/x-pdb", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0046/files/trajectory.xtc", "length": 56908008, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_00.jpg", "length": 16145, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_01.jpg", "length": 15379, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_02.jpg", "length": 17033, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_03.jpg", "length": 14695, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_04.jpg", "length": 15350, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_05.jpg", "length": 15414, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_06.jpg", "length": 16247, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_07.jpg", "length": 16830, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_08.jpg", "length": 15561, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_09.jpg", "length": 16363, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_10.jpg", "length": 17266, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_11.jpg", "length": 13877, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_12.jpg", "length": 16908, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_13.jpg", "length": 16218, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_14.jpg", "length": 16099, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_15.jpg", "length": 16204, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_16.jpg", "length": 15198, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_17.jpg", "length": 16401, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_18.jpg", "length": 17057, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_19.jpg", "length": 16042, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_20.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_20.jpg", "length": 17026, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_00_screenshot_21.jpg", "downloadUrl": "/projects/A0046/files/clusters_00_screenshot_21.jpg", "length": 16867, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_00.jpg", "length": 15382, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_01.jpg", "length": 14375, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_02.jpg", "length": 15517, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_03.jpg", "length": 13803, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_04.jpg", "length": 14712, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_05.jpg", "length": 14505, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_06.jpg", "length": 15045, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_07.jpg", "length": 16085, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_08.jpg", "length": 14541, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_09.jpg", "length": 14786, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_10.jpg", "length": 15941, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_11.jpg", "length": 12791, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_12.jpg", "length": 15739, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_13.jpg", "length": 14977, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_14.jpg", "length": 14902, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_15.jpg", "length": 15086, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_16.jpg", "length": 13629, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_17.jpg", "length": 15768, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_18.jpg", "length": 14628, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0046/files/clusters_01_screenshot_19.jpg", "length": 15527, "contentType": "application/octet-stream", "metadata": {"project": "6840aadb3d674274ef7d6e1e", "md": 0}}]}
A0049/project.json ADDED
@@ -0,0 +1,179 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0049",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 2XQR",
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
+ "2XQR"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "Q43866",
31
+ "O49908"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL",
38
+ "NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Beta-fructofuranosidase, insoluble isoenzyme CWINV1",
43
+ "",
44
+ "Pectinesterase inhibitor"
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": 10758,
56
+ "SYSTRES": 683,
57
+ "PROTATS": 10758,
58
+ "PROTRES": 683,
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": 11.0762,
90
+ "BOXSIZEY": 11.0762,
91
+ "BOXSIZEZ": 7.82367,
92
+ "mdName": "replica 1",
93
+ "mdAtoms": 10758,
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
+ "structure.pdb",
112
+ "trajectory.xtc",
113
+ "clusters_00_screenshot_00.jpg",
114
+ "clusters_00_screenshot_01.jpg",
115
+ "clusters_00_screenshot_02.jpg",
116
+ "clusters_00_screenshot_03.jpg",
117
+ "clusters_00_screenshot_04.jpg",
118
+ "clusters_00_screenshot_05.jpg",
119
+ "clusters_00_screenshot_06.jpg",
120
+ "clusters_00_screenshot_07.jpg",
121
+ "clusters_00_screenshot_08.jpg",
122
+ "clusters_00_screenshot_09.jpg",
123
+ "clusters_00_screenshot_10.jpg",
124
+ "clusters_00_screenshot_11.jpg",
125
+ "clusters_00_screenshot_12.jpg",
126
+ "clusters_00_screenshot_13.jpg",
127
+ "clusters_00_screenshot_14.jpg",
128
+ "clusters_00_screenshot_15.jpg",
129
+ "clusters_00_screenshot_16.jpg",
130
+ "clusters_00_screenshot_17.jpg",
131
+ "clusters_00_screenshot_18.jpg",
132
+ "clusters_00_screenshot_19.jpg",
133
+ "clusters_01_screenshot_00.jpg",
134
+ "clusters_01_screenshot_01.jpg",
135
+ "clusters_01_screenshot_02.jpg",
136
+ "clusters_01_screenshot_03.jpg",
137
+ "clusters_01_screenshot_04.jpg",
138
+ "clusters_01_screenshot_05.jpg",
139
+ "clusters_01_screenshot_06.jpg",
140
+ "clusters_01_screenshot_07.jpg",
141
+ "clusters_01_screenshot_08.jpg",
142
+ "clusters_01_screenshot_09.jpg",
143
+ "clusters_01_screenshot_10.jpg",
144
+ "clusters_01_screenshot_11.jpg",
145
+ "clusters_01_screenshot_12.jpg",
146
+ "clusters_01_screenshot_13.jpg",
147
+ "clusters_01_screenshot_14.jpg",
148
+ "clusters_01_screenshot_15.jpg",
149
+ "clusters_01_screenshot_16.jpg",
150
+ "clusters_01_screenshot_17.jpg",
151
+ "clusters_01_screenshot_18.jpg",
152
+ "clusters_01_screenshot_19.jpg",
153
+ "pocket_01.pdb"
154
+ ],
155
+ "analyses": [
156
+ "clusters",
157
+ "clusters-00",
158
+ "clusters-01",
159
+ "dist-perres",
160
+ "energies",
161
+ "fluctuation",
162
+ "hbonds",
163
+ "interactions",
164
+ "pca",
165
+ "pockets",
166
+ "rgyr",
167
+ "rmsd-pairwise",
168
+ "rmsd-perres",
169
+ "rmsds",
170
+ "sasa",
171
+ "tmscores"
172
+ ],
173
+ "mdIndex": 0,
174
+ "mdNumber": 1,
175
+ "refframe": 0,
176
+ "internalId": "6840b149c79430af3b36cc0d",
177
+ "creationDate": "2025-06-04T20:49:13.000Z",
178
+ "identifier": "A0049"
179
+ }
A0049/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A0049", "accession": "A0049", "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 2XQR", "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": ["2XQR"], "FORCED_REFERENCES": null, "REFERENCES": ["Q43866", "O49908"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL", "NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS"], "NUCLSEQ": [], "DOMAINS": ["Beta-fructofuranosidase, insoluble isoenzyme CWINV1", "", "Pectinesterase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 10758, "SYSTRES": 683, "PROTATS": 10758, "PROTRES": 683, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0762, "BOXSIZEY": 11.0762, "BOXSIZEZ": 7.82367, "mdName": "replica 1", "mdAtoms": 10758, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0049/files/topology.tpr", "length": 3202240, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0049/files/screenshot.jpg", "length": 30621, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0049/files/trajectory.bin", "length": 645609096, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 5001, "atoms": 10758}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_01.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_02.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_03.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_04.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_05.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0049/files/structure.pdb", "length": 871433, "contentType": "chemical/x-pdb", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0049/files/trajectory.xtc", "length": 204705032, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_00.jpg", "length": 26937, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_01.jpg", "length": 24543, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_02.jpg", "length": 22121, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_03.jpg", "length": 20250, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_04.jpg", "length": 24296, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_05.jpg", "length": 21804, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_06.jpg", "length": 21405, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_07.jpg", "length": 19837, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_08.jpg", "length": 21275, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_09.jpg", "length": 20084, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_10.jpg", "length": 21084, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_11.jpg", "length": 19977, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_12.jpg", "length": 18988, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_13.jpg", "length": 22410, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_14.jpg", "length": 23042, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_15.jpg", "length": 22009, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_16.jpg", "length": 19511, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_17.jpg", "length": 19756, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_18.jpg", "length": 21998, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_19.jpg", "length": 21205, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_00.jpg", "length": 26719, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_01.jpg", "length": 24547, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_02.jpg", "length": 21874, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_03.jpg", "length": 20519, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_04.jpg", "length": 24182, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_05.jpg", "length": 22713, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_06.jpg", "length": 22444, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_07.jpg", "length": 21010, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_08.jpg", "length": 19515, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_09.jpg", "length": 21054, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_10.jpg", "length": 21984, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_11.jpg", "length": 19574, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_12.jpg", "length": 21829, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_13.jpg", "length": 18970, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_14.jpg", "length": 22405, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_15.jpg", "length": 21821, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_16.jpg", "length": 18915, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_17.jpg", "length": 19210, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_18.jpg", "length": 18982, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_19.jpg", "length": 20125, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0049/files/pocket_01.pdb", "length": 4556, "contentType": "chemical/x-pdb", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}]}
2
