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+63.8	3.95	4.56	4.36
+63.9	4.04	4.38	4.22
+64.0	3.88	4.77	4.33
+64.1	3.83	4.86	3.92
+64.2	3.82	4.9	3.8
+64.3	4.23	4.92	3.88
+64.4	4.48	4.75	3.87
+64.5	3.65	4.93	4.13
+64.6	3.99	4.96	4.27
+64.7	4.17	4.75	4.1
+64.8	3.94	4.88	4.37
+64.9	4.17	4.96	4.16
+65.0	4.04	4.78	4.57
+65.1	4.41	4.95	4.47
+65.2	3.91	4.78	4.64
+65.3	3.98	4.85	4.62
+65.4	4.21	4.75	4.48
+65.5	4.11	4.98	4.55
+65.6	3.89	4.39	4.76
+65.7	4.12	4.39	4.51
+65.8	4.3	4.71	4.35
+65.9	4.2	5.02	4.3
+66.0	4.43	5.0	3.97
+66.1	4.02	5.14	3.77
+66.2	4.01	5.17	4.09
+66.3	4.1	4.9	4.4
+66.4	3.92	4.88	4.4
+66.5	3.81	5.67	4.17
+66.6	4.3	6.16	4.4
+66.7	3.95	5.65	4.33
+66.8	3.73	6.13	4.77
+66.9	4.16	5.63	4.57
+67.0	4.19	5.66	4.45
+67.1	3.86	5.64	4.93
+67.2	3.85	5.25	4.8
+67.3	4.12	5.54	4.99
+67.4	3.79	4.95	4.94
+67.5	4.1	5.11	4.36
+67.6	3.8	5.44	4.58
+67.7	3.52	5.38	4.68
+67.8	3.69	5.33	4.89
+67.9	4.5	4.9	4.93
+68.0	4.16	4.8	4.46
+68.1	4.07	4.55	5.09
+68.2	4.35	4.46	4.61
+68.3	4.17	4.39	4.86
+68.4	4.24	4.8	4.68
+68.5	4.47	5.04	4.34
+68.6	4.72	4.9	4.55
+68.7	4.64	4.99	4.56
+68.8	4.92	5.29	4.85
+68.9	4.44	5.45	4.58
+69.0	4.41	4.98	4.62
+69.1	4.16	5.11	4.48
+69.2	4.12	5.28	4.53
+69.3	4.1	4.94	4.7
+69.4	4.36	5.39	4.45
+69.5	4.45	4.83	4.74
+69.6	4.12	4.64	4.72
+69.7	4.06	5.14	4.3
+69.8	3.97	4.64	4.11
+69.9	3.87	4.88	4.26
+70.0	3.84	6.02	4.48
+70.1	3.92	5.44	4.12
+70.2	3.93	4.96	4.71
+70.3	3.97	5.51	4.3
+70.4	3.95	5.62	4.59
+70.5	3.87	4.74	4.46
+70.6	4.06	4.44	4.41
+70.7	4.35	4.61	4.72
+70.8	4.1	4.15	4.64
+70.9	4.21	4.15	4.67
+71.0	4.49	3.91	4.45
+71.1	4.19	3.88	4.61
+71.2	4.07	4.34	4.86
+71.3	3.92	4.67	4.34
+71.4	3.66	4.49	4.17
+71.5	4.14	5.1	4.16
+71.6	4.1	4.53	4.72
+71.7	4.0	4.94	4.03
+71.8	4.16	4.97	4.57
+71.9	3.98	5.56	4.55
+72.0	3.8	5.21	4.53
+72.1	3.91	4.82	4.71
+72.2	4.28	4.77	4.67
+72.3	3.88	4.92	4.72
+72.4	3.94	4.54	4.71
+72.5	3.69	4.7	4.58
+72.6	3.9	3.94	4.77
+72.7	3.95	4.17	4.28
+72.8	3.96	4.21	4.43
+72.9	4.16	4.01	4.78
+73.0	3.96	4.28	4.47
+73.1	4.07	3.74	4.42
+73.2	4.05	3.51	4.29
+73.3	3.99	3.55	4.4
+73.4	3.92	4.08	4.5
+73.5	3.87	3.91	4.81
+73.6	4.08	4.2	4.61
+73.7	3.98	4.09	4.71
+73.8	3.48	4.89	4.92
+73.9	3.8	4.96	4.82
+74.0	3.99	4.54	4.78
+74.1	3.93	4.48	4.76
+74.2	3.97	5.22	4.64
+74.3	4.02	5.11	4.87
+74.4	4.16	4.57	4.62
+74.5	4.03	4.91	4.81
+74.6	4.29	4.93	4.6
+74.7	4.5	5.0	4.33
+74.8	4.35	5.06	4.67
+74.9	4.3	5.3	4.68
+75.0	4.3	4.82	4.8
+75.1	4.21	4.56	4.51
+75.2	4.13	4.64	4.57
+75.3	3.91	4.89	4.59
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+75.5	4.09	4.69	4.23
+75.6	4.03	4.99	4.42
+75.7	4.67	4.69	4.21
+75.8	4.24	4.96	4.34
+75.9	4.22	5.06	4.75
+76.0	4.16	4.96	4.6
+76.1	4.43	4.89	5.0
+76.2	4.16	4.12	4.67
+76.3	4.6	3.66	4.9
+76.4	4.63	4.31	4.61
+76.5	4.76	3.9	4.51