+ {"project_identifier": "A0049", "accession": "A0049", "published": true, "md_index": 1, "md_name": "replica 2", "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 2XQR", "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": ["2XQR"], "FORCED_REFERENCES": null, "REFERENCES": ["Q43866", "O49908"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL", "NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS"], "NUCLSEQ": [], "DOMAINS": ["Beta-fructofuranosidase, insoluble isoenzyme CWINV1", "", "Pectinesterase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 10758, "SYSTRES": 683, "PROTATS": 10758, "PROTRES": 683, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0762, "BOXSIZEY": 11.0762, "BOXSIZEZ": 7.82367, "mdName": "replica 1", "mdAtoms": 10758, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0049/files/topology.tpr", "length": 3202240, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0049/files/screenshot.jpg", "length": 30621, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0049/files/trajectory.bin", "length": 645609096, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 5001, "atoms": 10758}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_01.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_02.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_03.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_04.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_05.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0049/files/structure.pdb", "length": 871433, "contentType": "chemical/x-pdb", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0049/files/trajectory.xtc", "length": 204705032, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_00.jpg", "length": 26937, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_01.jpg", "length": 24543, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_02.jpg", "length": 22121, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_03.jpg", "length": 20250, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_04.jpg", "length": 24296, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_05.jpg", "length": 21804, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_06.jpg", "length": 21405, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_07.jpg", "length": 19837, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_08.jpg", "length": 21275, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_09.jpg", "length": 20084, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_10.jpg", "length": 21084, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_11.jpg", "length": 19977, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_12.jpg", "length": 18988, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_13.jpg", "length": 22410, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_14.jpg", "length": 23042, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_15.jpg", "length": 22009, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_16.jpg", "length": 19511, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_17.jpg", "length": 19756, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_18.jpg", "length": 21998, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_19.jpg", "length": 21205, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_00.jpg", "length": 26719, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_01.jpg", "length": 24547, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_02.jpg", "length": 21874, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_03.jpg", "length": 20519, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_04.jpg", "length": 24182, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_05.jpg", "length": 22713, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_06.jpg", "length": 22444, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_07.jpg", "length": 21010, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_08.jpg", "length": 19515, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_09.jpg", "length": 21054, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_10.jpg", "length": 21984, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_11.jpg", "length": 19574, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_12.jpg", "length": 21829, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_13.jpg", "length": 18970, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_14.jpg", "length": 22405, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_15.jpg", "length": 21821, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_16.jpg", "length": 18915, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_17.jpg", "length": 19210, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_18.jpg", "length": 18982, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_19.jpg", "length": 20125, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0049/files/pocket_01.pdb", "length": 4556, "contentType": "chemical/x-pdb", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}]}
3
+ {"project_identifier": "A0049", "accession": "A0049", "published": true, "md_index": 2, "md_name": "replica 3", "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 2XQR", "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": ["2XQR"], "FORCED_REFERENCES": null, "REFERENCES": ["Q43866", "O49908"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["NLVETTCKNTPNYQLCLKTLLSDKRSATGDITTLALIMVDAIKAKANQAAVTISKLRHSNPPAAWKGPLKNCAFSYKVILTASLPEAIEALTKGDPKFAEDGMVGSSGDAQECEEYFKGSKSPFSALNIAVHELSDVGRAIVRNLL", "NQPYRTGFHFQPPKNWMNDPNGPMIYKGIYHLFYQWNPKGAVWGNIVWAHSTSTDLINWDPHPPAIFPSAPFDINGCWSGSATILPNGKPVILYTGIDPKNQQVQNIAEPKNLSDPYLREWKKSPLNPLMAPDAVNGINASSFRDPTTAWLGQDKKWRVIIGSKIHRRGLAITYTSKDFLKWEKSPEPLHYDDGSGMWECPDFFPVTRFGSNGVETSSFGEPNEILKHVLKISLDDTKHDYYTIGTYDRVKDKFVPDNGFKMDGTAPRYDYGKYYASKTFFDSAKNRRILWGWTNESSSVEDDVEKGWSGIQTIPRKIWLDRSGKQLIQWPVREVERLRTKQVKNLRNKVLKSGSRLEVYGVTAAQADVEVLFKVRDLEKADVIEPSWTDPQLICSKMNVSVKSGLGPFGLMVLASKNLEEYTSVYFRIFKARQNSNKYVVLMCSDQSRSSLKEDNDKTTYGAFVDINPHQPLSLRALIDHSVVESFGGKGRACITSRVYPKLAIGKSSHLFAFNYGYQSVDVLNLNAWSMNSAQIS"], "NUCLSEQ": [], "DOMAINS": ["Beta-fructofuranosidase, insoluble isoenzyme CWINV1", "", "Pectinesterase inhibitor"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 10758, "SYSTRES": 683, "PROTATS": 10758, "PROTRES": 683, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 11.0762, "BOXSIZEY": 11.0762, "BOXSIZEZ": 7.82367, "mdName": "replica 1", "mdAtoms": 10758, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0049/files/topology.tpr", "length": 3202240, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0049/files/screenshot.jpg", "length": 30621, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0049/files/trajectory.bin", "length": 645609096, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 5001, "atoms": 10758}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_01.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_02.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_03.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_04.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0049/files/pca_trajectory_05.bin", "length": 491760, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0, "frames": 20, "atoms": 2049}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0049/files/structure.pdb", "length": 871433, "contentType": "chemical/x-pdb", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0049/files/trajectory.xtc", "length": 204705032, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_00.jpg", "length": 26937, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_01.jpg", "length": 24543, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_02.jpg", "length": 22121, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_03.jpg", "length": 20250, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_04.jpg", "length": 24296, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_05.jpg", "length": 21804, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_06.jpg", "length": 21405, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_07.jpg", "length": 19837, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_08.jpg", "length": 21275, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_09.jpg", "length": 20084, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_10.jpg", "length": 21084, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_11.jpg", "length": 19977, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_12.jpg", "length": 18988, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_13.jpg", "length": 22410, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_14.jpg", "length": 23042, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_15.jpg", "length": 22009, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_16.jpg", "length": 19511, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_17.jpg", "length": 19756, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_18.jpg", "length": 21998, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0049/files/clusters_00_screenshot_19.jpg", "length": 21205, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_00.jpg", "length": 26719, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_01.jpg", "length": 24547, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_02.jpg", "length": 21874, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_03.jpg", "length": 20519, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_04.jpg", "length": 24182, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_05.jpg", "length": 22713, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_06.jpg", "length": 22444, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_07.jpg", "length": 21010, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_08.jpg", "length": 19515, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_09.jpg", "length": 21054, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_10.jpg", "length": 21984, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_11.jpg", "length": 19574, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_12.jpg", "length": 21829, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_13.jpg", "length": 18970, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_14.jpg", "length": 22405, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_15.jpg", "length": 21821, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_16.jpg", "length": 18915, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_17.jpg", "length": 19210, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_18.jpg", "length": 18982, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0049/files/clusters_01_screenshot_19.jpg", "length": 20125, "contentType": "application/octet-stream", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0049/files/pocket_01.pdb", "length": 4556, "contentType": "chemical/x-pdb", "metadata": {"project": "6840b149c79430af3b36cc0d", "md": 0}}]}
A004L/project.json ADDED
@@ -0,0 +1,199 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A004L",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 3C9A",
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
+ "3C9A"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "Q00805",
31
+ "Q01083"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "DRDVRILYQVGDSEEDLPVCAPNAVCSKIDLYETPWIERQCRCPDGRTCPSSLGVEDGHTIADKTRHYKMCQPVHKLPVCKHFRDYTWTLTTAAELNVTEQIVHCRCPRNSVTYLTKREPIGNDSPGYRYLFACSPLTRLRCQRKQPCKLFTVRKRQEFLDEVNINSLCQCPKGHRCPSHHTQSGVIAGESFLEDNIQTYSGYCMAN",
38
+ "PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Protein giant-lens",
43
+ "Protein spitz",
44
+ "EGF-like"
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": 3991,
56
+ "SYSTRES": 255,
57
+ "PROTATS": 3991,
58
+ "PROTRES": 255,
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": 8.55642,
90
+ "BOXSIZEY": 8.55642,
91
+ "BOXSIZEZ": 6.04081,
92
+ "mdName": "replica 1",
93
+ "mdAtoms": 3991,
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
+ "pca_trajectory_18.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_01_screenshot_00.jpg",
147
+ "clusters_01_screenshot_01.jpg",
148
+ "clusters_01_screenshot_02.jpg",
149
+ "clusters_01_screenshot_03.jpg",
150
+ "clusters_01_screenshot_04.jpg",
151
+ "clusters_01_screenshot_05.jpg",
152
+ "clusters_01_screenshot_06.jpg",
153
+ "clusters_01_screenshot_07.jpg",
154
+ "clusters_01_screenshot_08.jpg",
155
+ "clusters_01_screenshot_09.jpg",
156
+ "clusters_01_screenshot_10.jpg",
157
+ "clusters_01_screenshot_11.jpg",
158
+ "clusters_01_screenshot_12.jpg",
159
+ "clusters_01_screenshot_13.jpg",
160
+ "clusters_01_screenshot_14.jpg",
161
+ "clusters_01_screenshot_15.jpg",
162
+ "clusters_01_screenshot_16.jpg",
163
+ "clusters_01_screenshot_17.jpg",
164
+ "clusters_01_screenshot_18.jpg",
165
+ "clusters_01_screenshot_19.jpg",
166
+ "pocket_01.pdb",
167
+ "pocket_02.pdb",
168
+ "pocket_03.pdb",
169
+ "pocket_04.pdb",
170
+ "pocket_05.pdb",
171
+ "pocket_06.pdb",
172
+ "pocket_07.pdb",
173
+ "pocket_08.pdb"
174
+ ],
175
+ "analyses": [
176
+ "clusters",
177
+ "clusters-00",
178
+ "clusters-01",
179
+ "dist-perres",
180
+ "energies",
181
+ "fluctuation",
182
+ "hbonds",
183
+ "interactions",
184
+ "pca",
185
+ "pockets",
186
+ "rgyr",
187
+ "rmsd-pairwise",
188
+ "rmsd-perres",
189
+ "rmsds",
190
+ "sasa",
191
+ "tmscores"
192
+ ],
193
+ "mdIndex": 0,
194
+ "mdNumber": 1,
195
+ "refframe": 0,
196
+ "internalId": "6840cd477aee7e4da27517bb",
197
+ "creationDate": "2025-06-04T22:48:39.000Z",
198
+ "identifier": "A004L"
199
+ }
A004L/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A004L", "accession": "A004L", "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 3C9A", "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": ["3C9A"], "FORCED_REFERENCES": null, "REFERENCES": ["Q00805", "Q01083"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DRDVRILYQVGDSEEDLPVCAPNAVCSKIDLYETPWIERQCRCPDGRTCPSSLGVEDGHTIADKTRHYKMCQPVHKLPVCKHFRDYTWTLTTAAELNVTEQIVHCRCPRNSVTYLTKREPIGNDSPGYRYLFACSPLTRLRCQRKQPCKLFTVRKRQEFLDEVNINSLCQCPKGHRCPSHHTQSGVIAGESFLEDNIQTYSGYCMAN", "PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE"], "NUCLSEQ": [], "DOMAINS": ["Protein giant-lens", "Protein spitz", "EGF-like"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3991, "SYSTRES": 255, "PROTATS": 3991, "PROTRES": 255, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.55642, "BOXSIZEY": 8.55642, "BOXSIZEZ": 6.04081, "mdName": "replica 1", "mdAtoms": 3991, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A004L/files/topology.tpr", "length": 1370384, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A004L/files/screenshot.jpg", "length": 22328, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A004L/files/trajectory.bin", "length": 239507892, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 5001, "atoms": 3991}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_01.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_02.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_03.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_04.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_05.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_06.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_07.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_08.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_09.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_10.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_11.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_12.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_13.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_14.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_15.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_16.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_17.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_18.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "structure.pdb", "downloadUrl": "/projects/A004L/files/structure.pdb", "length": 323306, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A004L/files/trajectory.xtc", "length": 76203640, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_00.jpg", "length": 23646, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_01.jpg", "length": 24001, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_02.jpg", "length": 23926, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_03.jpg", "length": 24197, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_04.jpg", "length": 23914, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_05.jpg", "length": 24443, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_06.jpg", "length": 24495, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_07.jpg", "length": 24364, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_08.jpg", "length": 24347, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_09.jpg", "length": 24257, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_10.jpg", "length": 23639, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_11.jpg", "length": 23322, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_12.jpg", "length": 24237, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_13.jpg", "length": 23963, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_14.jpg", "length": 23508, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_15.jpg", "length": 24403, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_16.jpg", "length": 24385, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_17.jpg", "length": 24043, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_18.jpg", "length": 23891, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_19.jpg", "length": 24166, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_00.jpg", "length": 23386, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_01.jpg", "length": 23335, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_02.jpg", "length": 23650, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_03.jpg", "length": 22984, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_04.jpg", "length": 23651, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_05.jpg", "length": 23805, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_06.jpg", "length": 23657, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_07.jpg", "length": 23935, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_08.jpg", "length": 23126, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_09.jpg", "length": 23492, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_10.jpg", "length": 23961, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_11.jpg", "length": 23616, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_12.jpg", "length": 23886, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_13.jpg", "length": 23088, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_14.jpg", "length": 23257, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_15.jpg", "length": 23734, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_16.jpg", "length": 23626, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_17.jpg", "length": 23774, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_18.jpg", "length": 22998, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_19.jpg", "length": 23762, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A004L/files/pocket_01.pdb", "length": 58424, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A004L/files/pocket_02.pdb", "length": 22713, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A004L/files/pocket_03.pdb", "length": 13266, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A004L/files/pocket_04.pdb", "length": 12864, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A004L/files/pocket_05.pdb", "length": 10519, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A004L/files/pocket_06.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A004L/files/pocket_07.pdb", "length": 6365, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A004L/files/pocket_08.pdb", "length": 6030, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}]}
2
+ {"project_identifier": "A004L", "accession": "A004L", "published": true, "md_index": 1, "md_name": "replica 2", "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 3C9A", "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": ["3C9A"], "FORCED_REFERENCES": null, "REFERENCES": ["Q00805", "Q01083"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DRDVRILYQVGDSEEDLPVCAPNAVCSKIDLYETPWIERQCRCPDGRTCPSSLGVEDGHTIADKTRHYKMCQPVHKLPVCKHFRDYTWTLTTAAELNVTEQIVHCRCPRNSVTYLTKREPIGNDSPGYRYLFACSPLTRLRCQRKQPCKLFTVRKRQEFLDEVNINSLCQCPKGHRCPSHHTQSGVIAGESFLEDNIQTYSGYCMAN", "PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE"], "NUCLSEQ": [], "DOMAINS": ["Protein giant-lens", "Protein spitz", "EGF-like"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3991, "SYSTRES": 255, "PROTATS": 3991, "PROTRES": 255, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.55642, "BOXSIZEY": 8.55642, "BOXSIZEZ": 6.04081, "mdName": "replica 1", "mdAtoms": 3991, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A004L/files/topology.tpr", "length": 1370384, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A004L/files/screenshot.jpg", "length": 22328, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A004L/files/trajectory.bin", "length": 239507892, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 5001, "atoms": 3991}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_01.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_02.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_03.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_04.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_05.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_06.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_07.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_08.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_09.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_10.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_11.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_12.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_13.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_14.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_15.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_16.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_17.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_18.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "structure.pdb", "downloadUrl": "/projects/A004L/files/structure.pdb", "length": 323306, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A004L/files/trajectory.xtc", "length": 76203640, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_00.jpg", "length": 23646, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_01.jpg", "length": 24001, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_02.jpg", "length": 23926, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_03.jpg", "length": 24197, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_04.jpg", "length": 23914, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_05.jpg", "length": 24443, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_06.jpg", "length": 24495, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_07.jpg", "length": 24364, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_08.jpg", "length": 24347, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_09.jpg", "length": 24257, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_10.jpg", "length": 23639, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_11.jpg", "length": 23322, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_12.jpg", "length": 24237, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_13.jpg", "length": 23963, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_14.jpg", "length": 23508, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_15.jpg", "length": 24403, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_16.jpg", "length": 24385, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_17.jpg", "length": 24043, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_18.jpg", "length": 23891, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_19.jpg", "length": 24166, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_00.jpg", "length": 23386, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_01.jpg", "length": 23335, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_02.jpg", "length": 23650, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_03.jpg", "length": 22984, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_04.jpg", "length": 23651, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_05.jpg", "length": 23805, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_06.jpg", "length": 23657, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_07.jpg", "length": 23935, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_08.jpg", "length": 23126, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_09.jpg", "length": 23492, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_10.jpg", "length": 23961, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_11.jpg", "length": 23616, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_12.jpg", "length": 23886, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_13.jpg", "length": 23088, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_14.jpg", "length": 23257, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_15.jpg", "length": 23734, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_16.jpg", "length": 23626, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_17.jpg", "length": 23774, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_18.jpg", "length": 22998, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_19.jpg", "length": 23762, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A004L/files/pocket_01.pdb", "length": 58424, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A004L/files/pocket_02.pdb", "length": 22713, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A004L/files/pocket_03.pdb", "length": 13266, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A004L/files/pocket_04.pdb", "length": 12864, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A004L/files/pocket_05.pdb", "length": 10519, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A004L/files/pocket_06.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A004L/files/pocket_07.pdb", "length": 6365, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A004L/files/pocket_08.pdb", "length": 6030, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}]}
3
+ {"project_identifier": "A004L", "accession": "A004L", "published": true, "md_index": 2, "md_name": "replica 3", "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 3C9A", "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": ["3C9A"], "FORCED_REFERENCES": null, "REFERENCES": ["Q00805", "Q01083"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["DRDVRILYQVGDSEEDLPVCAPNAVCSKIDLYETPWIERQCRCPDGRTCPSSLGVEDGHTIADKTRHYKMCQPVHKLPVCKHFRDYTWTLTTAAELNVTEQIVHCRCPRNSVTYLTKREPIGNDSPGYRYLFACSPLTRLRCQRKQPCKLFTVRKRQEFLDEVNINSLCQCPKGHRCPSHHTQSGVIAGESFLEDNIQTYSGYCMAN", "PTYKCPETFDAWYCLNDAHCFAVKIADLPVYSCECAIGFMGQRCEYKE"], "NUCLSEQ": [], "DOMAINS": ["Protein giant-lens", "Protein spitz", "EGF-like"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3991, "SYSTRES": 255, "PROTATS": 3991, "PROTRES": 255, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.55642, "BOXSIZEY": 8.55642, "BOXSIZEZ": 6.04081, "mdName": "replica 1", "mdAtoms": 3991, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A004L/files/topology.tpr", "length": 1370384, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A004L/files/screenshot.jpg", "length": 22328, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A004L/files/trajectory.bin", "length": 239507892, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 5001, "atoms": 3991}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_01.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_02.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_03.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_04.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_05.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_06.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_07.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_08.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_09.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_10.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_10.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_11.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_11.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_12.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_12.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_13.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_13.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_14.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_14.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_15.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_15.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_16.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_16.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_17.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_17.