+76.6	4.54	4.43	4.67
+76.7	4.67	3.77	4.57
+76.8	3.94	3.21	4.73
+76.9	4.32	3.43	4.62
+77.0	4.31	4.15	4.48
+77.1	4.46	4.54	4.29
+77.2	4.64	4.47	4.19
+77.3	4.32	4.71	3.69
+77.4	4.18	4.36	4.24
+77.5	4.05	5.03	4.5
+77.6	3.95	5.19	4.58
+77.7	3.8	4.99	4.04
+77.8	3.88	5.17	4.34
+77.9	3.63	4.67	4.42
+78.0	3.58	4.84	4.21
+78.1	4.22	4.64	4.39
+78.2	3.92	4.75	4.22
+78.3	4.1	5.27	4.45
+78.4	3.72	4.92	4.23
+78.5	4.39	5.13	4.22
+78.6	3.74	5.9	4.16
+78.7	3.71	6.53	3.8
+78.8	4.05	6.37	4.04
+78.9	3.92	5.74	4.52
+79.0	4.05	5.09	4.2
+79.1	3.59	4.55	4.19
+79.2	3.95	3.85	4.25
+79.3	3.7	3.89	4.22
+79.4	3.47	3.98	4.52
+79.5	3.83	3.75	4.12
+79.6	4.21	3.87	4.56
+79.7	3.75	4.07	4.32
+79.8	4.28	3.56	4.15
+79.9	3.93	4.34	3.92
+80.0	4.11	4.25	3.96
+80.1	3.76	4.04	4.37
+80.2	4.36	4.79	3.97
+80.3	4.13	4.68	4.45
+80.4	3.92	4.51	4.59
+80.5	4.3	5.01	4.86
+80.6	4.35	5.77	4.48
+80.7	3.86	5.78	4.34
+80.8	4.38	4.98	4.45
+80.9	4.12	5.03	4.37
+81.0	4.39	5.24	3.97
+81.1	4.49	5.08	4.04
+81.2	4.32	4.77	3.81
+81.3	4.18	5.29	3.77
+81.4	4.55	5.23	3.68
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+81.6	4.27	4.66	3.37
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+81.9	3.88	4.95	3.61
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+82.2	4.06	5.17	3.48
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+82.4	3.69	3.97	3.52
+82.5	3.99	4.2	3.69
+82.6	3.99	3.8	3.91
+82.7	3.92	4.47	3.71
+82.8	3.85	4.38	3.88
+82.9	3.48	4.48	3.79
+83.0	3.9	4.37	3.34
+83.1	4.18	4.21	3.83
+83.2	3.95	4.84	3.42
+83.3	4.34	4.56	3.63
+83.4	4.01	4.46	3.53
+83.5	3.94	4.37	3.7
+83.6	3.83	4.41	3.71
+83.7	3.64	4.37	3.38
+83.8	3.38	3.81	3.72
+83.9	3.85	4.04	3.66
+84.0	4.51	4.04	3.89
+84.1	4.05	4.04	3.65
+84.2	4.24	3.81	3.81
+84.3	4.43	3.83	3.84
+84.4	4.28	3.91	3.79
+84.5	4.48	4.71	3.89
+84.6	4.64	4.37	3.64
+84.7	4.39	4.32	3.8
+84.8	4.05	4.09	3.79
+84.9	3.79	3.98	3.94
+85.0	3.99	4.42	3.79
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+85.2	3.98	4.12	3.46
+85.3	3.75	4.03	3.77
+85.4	3.95	3.48	3.47
+85.5	4.31	3.71	3.73
+85.6	3.92	4.44	3.48
+85.7	3.83	4.56	3.67
+85.8	3.9	5.13	3.6
+85.9	3.94	5.25	3.77
+86.0	4.1	5.32	3.96
+86.1	3.95	5.42	3.78
+86.2	3.77	5.28	3.74
+86.3	3.7	4.74	3.9
+86.4	3.82	5.06	3.85
+86.5	3.95	5.17	3.62
+86.6	3.99	5.21	3.67
+86.7	3.61	4.83	3.71
+86.8	3.95	4.73	3.85
+86.9	3.93	4.36	3.97
+87.0	3.94	4.8	3.98
+87.1	3.88	4.77	4.02
+87.2	3.92	5.18	3.81
+87.3	3.78	4.43	3.75
+87.4	3.82	4.84	3.79
+87.5	3.98	3.83	3.34
+87.6	3.66	4.5	3.46
+87.7	3.98	3.34	3.75
+87.8	3.94	3.97	3.37
+87.9	4.08	3.73	3.5
+88.0	3.79	3.32	3.7
+88.1	3.98	2.95	3.69
+88.2	3.8	3.63	3.72
+88.3	4.02	3.03	3.57
+88.4	3.66	2.81	3.7
+88.5	4.02	3.65	4.13
+88.6	3.96	3.15	4.27
+88.7	3.55	3.98	4.41
+88.8	3.64	3.53	4.23
+88.9	3.52	3.93	4.38
+89.0	3.36	4.19	4.26