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "pca_trajectory_18.bin", "downloadUrl": "/projects/A004L/files/pca_trajectory_18.bin", "length": 183600, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0, "frames": 20, "atoms": 765}}, {"name": "structure.pdb", "downloadUrl": "/projects/A004L/files/structure.pdb", "length": 323306, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A004L/files/trajectory.xtc", "length": 76203640, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_00.jpg", "length": 23646, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_01.jpg", "length": 24001, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_02.jpg", "length": 23926, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_03.jpg", "length": 24197, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_04.jpg", "length": 23914, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_05.jpg", "length": 24443, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_06.jpg", "length": 24495, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_07.jpg", "length": 24364, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_08.jpg", "length": 24347, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_09.jpg", "length": 24257, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_10.jpg", "length": 23639, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_11.jpg", "length": 23322, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_12.jpg", "length": 24237, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_13.jpg", "length": 23963, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_14.jpg", "length": 23508, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_15.jpg", "length": 24403, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_16.jpg", "length": 24385, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_17.jpg", "length": 24043, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_18.jpg", "length": 23891, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A004L/files/clusters_00_screenshot_19.jpg", "length": 24166, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_00.jpg", "length": 23386, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_01.jpg", "length": 23335, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_02.jpg", "length": 23650, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_03.jpg", "length": 22984, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_04.jpg", "length": 23651, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_05.jpg", "length": 23805, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_06.jpg", "length": 23657, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_07.jpg", "length": 23935, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_08.jpg", "length": 23126, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_09.jpg", "length": 23492, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_10.jpg", "length": 23961, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_11.jpg", "length": 23616, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_12.jpg", "length": 23886, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_13.jpg", "length": 23088, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_14.jpg", "length": 23257, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_15.jpg", "length": 23734, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_16.jpg", "length": 23626, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_17.jpg", "length": 23774, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_18.jpg", "length": 22998, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A004L/files/clusters_01_screenshot_19.jpg", "length": 23762, "contentType": "application/octet-stream", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A004L/files/pocket_01.pdb", "length": 58424, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A004L/files/pocket_02.pdb", "length": 22713, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A004L/files/pocket_03.pdb", "length": 13266, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A004L/files/pocket_04.pdb", "length": 12864, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A004L/files/pocket_05.pdb", "length": 10519, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A004L/files/pocket_06.pdb", "length": 6901, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A004L/files/pocket_07.pdb", "length": 6365, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A004L/files/pocket_08.pdb", "length": 6030, "contentType": "chemical/x-pdb", "metadata": {"project": "6840cd477aee7e4da27517bb", "md": 0}}]}
A004M/project.json ADDED
@@ -0,0 +1,306 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A004M",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 3CQX",
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
+ "3CQX"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P63017",
31
+ "Q91YN9"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "SEESLKHATRIIDEVVSKFLDDLGNAKSHLMSLYSACSSEVPPGPVDQKFQSIVIGCALEDQKKIKRRLETLLRNIDNSDKAIK",
38
+ "PAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS",
39
+ "ESLKHATRIIDEVVSKFLDDLGNAKSHLMSLYSACSSEVPPGPVDQKFQSIVIGCALEDQKKIKRRLETLLRNIDNSDKAI",
40
+ "AVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS"
41
+ ],
42
+ "NUCLSEQ": [],
43
+ "DOMAINS": [
44
+ "Heat shock cognate 71 kDa protein",
45
+ "Nucleotide-binding domain (NBD)",
46
+ "Interaction with BAG1",
47
+ "BAG family molecular chaperone regulator 2",
48
+ "BAG"
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": 14320,
60
+ "SYSTRES": 918,
61
+ "PROTATS": 14320,
62
+ "PROTRES": 918,
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 C interaction",
77
+ "agent_1": "chain A",
78
+ "agent_2": "chain C",
79
+ "selection_1": "chain A",
80
+ "selection_2": "chain B",
81
+ "type": "protein-protein"
82
+ },
83
+ {
84
+ "name": "chain A-chain D interaction",
85
+ "agent_1": "chain A",
86
+ "agent_2": "chain D",
87
+ "selection_1": "chain A",
88
+ "selection_2": "chain C",
89
+ "type": "protein-protein"
90
+ },
91
+ {
92
+ "name": "chain B-chain C interaction",
93
+ "agent_1": "chain B",
94
+ "agent_2": "chain C",
95
+ "selection_1": "chain A",
96
+ "selection_2": "chain D",
97
+ "type": "protein-protein"
98
+ },
99
+ {
100
+ "name": "chain B-chain D interaction",
101
+ "agent_1": "chain B",
102
+ "agent_2": "chain D",
103
+ "selection_1": "chain B",
104
+ "selection_2": "chain C",
105
+ "type": "protein-protein"
106
+ },
107
+ {
108
+ "name": "chain C-chain D interaction",
109
+ "agent_1": "chain C",
110
+ "agent_2": "chain D",
111
+ "selection_1": "chain B",
112
+ "selection_2": "chain D",
113
+ "type": "protein-protein"
114
+ }
115
+ ],
116
+ "PBC_SELECTION": null,
117
+ "CHAINNAMES": null,
118
+ "MEMBRANES": null,
119
+ "CUSTOMS": null,
120
+ "ORIENTATION": null,
121
+ "PTM": [],
122
+ "MULTIMERIC": null,
123
+ "COLLECTIONS": "dynarepo",
124
+ "WARNINGS": [],
125
+ "BOXSIZEX": 14.6656,
126
+ "BOXSIZEY": 14.6656,
127
+ "BOXSIZEZ": 10.3637,
128
+ "mdName": "replica 1",
129
+ "mdAtoms": 14320,
130
+ "mdFrames": 5001
131
+ },
132
+ "mds": [
133
+ "replica 1",
134
+ "replica 2",
135
+ "replica 3"
136
+ ],
137
+ "mdref": 0,
138
+ "files": [
139
+ "topology.tpr",
140
+ "screenshot.jpg",
141
+ "trajectory.bin",
142
+ "pca_trajectory_01.bin",
143
+ "pca_trajectory_02.bin",
144
+ "pca_trajectory_03.bin",
145
+ "pca_trajectory_04.bin",
146
+ "pca_trajectory_05.bin",
147
+ "pca_trajectory_06.bin",
148
+ "structure.pdb",
149
+ "trajectory.xtc",
150
+ "clusters_00_screenshot_00.jpg",
151
+ "clusters_00_screenshot_01.jpg",
152
+ "clusters_00_screenshot_02.jpg",
153
+ "clusters_00_screenshot_03.jpg",
154
+ "clusters_00_screenshot_04.jpg",
155
+ "clusters_00_screenshot_05.jpg",
156
+ "clusters_00_screenshot_06.jpg",
157
+ "clusters_00_screenshot_07.jpg",
158
+ "clusters_00_screenshot_08.jpg",
159
+ "clusters_00_screenshot_09.jpg",
160
+ "clusters_00_screenshot_10.jpg",
161
+ "clusters_00_screenshot_11.jpg",
162
+ "clusters_00_screenshot_12.jpg",
163
+ "clusters_00_screenshot_13.jpg",
164
+ "clusters_00_screenshot_14.jpg",
165
+ "clusters_00_screenshot_15.jpg",
166
+ "clusters_00_screenshot_16.jpg",
167
+ "clusters_00_screenshot_17.jpg",
168
+ "clusters_00_screenshot_18.jpg",
169
+ "clusters_00_screenshot_19.jpg",
170
+ "clusters_01_screenshot_00.jpg",
171
+ "clusters_01_screenshot_01.jpg",
172
+ "clusters_01_screenshot_02.jpg",
173
+ "clusters_01_screenshot_03.jpg",
174
+ "clusters_01_screenshot_04.jpg",
175
+ "clusters_01_screenshot_05.jpg",
176
+ "clusters_01_screenshot_06.jpg",
177
+ "clusters_01_screenshot_07.jpg",
178
+ "clusters_01_screenshot_08.jpg",
179
+ "clusters_01_screenshot_09.jpg",
180
+ "clusters_01_screenshot_10.jpg",
181
+ "clusters_01_screenshot_11.jpg",
182
+ "clusters_01_screenshot_12.jpg",
183
+ "clusters_01_screenshot_13.jpg",
184
+ "clusters_01_screenshot_14.jpg",
185
+ "clusters_01_screenshot_15.jpg",
186
+ "clusters_01_screenshot_16.jpg",
187
+ "clusters_01_screenshot_17.jpg",
188
+ "clusters_01_screenshot_18.jpg",
189
+ "clusters_02_screenshot_00.jpg",
190
+ "clusters_02_screenshot_01.jpg",
191
+ "clusters_02_screenshot_02.jpg",
192
+ "clusters_02_screenshot_03.jpg",
193
+ "clusters_02_screenshot_04.jpg",
194
+ "clusters_02_screenshot_05.jpg",
195
+ "clusters_02_screenshot_06.jpg",
196
+ "clusters_02_screenshot_07.jpg",
197
+ "clusters_02_screenshot_08.jpg",
198
+ "clusters_02_screenshot_09.jpg",
199
+ "clusters_02_screenshot_10.jpg",
200
+ "clusters_02_screenshot_11.jpg",
201
+ "clusters_02_screenshot_12.jpg",
202
+ "clusters_02_screenshot_13.jpg",
203
+ "clusters_02_screenshot_14.jpg",
204
+ "clusters_02_screenshot_15.jpg",
205
+ "clusters_02_screenshot_16.jpg",
206
+ "clusters_02_screenshot_17.jpg",
207
+ "clusters_02_screenshot_18.jpg",
208
+ "clusters_02_screenshot_19.jpg",
209
+ "clusters_03_screenshot_00.jpg",
210
+ "clusters_03_screenshot_01.jpg",
211
+ "clusters_03_screenshot_02.jpg",
212
+ "clusters_03_screenshot_03.jpg",
213
+ "clusters_03_screenshot_04.jpg",
214
+ "clusters_03_screenshot_05.jpg",
215
+ "clusters_03_screenshot_06.jpg",
216
+ "clusters_03_screenshot_07.jpg",
217
+ "clusters_03_screenshot_08.jpg",
218
+ "clusters_03_screenshot_09.jpg",
219
+ "clusters_03_screenshot_10.jpg",
220
+ "clusters_03_screenshot_11.jpg",
221
+ "clusters_03_screenshot_12.jpg",
222
+ "clusters_03_screenshot_13.jpg",
223
+ "clusters_03_screenshot_14.jpg",
224
+ "clusters_03_screenshot_15.jpg",
225
+ "clusters_03_screenshot_16.jpg",
226
+ "clusters_03_screenshot_17.jpg",
227
+ "clusters_03_screenshot_18.jpg",
228
+ "clusters_04_screenshot_00.jpg",
229
+ "clusters_04_screenshot_01.jpg",
230
+ "clusters_04_screenshot_02.jpg",
231
+ "clusters_04_screenshot_03.jpg",
232
+ "clusters_04_screenshot_04.jpg",
233
+ "clusters_04_screenshot_05.jpg",
234
+ "clusters_04_screenshot_06.jpg",
235
+ "clusters_04_screenshot_07.jpg",
236
+ "clusters_04_screenshot_08.jpg",
237
+ "clusters_04_screenshot_09.jpg",
238
+ "clusters_04_screenshot_10.jpg",
239
+ "clusters_04_screenshot_11.jpg",
240
+ "clusters_04_screenshot_12.jpg",
241
+ "clusters_04_screenshot_13.jpg",
242
+ "clusters_04_screenshot_14.jpg",
243
+ "clusters_04_screenshot_15.jpg",
244
+ "clusters_04_screenshot_16.jpg",
245
+ "clusters_04_screenshot_17.jpg",
246
+ "clusters_04_screenshot_18.jpg",
247
+ "clusters_05_screenshot_00.jpg",
248
+ "clusters_05_screenshot_01.jpg",
249
+ "clusters_05_screenshot_02.jpg",
250
+ "clusters_05_screenshot_03.jpg",
251
+ "clusters_05_screenshot_04.jpg",
252
+ "clusters_05_screenshot_05.jpg",
253
+ "clusters_05_screenshot_06.jpg",
254
+ "clusters_05_screenshot_07.jpg",
255
+ "clusters_05_screenshot_08.jpg",
256
+ "clusters_05_screenshot_09.jpg",
257
+ "clusters_05_screenshot_10.jpg",
258
+ "clusters_05_screenshot_11.jpg",
259
+ "clusters_05_screenshot_12.jpg",
260
+ "clusters_05_screenshot_13.jpg",
261
+ "clusters_05_screenshot_14.jpg",
262
+ "clusters_05_screenshot_15.jpg",
263
+ "clusters_05_screenshot_16.jpg",
264
+ "clusters_05_screenshot_17.jpg",
265
+ "clusters_05_screenshot_18.jpg",
266
+ "clusters_05_screenshot_19.jpg",
267
+ "pocket_01.pdb",
268
+ "pocket_02.pdb",
269
+ "pocket_03.pdb",
270
+ "pocket_04.pdb",
271
+ "pocket_05.pdb",
272
+ "pocket_06.pdb",
273
+ "pocket_07.pdb",
274
+ "pocket_08.pdb",
275
+ "pocket_09.pdb",
276
+ "pocket_10.pdb"
277
+ ],
278
+ "analyses": [
279
+ "clusters",
280
+ "clusters-00",
281
+ "clusters-01",
282
+ "clusters-02",
283
+ "clusters-03",
284
+ "clusters-04",
285
+ "clusters-05",
286
+ "dist-perres",
287
+ "energies",
288
+ "fluctuation",
289
+ "hbonds",
290
+ "interactions",
291
+ "pca",
292
+ "pockets",
293
+ "rgyr",
294
+ "rmsd-pairwise",
295
+ "rmsd-perres",
296
+ "rmsds",
297
+ "sasa",
298
+ "tmscores"
299
+ ],
300
+ "mdIndex": 0,
301
+ "mdNumber": 1,
302
+ "refframe": 0,
303
+ "internalId": "6840d07cf45b2d4b2577a8af",
304
+ "creationDate": "2025-06-04T23:02:20.000Z",
305
+ "identifier": "A004M"
306
+ }
A004M/records.jsonl ADDED
The diff for this file is too large to render. See raw diff
 
A004S/project.json ADDED
@@ -0,0 +1,185 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A004S",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 3EJH",
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
+ "3EJH"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P02751",
31
+ "P02452"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "VVGLPGQRGERGFPG",
38
+ "DQCIVDDITYNVQDTFHKKHEEGHMLNCTCFGQGRGRWKCDPVDQCQDSETGTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQPLQTYP"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "Fibronectin",
43
+ "Fibronectin type-I 8",
44
+ "Fibronectin type-I 9",
45
+ "Collagen-binding",
46
+ "Collagen alpha-1(I) chain",
47
+ "Disordered",
48
+ "Triple-helical region"
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": 1629,
60
+ "SYSTRES": 106,
61
+ "PROTATS": 1629,
62
+ "PROTRES": 106,
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": 8.7781,
94
+ "BOXSIZEY": 8.7781,
95
+ "BOXSIZEZ": 6.21161,
96
+ "mdName": "replica 1",
97
+ "mdAtoms": 1629,
98
+ "mdFrames": 5001
99
+ },
100
+ "mds": [
101
+ "replica 1",
102
+ "replica 2",
103
+ "replica 3"
104
+ ],
105
+ "mdref": 0,
106
+ "files": [
107
+ "topology.tpr",
108
+ "screenshot.jpg",
109
+ "trajectory.bin",
110
+ "pca_trajectory_01.bin",
111
+ "pca_trajectory_02.bin",
112
+ "pca_trajectory_03.bin",
113
+ "pca_trajectory_04.bin",
114
+ "pca_trajectory_05.bin",
115
+ "pca_trajectory_06.bin",
116
+ "pca_trajectory_07.bin",
117
+ "pca_trajectory_08.bin",
118
+ "pca_trajectory_09.bin",
119
+ "structure.pdb",
120
+ "trajectory.xtc",
121
+ "clusters_00_screenshot_00.jpg",
122
+ "clusters_00_screenshot_01.jpg",
123
+ "clusters_00_screenshot_02.jpg",
124
+ "clusters_00_screenshot_03.jpg",
125
+ "clusters_00_screenshot_04.jpg",
126
+ "clusters_00_screenshot_05.jpg",
127
+ "clusters_00_screenshot_06.jpg",
128
+ "clusters_00_screenshot_07.jpg",
129
+ "clusters_00_screenshot_08.jpg",
130
+ "clusters_00_screenshot_09.jpg",
131
+ "clusters_00_screenshot_10.jpg",
132
+ "clusters_00_screenshot_11.jpg",
133
+ "clusters_00_screenshot_12.jpg",
134
+ "clusters_00_screenshot_13.jpg",
135
+ "clusters_00_screenshot_14.jpg",
136
+ "clusters_00_screenshot_15.jpg",
137
+ "clusters_00_screenshot_16.jpg",
138
+ "clusters_00_screenshot_17.jpg",
139
+ "clusters_00_screenshot_18.jpg",
140
+ "clusters_00_screenshot_19.jpg",
141
+ "clusters_01_screenshot_00.jpg",
142
+ "clusters_01_screenshot_01.jpg",
143
+ "clusters_01_screenshot_02.jpg",
144
+ "clusters_01_screenshot_03.jpg",
145
+ "clusters_01_screenshot_04.jpg",
146
+ "clusters_01_screenshot_05.jpg",
147
+ "clusters_01_screenshot_06.jpg",
148
+ "clusters_01_screenshot_07.jpg",
149
+ "clusters_01_screenshot_08.jpg",
150
+ "clusters_01_screenshot_09.jpg",
151
+ "clusters_01_screenshot_10.jpg",
152
+ "clusters_01_screenshot_11.jpg",
153
+ "clusters_01_screenshot_12.jpg",
154
+ "clusters_01_screenshot_13.jpg",
155
+ "clusters_01_screenshot_14.jpg",
156
+ "clusters_01_screenshot_15.jpg",
157
+ "clusters_01_screenshot_16.jpg",
158
+ "clusters_01_screenshot_17.jpg",
159
+ "clusters_01_screenshot_18.jpg",
160
+ "clusters_01_screenshot_19.jpg"
161
+ ],
162
+ "analyses": [
163
+ "clusters",
164
+ "clusters-00",
165
+ "clusters-01",
166
+ "dist-perres",
167
+ "energies",
168
+ "fluctuation",
169
+ "hbonds",
170
+ "interactions",
171
+ "pca",
172
+ "rgyr",
173
+ "rmsd-pairwise",
174
+ "rmsd-perres",
175
+ "rmsds",
176
+ "sasa",
177
+ "tmscores"
178
+ ],
179
+ "mdIndex": 0,
180
+ "mdNumber": 1,
181
+ "refframe": 0,
182
+ "internalId": "6840daf1c6c220e2c0412a8d",
183
+ "creationDate": "2025-06-04T23:46:57.000Z",
184
+ "identifier": "A004S"
185
+ }
A004S/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A004S", "accession": "A004S", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 3EJH", "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": ["3EJH"], "FORCED_REFERENCES": null, "REFERENCES": ["P02751", "P02452"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VVGLPGQRGERGFPG", "DQCIVDDITYNVQDTFHKKHEEGHMLNCTCFGQGRGRWKCDPVDQCQDSETGTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQPLQTYP"], "NUCLSEQ": [], "DOMAINS": ["Fibronectin", "Fibronectin type-I 8", "Fibronectin type-I 9", "Collagen-binding", "Collagen alpha-1(I) chain", "Disordered", "Triple-helical region"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 1629, "SYSTRES": 106, "PROTATS": 1629, "PROTRES": 106, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.7781, "BOXSIZEY": 8.7781, "BOXSIZEZ": 6.21161, "mdName": "replica 1", "mdAtoms": 1629, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A004S/files/topology.tpr", "length": 765088, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A004S/files/screenshot.jpg", "length": 14175, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A004S/files/trajectory.bin", "length": 97759548, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 5001, "atoms": 1629}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_01.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_02.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_03.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_04.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_05.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_06.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_07.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_08.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_09.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "structure.pdb", "downloadUrl": "/projects/A004S/files/structure.pdb", "length": 131984, "contentType": "chemical/x-pdb", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A004S/files/trajectory.xtc", "length": 31319064, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_00.jpg", "length": 11465, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_01.jpg", "length": 11263, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_02.jpg", "length": 11346, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_03.jpg", "length": 11930, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_04.jpg", "length": 11723, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_05.jpg", "length": 11459, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_06.jpg", "length": 11700, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_07.jpg", "length": 11741, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_08.jpg", "length": 11868, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_09.jpg", "length": 11859, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_10.jpg", "length": 11231, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_11.jpg", "length": 11022, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_12.jpg", "length": 11078, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_13.jpg", "length": 11021, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_14.jpg", "length": 10823, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_15.jpg", "length": 11373, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_16.jpg", "length": 11405, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_17.jpg", "length": 11256, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_18.jpg", "length": 10769, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_19.jpg", "length": 11047, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_00.jpg", "length": 13040, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_01.jpg", "length": 13241, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_02.jpg", "length": 13115, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_03.jpg", "length": 12937, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_04.jpg", "length": 13366, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_05.jpg", "length": 13030, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_06.jpg", "length": 12865, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_07.jpg", "length": 13308, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_08.jpg", "length": 12558, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_09.jpg", "length": 13353, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_10.jpg", "length": 13270, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_11.jpg", "length": 12946, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_12.jpg", "length": 12550, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_13.jpg", "length": 13048, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_14.jpg", "length": 12800, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_15.jpg", "length": 11989, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_16.jpg", "length": 12309, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_17.jpg", "length": 12532, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_18.jpg", "length": 12202, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_19.jpg", "length": 12771, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}]}
2
+ {"project_identifier": "A004S", "accession": "A004S", "published": true, "md_index": 1, "md_name": "replica 2", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 3EJH", "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": ["3EJH"], "FORCED_REFERENCES": null, "REFERENCES": ["P02751", "P02452"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VVGLPGQRGERGFPG", "DQCIVDDITYNVQDTFHKKHEEGHMLNCTCFGQGRGRWKCDPVDQCQDSETGTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQPLQTYP"], "NUCLSEQ": [], "DOMAINS": ["Fibronectin", "Fibronectin type-I 8", "Fibronectin type-I 9", "Collagen-binding", "Collagen alpha-1(I) chain", "Disordered", "Triple-helical region"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 1629, "SYSTRES": 106, "PROTATS": 1629, "PROTRES": 106, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.7781, "BOXSIZEY": 8.7781, "BOXSIZEZ": 6.21161, "mdName": "replica 1", "mdAtoms": 1629, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A004S/files/topology.tpr", "length": 765088, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A004S/files/screenshot.jpg", "length": 14175, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A004S/files/trajectory.bin", "length": 97759548, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 5001, "atoms": 1629}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_01.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_02.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_03.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_04.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_05.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_06.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_07.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_08.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_09.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "structure.pdb", "downloadUrl": "/projects/A004S/files/structure.pdb", "length": 131984, "contentType": "chemical/x-pdb", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A004S/files/trajectory.xtc", "length": 31319064, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_00.jpg", "length": 11465, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_01.jpg", "length": 11263, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_02.jpg", "length": 11346, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_03.jpg", "length": 11930, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_04.jpg", "length": 11723, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_05.jpg", "length": 11459, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_06.jpg", "length": 11700, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_07.jpg", "length": 11741, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_08.jpg", "length": 11868, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_09.jpg", "length": 11859, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_10.jpg", "length": 11231, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_11.jpg", "length": 11022, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_12.jpg", "length": 11078, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_13.jpg", "length": 11021, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_14.jpg", "length": 10823, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_15.jpg", "length": 11373, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_16.jpg", "length": 11405, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_17.jpg", "length": 11256, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_18.jpg", "length": 10769, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_19.jpg", "length": 11047, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_00.jpg", "length": 13040, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_01.jpg", "length": 13241, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_02.jpg", "length": 13115, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_03.jpg", "length": 12937, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_04.jpg", "length": 13366, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_05.jpg", "length": 13030, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_06.jpg", "length": 12865, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_07.jpg", "length": 13308, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_08.jpg", "length": 12558, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_09.jpg", "length": 13353, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_10.jpg", "length": 13270, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_11.jpg", "length": 12946, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_12.jpg", "length": 12550, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_13.jpg", "length": 13048, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_14.jpg", "length": 12800, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_15.jpg", "length": 11989, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_16.jpg", "length": 12309, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_17.jpg", "length": 12532, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_18.jpg", "length": 12202, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_19.jpg", "length": 12771, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}]}
3
+ {"project_identifier": "A004S", "accession": "A004S", "published": true, "md_index": 2, "md_name": "replica 3", "analyses": ["clusters", "clusters-00", "clusters-01", "dist-perres", "energies", "fluctuation", "hbonds", "interactions", "pca", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 3EJH", "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": ["3EJH"], "FORCED_REFERENCES": null, "REFERENCES": ["P02751", "P02452"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["VVGLPGQRGERGFPG", "DQCIVDDITYNVQDTFHKKHEEGHMLNCTCFGQGRGRWKCDPVDQCQDSETGTFYQIGDSWEKYVHGVRYQCYCYGRGIGEWHCQPLQTYP"], "NUCLSEQ": [], "DOMAINS": ["Fibronectin", "Fibronectin type-I 8", "Fibronectin type-I 9", "Collagen-binding", "Collagen alpha-1(I) chain", "Disordered", "Triple-helical region"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 1629, "SYSTRES": 106, "PROTATS": 1629, "PROTRES": 106, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.7781, "BOXSIZEY": 8.7781, "BOXSIZEZ": 6.21161, "mdName": "replica 1", "mdAtoms": 1629, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A004S/files/topology.tpr", "length": 765088, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A004S/files/screenshot.jpg", "length": 14175, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A004S/files/trajectory.bin", "length": 97759548, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 5001, "atoms": 1629}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_01.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_02.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_03.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_04.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_05.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_06.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_07.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_08.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_08.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "pca_trajectory_09.bin", "downloadUrl": "/projects/A004S/files/pca_trajectory_09.bin", "length": 76320, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0, "frames": 20, "atoms": 318}}, {"name": "structure.pdb", "downloadUrl": "/projects/A004S/files/structure.pdb", "length": 131984, "contentType": "chemical/x-pdb", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A004S/files/trajectory.xtc", "length": 31319064, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_00.jpg", "length": 11465, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_01.jpg", "length": 11263, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_02.jpg", "length": 11346, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_03.jpg", "length": 11930, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_04.jpg", "length": 11723, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_05.jpg", "length": 11459, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_06.jpg", "length": 11700, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_07.jpg", "length": 11741, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_08.jpg", "length": 11868, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_09.jpg", "length": 11859, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_10.jpg", "length": 11231, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_11.jpg", "length": 11022, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_12.jpg", "length": 11078, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_13.jpg", "length": 11021, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_14.jpg", "length": 10823, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_15.jpg", "length": 11373, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_16.jpg", "length": 11405, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_17.jpg", "length": 11256, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_18.jpg", "length": 10769, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A004S/files/clusters_00_screenshot_19.jpg", "length": 11047, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_00.jpg", "length": 13040, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_01.jpg", "length": 13241, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_02.jpg", "length": 13115, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_03.jpg", "length": 12937, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_04.jpg", "length": 13366, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_05.jpg", "length": 13030, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_06.jpg", "length": 12865, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_07.jpg", "length": 13308, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_08.jpg", "length": 12558, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_09.jpg", "length": 13353, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_10.jpg", "length": 13270, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_11.jpg", "length": 12946, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_12.jpg", "length": 12550, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_13.jpg", "length": 13048, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_14.jpg", "length": 12800, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_15.jpg", "length": 11989, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_16.jpg", "length": 12309, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_17.jpg", "length": 12532, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_18.jpg", "length": 12202, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A004S/files/clusters_01_screenshot_19.jpg", "length": 12771, "contentType": "application/octet-stream", "metadata": {"project": "6840daf1c6c220e2c0412a8d", "md": 0}}]}
A0050/project.json ADDED
@@ -0,0 +1,191 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0050",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 3GJ8",
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
+ "3GJ8"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "P62826",
31
+ "P49791"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "EPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTAL",
38
+ "GSWDXEVXLVQNKADSTKXIAXESAKP"
39
+ ],
40
+ "NUCLSEQ": [],
41
+ "DOMAINS": [
42
+ "GTP-binding nuclear protein Ran",
43
+ "Essential for GTP hydrolysis",
44
+ "Nuclear pore complex protein Nup153",
45
+ "29 X 2 AA repeats of F-G"
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": 3669,
57
+ "SYSTRES": 231,
58
+ "PROTATS": 3669,
59
+ "PROTRES": 231,
60
+ "NUCLATS": 0,
61
+ "NUCLRES": 0,
62
+ "LIPIATS": 0,
63
+ "LIPIRES": 0,
64
+ "CARBATS": 0,
65
+ "CARBRES": 0,
66
+ "SOLVATS": 0,
67
+ "SOLVRES": 0,
68
+ "COUNCAT": 0,
69
+ "COUNANI": 0,
70
+ "COUNION": 0,
71
+ "INTERACTIONS": [
72
+ {
73
+ "name": "chain A-chain B interaction",
74
+ "agent_1": "chain A",
75
+ "agent_2": "chain B",
76
+ "selection_1": "chain A",
77
+ "selection_2": "chain B",
78
+ "type": "protein-protein"
79
+ }
80
+ ],
81
+ "PBC_SELECTION": null,
82
+ "CHAINNAMES": null,
83
+ "MEMBRANES": null,
84
+ "CUSTOMS": null,
85
+ "ORIENTATION": null,
86
+ "PTM": [],
87
+ "MULTIMERIC": null,
88
+ "COLLECTIONS": "dynarepo",
89
+ "WARNINGS": [],
90
+ "BOXSIZEX": 8.34008,
91
+ "BOXSIZEY": 8.34008,
92
+ "BOXSIZEZ": 5.91347,
93
+ "mdName": "replica 1",
94
+ "mdAtoms": 3669,
95
+ "mdFrames": 5001
96
+ },
97
+ "mds": [
98
+ "replica 1",
99
+ "replica 2",
100
+ "replica 3"
101
+ ],
102
+ "mdref": 0,
103
+ "files": [
104
+ "topology.tpr",
105
+ "screenshot.jpg",
106
+ "trajectory.bin",
107
+ "pca_trajectory_01.bin",
108
+ "pca_trajectory_02.bin",
109
+ "pca_trajectory_03.bin",
110
+ "pca_trajectory_04.bin",
111
+ "pca_trajectory_05.bin",
112
+ "pca_trajectory_06.bin",
113
+ "pca_trajectory_07.bin",
114
+ "structure.pdb",
115
+ "trajectory.xtc",
116
+ "clusters_00_screenshot_00.jpg",
117
+ "clusters_00_screenshot_01.jpg",
118
+ "clusters_00_screenshot_02.jpg",
119
+ "clusters_00_screenshot_03.jpg",
120
+ "clusters_00_screenshot_04.jpg",
121
+ "clusters_00_screenshot_05.jpg",
122
+ "clusters_00_screenshot_06.jpg",
123
+ "clusters_00_screenshot_07.jpg",
124
+ "clusters_00_screenshot_08.jpg",
125
+ "clusters_00_screenshot_09.jpg",
126
+ "clusters_00_screenshot_10.jpg",
127
+ "clusters_00_screenshot_11.jpg",
128
+ "clusters_00_screenshot_12.jpg",
129
+ "clusters_00_screenshot_13.jpg",
130
+ "clusters_00_screenshot_14.jpg",
131
+ "clusters_00_screenshot_15.jpg",
132
+ "clusters_00_screenshot_16.jpg",
133
+ "clusters_00_screenshot_17.jpg",
134
+ "clusters_00_screenshot_18.jpg",
135
+ "clusters_00_screenshot_19.jpg",
136
+ "clusters_01_screenshot_00.jpg",
137
+ "clusters_01_screenshot_01.jpg",
138
+ "clusters_01_screenshot_02.jpg",
139
+ "clusters_01_screenshot_03.jpg",
140
+ "clusters_01_screenshot_04.jpg",
141
+ "clusters_01_screenshot_05.jpg",
142
+ "clusters_01_screenshot_06.jpg",
143
+ "clusters_01_screenshot_07.jpg",
144
+ "clusters_01_screenshot_08.jpg",
145
+ "clusters_01_screenshot_09.jpg",
146
+ "clusters_01_screenshot_10.jpg",
147
+ "clusters_01_screenshot_11.jpg",
148
+ "clusters_01_screenshot_12.jpg",
149
+ "clusters_01_screenshot_13.jpg",
150
+ "clusters_01_screenshot_14.jpg",
151
+ "clusters_01_screenshot_15.jpg",
152
+ "clusters_01_screenshot_16.jpg",
153
+ "clusters_01_screenshot_17.jpg",
154
+ "clusters_01_screenshot_18.jpg",
155
+ "clusters_01_screenshot_19.jpg",
156
+ "pocket_01.pdb",
157
+ "pocket_02.pdb",
158
+ "pocket_03.pdb",
159
+ "pocket_04.pdb",
160
+ "pocket_05.pdb",
161
+ "pocket_06.pdb",
162
+ "pocket_07.pdb",
163
+ "pocket_08.pdb",
164
+ "pocket_09.pdb",
165
+ "pocket_10.pdb"
166
+ ],
167
+ "analyses": [
168
+ "clusters",
169
+ "clusters-00",
170
+ "clusters-01",
171
+ "dist-perres",
172
+ "energies",
173
+ "fluctuation",
174
+ "hbonds",
175
+ "interactions",
176
+ "pca",
177
+ "pockets",
178
+ "rgyr",
179
+ "rmsd-pairwise",
180
+ "rmsd-perres",
181
+ "rmsds",
182
+ "sasa",
183
+ "tmscores"
184
+ ],
185
+ "mdIndex": 0,
186
+ "mdNumber": 1,
187
+ "refframe": 0,
188
+ "internalId": "6840eaf9e938e1d5bd218352",
189
+ "creationDate": "2025-06-05T00:55:21.000Z",
190
+ "identifier": "A0050"
191
+ }
A0050/records.jsonl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ {"project_identifier": "A0050", "accession": "A0050", "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 3GJ8", "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": ["3GJ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P62826", "P49791"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTAL", "GSWDXEVXLVQNKADSTKXIAXESAKP"], "NUCLSEQ": [], "DOMAINS": ["GTP-binding nuclear protein Ran", "Essential for GTP hydrolysis", "Nuclear pore complex protein Nup153", "29 X 2 AA repeats of F-G"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3669, "SYSTRES": 231, "PROTATS": 3669, "PROTRES": 231, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.34008, "BOXSIZEY": 8.34008, "BOXSIZEZ": 5.91347, "mdName": "replica 1", "mdAtoms": 3669, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0050/files/topology.tpr", "length": 1281032, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0050/files/screenshot.jpg", "length": 19181, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0050/files/trajectory.bin", "length": 220184028, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 5001, "atoms": 3669}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_01.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_02.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_03.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_04.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_05.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_06.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_07.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0050/files/structure.pdb", "length": 297224, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0050/files/trajectory.xtc", "length": 69796556, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_00.jpg", "length": 19947, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_01.jpg", "length": 19933, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_02.jpg", "length": 19786, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_03.jpg", "length": 19779, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_04.jpg", "length": 20189, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_05.jpg", "length": 20409, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_06.jpg", "length": 20238, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_07.jpg", "length": 20312, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_08.jpg", "length": 19927, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_09.jpg", "length": 20201, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_10.jpg", "length": 19816, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_11.jpg", "length": 20112, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_12.jpg", "length": 20307, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_13.jpg", "length": 20141, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_14.jpg", "length": 20219, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_15.jpg", "length": 20646, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_16.jpg", "length": 20009, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_17.jpg", "length": 20488, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_18.jpg", "length": 19666, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_19.jpg", "length": 20804, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_00.jpg", "length": 21264, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_01.jpg", "length": 21563, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_02.jpg", "length": 21064, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_03.jpg", "length": 21176, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_04.jpg", "length": 21420, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_05.jpg", "length": 20809, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_06.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_07.jpg", "length": 21061, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_08.jpg", "length": 21233, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_09.jpg", "length": 21483, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_10.jpg", "length": 20826, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_11.jpg", "length": 20770, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_12.jpg", "length": 21592, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_13.jpg", "length": 21051, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_14.jpg", "length": 21536, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_15.jpg", "length": 21760, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_16.jpg", "length": 21255, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_17.jpg", "length": 21302, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_18.jpg", "length": 21224, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_19.jpg", "length": 21028, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0050/files/pocket_01.pdb", "length": 14271, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0050/files/pocket_02.pdb", "length": 10385, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0050/files/pocket_03.pdb", "length": 9380, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0050/files/pocket_04.pdb", "length": 7906, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0050/files/pocket_05.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0050/files/pocket_06.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0050/files/pocket_07.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0050/files/pocket_08.pdb", "length": 7035, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0050/files/pocket_09.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0050/files/pocket_10.pdb", "length": 1608, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}]}
2
+ {"project_identifier": "A0050", "accession": "A0050", "published": true, "md_index": 1, "md_name": "replica 2", "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 3GJ8", "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": ["3GJ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P62826", "P49791"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTAL", "GSWDXEVXLVQNKADSTKXIAXESAKP"], "NUCLSEQ": [], "DOMAINS": ["GTP-binding nuclear protein Ran", "Essential for GTP hydrolysis", "Nuclear pore complex protein Nup153", "29 X 2 AA repeats of F-G"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3669, "SYSTRES": 231, "PROTATS": 3669, "PROTRES": 231, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.34008, "BOXSIZEY": 8.34008, "BOXSIZEZ": 5.91347, "mdName": "replica 1", "mdAtoms": 3669, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0050/files/topology.tpr", "length": 1281032, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0050/files/screenshot.jpg", "length": 19181, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0050/files/trajectory.bin", "length": 220184028, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 5001, "atoms": 3669}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_01.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_02.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_03.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_04.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_05.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_06.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_07.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0050/files/structure.pdb", "length": 297224, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0050/files/trajectory.xtc", "length": 69796556, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_00.jpg", "length": 19947, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_01.jpg", "length": 19933, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_02.jpg", "length": 19786, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_03.jpg", "length": 19779, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_04.jpg", "length": 20189, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_05.jpg", "length": 20409, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_06.jpg", "length": 20238, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_07.jpg", "length": 20312, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_08.jpg", "length": 19927, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_09.jpg", "length": 20201, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_10.jpg", "length": 19816, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_11.jpg", "length": 20112, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_12.jpg", "length": 20307, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_13.jpg", "length": 20141, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_14.jpg", "length": 20219, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_15.jpg", "length": 20646, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_16.jpg", "length": 20009, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_17.jpg", "length": 20488, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_18.jpg", "length": 19666, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_19.jpg", "length": 20804, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_00.jpg", "length": 21264, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_01.jpg", "length": 21563, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_02.jpg", "length": 21064, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_03.jpg", "length": 21176, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_04.jpg", "length": 21420, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_05.jpg", "length": 20809, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_06.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_07.jpg", "length": 21061, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_08.jpg", "length": 21233, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_09.jpg", "length": 21483, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_10.jpg", "length": 20826, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_11.jpg", "length": 20770, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_12.jpg", "length": 21592, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_13.jpg", "length": 21051, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_14.jpg", "length": 21536, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_15.jpg", "length": 21760, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_16.jpg", "length": 21255, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_17.jpg", "length": 21302, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_18.jpg", "length": 21224, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_19.jpg", "length": 21028, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0050/files/pocket_01.pdb", "length": 14271, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0050/files/pocket_02.pdb", "length": 10385, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0050/files/pocket_03.pdb", "length": 9380, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0050/files/pocket_04.pdb", "length": 7906, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0050/files/pocket_05.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0050/files/pocket_06.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0050/files/pocket_07.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0050/files/pocket_08.pdb", "length": 7035, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0050/files/pocket_09.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0050/files/pocket_10.pdb", "length": 1608, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}]}
3
+ {"project_identifier": "A0050", "accession": "A0050", "published": true, "md_index": 2, "md_name": "replica 3", "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 3GJ8", "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": ["3GJ8"], "FORCED_REFERENCES": null, "REFERENCES": ["P62826", "P49791"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": ["EPQVQFKLVLVGDGGTGKTTFVKRHLTGESEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTAL", "GSWDXEVXLVQNKADSTKXIAXESAKP"], "NUCLSEQ": [], "DOMAINS": ["GTP-binding nuclear protein Ran", "Essential for GTP hydrolysis", "Nuclear pore complex protein Nup153", "29 X 2 AA repeats of F-G"], "FRAMESTEP": 0.1, "TIMESTEP": 2, "TEMP": 310, "ENSEMBLE": "NPT", "FF": ["CHARMM36m"], "WAT": "TIP3P", "BOXTYPE": "Dodecahedron", "SYSTATS": 3669, "SYSTRES": 231, "PROTATS": 3669, "PROTRES": 231, "NUCLATS": 0, "NUCLRES": 0, "LIPIATS": 0, "LIPIRES": 0, "CARBATS": 0, "CARBRES": 0, "SOLVATS": 0, "SOLVRES": 0, "COUNCAT": 0, "COUNANI": 0, "COUNION": 0, "INTERACTIONS": [{"name": "chain A-chain B interaction", "agent_1": "chain A", "agent_2": "chain B", "selection_1": "chain A", "selection_2": "chain B", "type": "protein-protein"}], "PBC_SELECTION": null, "CHAINNAMES": null, "MEMBRANES": null, "CUSTOMS": null, "ORIENTATION": null, "PTM": [], "MULTIMERIC": null, "COLLECTIONS": "dynarepo", "WARNINGS": [], "BOXSIZEX": 8.34008, "BOXSIZEY": 8.34008, "BOXSIZEZ": 5.91347, "mdName": "replica 1", "mdAtoms": 3669, "mdFrames": 5001}, "files": [{"name": "topology.tpr", "downloadUrl": "/projects/A0050/files/topology.tpr", "length": 1281032, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": null}}, {"name": "screenshot.jpg", "downloadUrl": "/projects/A0050/files/screenshot.jpg", "length": 19181, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": null}}, {"name": "trajectory.bin", "downloadUrl": "/projects/A0050/files/trajectory.bin", "length": 220184028, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 5001, "atoms": 3669}}, {"name": "pca_trajectory_01.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_01.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_02.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_02.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_03.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_03.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_04.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_04.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_05.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_05.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_06.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_06.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "pca_trajectory_07.bin", "downloadUrl": "/projects/A0050/files/pca_trajectory_07.bin", "length": 166320, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0, "frames": 20, "atoms": 693}}, {"name": "structure.pdb", "downloadUrl": "/projects/A0050/files/structure.pdb", "length": 297224, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "trajectory.xtc", "downloadUrl": "/projects/A0050/files/trajectory.xtc", "length": 69796556, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_00.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_00.jpg", "length": 19947, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_01.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_01.jpg", "length": 19933, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_02.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_02.jpg", "length": 19786, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_03.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_03.jpg", "length": 19779, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_04.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_04.jpg", "length": 20189, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_05.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_05.jpg", "length": 20409, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_06.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_06.jpg", "length": 20238, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_07.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_07.jpg", "length": 20312, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_08.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_08.jpg", "length": 19927, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_09.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_09.jpg", "length": 20201, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_10.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_10.jpg", "length": 19816, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_11.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_11.jpg", "length": 20112, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_12.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_12.jpg", "length": 20307, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_13.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_13.jpg", "length": 20141, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_14.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_14.jpg", "length": 20219, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_15.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_15.jpg", "length": 20646, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_16.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_16.jpg", "length": 20009, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_17.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_17.jpg", "length": 20488, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_18.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_18.jpg", "length": 19666, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_00_screenshot_19.jpg", "downloadUrl": "/projects/A0050/files/clusters_00_screenshot_19.jpg", "length": 20804, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_00.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_00.jpg", "length": 21264, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_01.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_01.jpg", "length": 21563, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_02.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_02.jpg", "length": 21064, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_03.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_03.jpg", "length": 21176, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_04.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_04.jpg", "length": 21420, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_05.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_05.jpg", "length": 20809, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_06.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_06.jpg", "length": 20906, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_07.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_07.jpg", "length": 21061, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_08.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_08.jpg", "length": 21233, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_09.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_09.jpg", "length": 21483, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_10.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_10.jpg", "length": 20826, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_11.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_11.jpg", "length": 20770, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_12.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_12.jpg", "length": 21592, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_13.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_13.jpg", "length": 21051, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_14.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_14.jpg", "length": 21536, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_15.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_15.jpg", "length": 21760, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_16.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_16.jpg", "length": 21255, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_17.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_17.jpg", "length": 21302, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_18.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_18.jpg", "length": 21224, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "clusters_01_screenshot_19.jpg", "downloadUrl": "/projects/A0050/files/clusters_01_screenshot_19.jpg", "length": 21028, "contentType": "application/octet-stream", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_01.pdb", "downloadUrl": "/projects/A0050/files/pocket_01.pdb", "length": 14271, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_02.pdb", "downloadUrl": "/projects/A0050/files/pocket_02.pdb", "length": 10385, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_03.pdb", "downloadUrl": "/projects/A0050/files/pocket_03.pdb", "length": 9380, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_04.pdb", "downloadUrl": "/projects/A0050/files/pocket_04.pdb", "length": 7906, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_05.pdb", "downloadUrl": "/projects/A0050/files/pocket_05.pdb", "length": 7772, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_06.pdb", "downloadUrl": "/projects/A0050/files/pocket_06.pdb", "length": 7370, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_07.pdb", "downloadUrl": "/projects/A0050/files/pocket_07.pdb", "length": 7102, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_08.pdb", "downloadUrl": "/projects/A0050/files/pocket_08.pdb", "length": 7035, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_09.pdb", "downloadUrl": "/projects/A0050/files/pocket_09.pdb", "length": 3618, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}, {"name": "pocket_10.pdb", "downloadUrl": "/projects/A0050/files/pocket_10.pdb", "length": 1608, "contentType": "chemical/x-pdb", "metadata": {"project": "6840eaf9e938e1d5bd218352", "md": 0}}]}
A0051/project.json ADDED
@@ -0,0 +1,340 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "accession": "A0051",
3
+ "published": true,
4
+ "metadata": {
5
+ "NAME": "Dynarepo 3GS2",
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
+ "3GS2"
27
+ ],
28
+ "FORCED_REFERENCES": null,
29
+ "REFERENCES": [
30
+ "Q99496",
31
+ "O95931"
32
+ ],
33
+ "INPUT_LIGANDS": null,
34
+ "LIGANDS": [],
35
+ "LIGANDNAMES": null,
36
+ "PROTSEQ": [
37
+ "EVTVTDITANSITVTFREAQAAEGFFRDRS",
38
+ "SEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLDGSFSLELVSEKYWKVNKPMELYYAPTK",
39
+ "EVTVTDITANSITVTFREAQAAEGFFRDR",
40
+ "ASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYTIYIATASGQFTVLDGSFSLELVSEKYWKVNKPMELYYAPTK"
41
+ ],
42
+ "NUCLSEQ": [],
43
+ "DOMAINS": [
44
+ "E3 ubiquitin-protein ligase RING2",
45
+ "Chromobox protein homolog 7",
46
+ "Disordered",
47
+ "Required for cellular lifespan extension"
48
+ ],
49
+ "FRAMESTEP": 0.1,
50
+ "TIMESTEP": 2,
51
+ "TEMP": 310,
52
+ "ENSEMBLE": "NPT",
53
+ "FF": [
54
+ "CHARMM36m"
55
+ ],
56
+ "WAT": "TIP3P",
57
+ "BOXTYPE": "Dodecahedron",
58
+ "SYSTATS": 4435,
59
+ "SYSTRES": 280,
60
+ "PROTATS": 4435,
61
+ "PROTRES": 280,
62
+ "NUCLATS": 0,
63
+ "NUCLRES": 0,
64
+ "LIPIATS": 0,
65
+ "LIPIRES": 0,
66
+ "CARBATS": 0,
67
+ "CARBRES": 0,
68
+ "SOLVATS": 0,
69
+ "SOLVRES": 0,
70
+ "COUNCAT": 0,
71
+ "COUNANI": 0,
72
+ "COUNION": 0,
73
+ "INTERACTIONS": [
74
+ {
75
+ "name": "chain A-chain B interaction",
76
+ "agent_1": "chain A",
77
+ "agent_2": "chain B",
78
+ "selection_1": "chain A",
79
+ "selection_2": "chain B",
80
+ "type": "protein-protein"
81
+ },
82
+ {
83
+ "name": "chain A-chain C interaction",
84
+ "agent_1": "chain A",
85
+ "agent_2": "chain C",
86
+ "selection_1": "chain A",
87
+ "selection_2": "chain C",
88
+ "type": "protein-protein"
89
+ },
90
+ {
91
+ "name": "chain A-chain D interaction",
92
+ "agent_1": "chain A",
93
+ "agent_2": "chain D",
94
+ "selection_1": "chain A",
95
+ "selection_2": "chain D",
96
+ "type": "protein-protein"
97
+ },
98
+ {
99
+ "name": "chain B-chain C interaction",
100
+ "agent_1": "chain B",
101
+ "agent_2": "chain C",
102
+ "selection_1": "chain B",
103
+ "selection_2": "chain C",
104
+ "type": "protein-protein"
105
+ },
106
+ {
107
+ "name": "chain B-chain D interaction",
108
+ "agent_1": "chain B",
109
+ "agent_2": "chain D",
110
+ "selection_1": "chain B",
111
+ "selection_2": "chain D",
112
+ "type": "protein-protein"
113
+ },
114
+ {
115
+ "name": "chain C-chain D interaction",
116
+ "agent_1": "chain C",
117
+ "agent_2": "chain D",
118
+ "selection_1": "chain C",
119
+ "selection_2": "chain D",
120
+ "type": "protein-protein"
121
+ }
122
+ ],
123
+ "PBC_SELECTION": null,
124
+ "CHAINNAMES": null,
125
+ "MEMBRANES": null,
126
+ "CUSTOMS": null,
127
+ "ORIENTATION": null,
128
+ "PTM": [],
129
+ "MULTIMERIC": null,
130
+ "COLLECTIONS": "dynarepo",
131
+ "WARNINGS": [],
132
+ "BOXSIZEX": 10.1338,
133
+ "BOXSIZEY": 10.1338,
134
+ "BOXSIZEZ": 7.1493,
135
+ "mdName": "replica 1",
136
+ "mdAtoms": 4435,
137
+ "mdFrames": 5001
138
+ },
139
+ "mds": [
140
+ "replica 1",
141
+ "replica 2",
142
+ "replica 3"
143
+ ],
144
+ "mdref": 0,
145
+ "files": [
146
+ "topology.tpr",
147
+ "screenshot.jpg",
148
+ "trajectory.bin",
149
+ "pca_trajectory_01.bin",
150
+ "pca_trajectory_02.bin",
151
+ "pca_trajectory_03.bin",
152
+ "pca_trajectory_04.bin",
153
+ "pca_trajectory_05.bin",
154
+ "pca_trajectory_06.bin",
155
+ "pca_trajectory_07.bin",
156
+ "pca_trajectory_08.bin",
157
+ "pca_trajectory_09.bin",
158
+ "pca_trajectory_10.bin",
159
+ "pca_trajectory_11.bin",
160
+ "pca_trajectory_12.bin",
161
+ "structure.pdb",
162
+ "trajectory.xtc",
163
+ "clusters_00_screenshot_00.jpg",
164
+ "clusters_00_screenshot_01.jpg",
165
+ "clusters_00_screenshot_02.jpg",
166
+ "clusters_00_screenshot_03.jpg",
167
+ "clusters_00_screenshot_04.jpg",
168
+ "clusters_00_screenshot_05.jpg",
169
+ "clusters_00_screenshot_06.jpg",
170
+ "clusters_00_screenshot_07.jpg",
171
+ "clusters_00_screenshot_08.jpg",
172
+ "clusters_00_screenshot_09.jpg",
173
+ "clusters_00_screenshot_10.jpg",
174
+ "clusters_00_screenshot_11.jpg",
175
+ "clusters_00_screenshot_12.jpg",
176
+ "clusters_00_screenshot_13.jpg",
177
+ "clusters_00_screenshot_14.jpg",
178
+ "clusters_00_screenshot_15.jpg",
179
+ "clusters_00_screenshot_16.jpg",
180
+ "clusters_00_screenshot_17.jpg",
181
+ "clusters_00_screenshot_18.jpg",
182
+ "clusters_00_screenshot_19.jpg",
183
+ "clusters_00_screenshot_20.jpg",
184
+ "clusters_00_screenshot_21.jpg",
185
+ "clusters_00_screenshot_22.jpg",
186
+ "clusters_01_screenshot_00.jpg",
187
+ "clusters_01_screenshot_01.jpg",
188
+ "clusters_01_screenshot_02.jpg",
189
+ "clusters_01_screenshot_03.jpg",
190
+ "clusters_01_screenshot_04.jpg",
191
+ "clusters_01_screenshot_05.jpg",
192
+ "clusters_01_screenshot_06.jpg",
193
+ "clusters_01_screenshot_07.jpg",
194
+ "clusters_01_screenshot_08.jpg",
195
+ "clusters_01_screenshot_09.jpg",
196
+ "clusters_01_screenshot_10.jpg",
197
+ "clusters_01_screenshot_11.jpg",
198
+ "clusters_01_screenshot_12.jpg",
199
+ "clusters_01_screenshot_13.jpg",
200
+ "clusters_01_screenshot_14.jpg",
201
+ "clusters_01_screenshot_15.jpg",
202
+ "clusters_01_screenshot_16.jpg",
203
+ "clusters_01_screenshot_17.jpg",
204
+ "clusters_01_screenshot_18.jpg",
205
+ "clusters_01_screenshot_19.jpg",
206
+ "clusters_02_screenshot_00.jpg",
207
+ "clusters_02_screenshot_01.jpg",
208
+ "clusters_02_screenshot_02.jpg",
209
+ "clusters_02_screenshot_03.jpg",
210
+ "clusters_02_screenshot_04.jpg",
211
+ "clusters_02_screenshot_05.jpg",
212
+ "clusters_02_screenshot_06.jpg",
213
+ "clusters_02_screenshot_07.jpg",
214
+ "clusters_02_screenshot_08.jpg",
215
+ "clusters_02_screenshot_09.jpg",
216
+ "clusters_02_screenshot_10.jpg",
217
+ "clusters_02_screenshot_11.jpg",
218
+ "clusters_02_screenshot_12.jpg",
219
+ "clusters_02_screenshot_13.jpg",
220
+ "clusters_02_screenshot_14.jpg",
221
+ "clusters_02_screenshot_15.jpg",
222
+ "clusters_02_screenshot_16.jpg",
223
+ "clusters_02_screenshot_17.jpg",
224
+ "clusters_02_screenshot_18.jpg",
225
+ "clusters_03_screenshot_00.jpg",
226
+ "clusters_03_screenshot_01.jpg",
227
+ "clusters_03_screenshot_02.jpg",
228
+ "clusters_03_screenshot_03.jpg",
229
+ "clusters_03_screenshot_04.jpg",
230
+ "clusters_03_screenshot_05.jpg",
231
+ "clusters_03_screenshot_06.jpg",
232
+ "clusters_03_screenshot_07.jpg",
233
+ "clusters_03_screenshot_08.jpg",
234
+ "clusters_03_screenshot_09.jpg",
235
+ "clusters_03_screenshot_10.jpg",
236
+ "clusters_03_screenshot_11.jpg",
237
+ "clusters_03_screenshot_12.jpg",
238
+ "clusters_03_screenshot_13.jpg",
239
+ "clusters_03_screenshot_14.jpg",
240
+ "clusters_03_screenshot_15.jpg",
241
+ "clusters_03_screenshot_16.jpg",
242
+ "clusters_04_screenshot_00.jpg",
243
+ "clusters_04_screenshot_01.jpg",
244
+ "clusters_04_screenshot_02.jpg",
245
+ "clusters_04_screenshot_03.jpg",
246
+ "clusters_04_screenshot_04.jpg",
247
+ "clusters_04_screenshot_05.jpg",
248
+ "clusters_04_screenshot_06.jpg",
249
+ "clusters_04_screenshot_07.jpg",
250
+ "clusters_04_screenshot_08.jpg",
251
+ "clusters_04_screenshot_09.jpg",
252
+ "clusters_04_screenshot_10.jpg",
253
+ "clusters_04_screenshot_11.jpg",
254
+ "clusters_04_screenshot_12.jpg",
255
+ "clusters_04_screenshot_13.jpg",
256
+ "clusters_04_screenshot_14.jpg",
257
+ "clusters_04_screenshot_15.jpg",
258
+ "clusters_04_screenshot_16.jpg",
259
+ "clusters_04_screenshot_17.jpg",
260
+ "clusters_04_screenshot_18.jpg",
261
+ "clusters_04_screenshot_19.jpg",
262
+ "clusters_05_screenshot_00.jpg",
263
+ "clusters_05_screenshot_01.jpg",
264
+ "clusters_05_screenshot_02.jpg",
265
+ "clusters_05_screenshot_03.jpg",
266
+ "clusters_05_screenshot_04.jpg",
267
+ "clusters_05_screenshot_05.jpg",
268
+ "clusters_05_screenshot_06.jpg",
269
+ "clusters_05_screenshot_07.jpg",
270
+ "clusters_05_screenshot_08.jpg",
271
+ "clusters_05_screenshot_09.jpg",
272
+ "clusters_05_screenshot_10.jpg",
273
+ "clusters_05_screenshot_11.jpg",
274
+ "clusters_05_screenshot_12.jpg",
275
+ "clusters_05_screenshot_13.jpg",
276
+ "clusters_05_screenshot_14.jpg",
277
+ "clusters_05_screenshot_15.jpg",
278
+ "clusters_05_screenshot_16.jpg",
279
+ "clusters_05_screenshot_17.jpg",
280
+ "clusters_05_screenshot_18.jpg",
281
+ "clusters_05_screenshot_19.jpg",
282
+ "clusters_06_screenshot_00.jpg",
283
+ "clusters_06_screenshot_01.jpg",
284
+ "clusters_06_screenshot_02.jpg",
285
+ "clusters_06_screenshot_03.jpg",
286
+ "clusters_06_screenshot_04.jpg",
287
+ "clusters_06_screenshot_05.jpg",
288
+ "clusters_06_screenshot_06.jpg",
289
+ "clusters_06_screenshot_07.jpg",
290
+ "clusters_06_screenshot_08.jpg",
291
+ "clusters_06_screenshot_09.jpg",
292
+ "clusters_06_screenshot_10.jpg",
293
+ "clusters_06_screenshot_11.jpg",
294
+ "clusters_06_screenshot_12.jpg",
295
+ "clusters_06_screenshot_13.jpg",
296
+ "clusters_06_screenshot_14.jpg",
297
+ "clusters_06_screenshot_15.jpg",
298
+ "clusters_06_screenshot_16.jpg",
299
+ "clusters_06_screenshot_17.jpg",
300
+ "clusters_06_screenshot_18.jpg",
301
+ "clusters_06_screenshot_19.jpg",
302
+ "pocket_01.pdb",
303
+ "pocket_02.pdb",
304
+ "pocket_03.pdb",
305
+ "pocket_04.pdb",
306
+ "pocket_05.pdb",
307
+ "pocket_06.pdb",
308
+ "pocket_07.pdb",
309
+ "pocket_08.pdb"
310
+ ],
311
+ "analyses": [
312
+ "clusters",
313
+ "clusters-00",
314
+ "clusters-01",
315
+ "clusters-02",
316
+ "clusters-03",
317
+ "clusters-04",
318
+ "clusters-05",
319
+ "clusters-06",
320
+ "dist-perres",
321
+ "energies",
322
+ "fluctuation",
323
+ "hbonds",
324
+ "interactions",
325
+ "pca",
326
+ "pockets",
327
+ "rgyr",
328
+ "rmsd-pairwise",
329
+ "rmsd-perres",
330
+ "rmsds",
331
+ "sasa",
332
+ "tmscores"
333
+ ],
334
+ "mdIndex": 0,
335
+ "mdNumber": 1,
336
+ "refframe": 0,
337
+ "internalId": "6840ecbfd7b6ed7c446d96e7",
338
+ "creationDate": "2025-06-05T01:02:55.000Z",
339
+ "identifier": "A0051"
340
+ }
A0051/records.jsonl ADDED
The diff for this file is too large to render. See raw diff