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+89.2	3.72	3.91	3.76
+89.3	3.74	5.16	3.85
+89.4	3.63	5.55	4.13
+89.5	3.57	5.71	4.1
+89.6	4.02	5.49	3.63
+89.7	3.97	5.3	3.72
+89.8	4.31	5.38	3.64
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+90.2	4.07	4.27	3.55
+90.3	3.98	3.55	3.58
+90.4	3.96	3.67	3.38
+90.5	3.99	4.74	3.8
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+90.7	4.23	4.25	3.72
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+90.9	3.8	4.12	3.7
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+91.1	3.94	4.81	4.13
+91.2	3.94	4.18	3.97
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+91.8	4.32	3.37	4.07
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+92.7	4.05	3.87	4.05
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+95.2	4.17	3.54	4.25
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+95.4	3.83	5.04	3.88
+95.5	3.92	5.89	4.37
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+95.7	3.86	6.61	4.16
+95.8	3.89	6.74	3.89
+95.9	3.88	6.9	3.7
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+96.6	3.77	6.53	4.04
+96.7	3.54	6.47	4.07
+96.8	3.79	6.92	3.82
+96.9	3.42	7.17	3.6
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+97.4	3.39	6.97	4.11
+97.5	3.72	6.99	3.91
+97.6	3.53	6.4	3.96
+97.7	3.33	6.96	3.84
+97.8	3.71	5.91	3.42
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+98.0	3.46	6.4	3.91
+98.1	3.79	6.64	3.9
+98.2	3.81	6.46	3.71
+98.3	3.91	6.46	3.64
+98.4	4.11	6.42	3.82
+98.5	3.86	6.27	3.72
+98.6	4.01	6.08	3.46
+98.7	3.82	6.42	3.4
+98.8	3.58	6.18	3.7
+98.9	3.93	6.14	3.55
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+99.1	4.07	6.58	3.78
+99.2	3.95	6.04	3.88
+99.3	3.52	6.52	3.93
+99.4	3.22	6.58	3.95
+99.5	3.51	6.87	3.53
+99.6	3.7	6.84	3.93
+99.7	3.96	6.74	4.48
+99.8	3.98	6.87	4.33
+99.9	3.88	6.91	3.98
+100.0	3.92	7.17	3.82

atlas_1000_analysis/1dk8_A/1dk8_A_RMSF.tsv

@@ -0,0 +1,148 @@
+seq	RMSF_R1	RMSF_R2	RMSF_R3
+G	11.75	13.36	11.7
+S	9.45	11.03	9.27
+A	7.69	9.43	7.29
+S	6.03	7.09	5.36
+P	3.77	5.03	3.31
+T	2.84	4.05	2.41
+P	1.9	3.09	1.89
+P	1.78	3.15	1.9
+Y	1.93	2.93	1.75
+L	2.01	2.79	1.66
+K	1.61	2.48	1.61
+W	1.2	2.07	1.35
+A	1.31	2.07	1.31
+E	1.45	2.26	1.49
+S	1.3	1.94	1.33
+L	1.08	1.56	1.18
+H	1.26	1.81	1.35
+S	1.34	2.08	1.37
+L	1.14	1.82	1.21
+L	1.16	1.72	1.33
+D	1.38	2.18	1.55
+D	1.38	2.42	1.53
+Q	1.41	2.47	1.64
+D	1.4	2.53	1.54
+G	1.18	2.11	1.31
+I	1.05	1.87	1.3
+S	1.16	2.13	1.35
+L	1.13	2.06	1.26
+F	0.91	1.59	1.09
+R	0.9	1.63	1.16
+T	1.08	1.99	1.28
+F	0.97	1.7	1.14
+L	0.81	1.41	1.08
+K	0.97	1.88	1.25
+Q	1.16	2.17	1.48
+E	1.04	1.85	1.44
+G	0.99	1.99	1.54
+C	0.82	1.6	1.49
+A	0.78	1.2	0.97
+D	0.72	1.02	0.97
+L	0.62	0.82	0.87
+L	0.7	0.94	0.92
+D	0.75	0.99	0.96
+F	0.58	0.68	0.77
+W	0.65	0.81	0.78
+F	0.84	1.07	1.02
+A	0.71	0.88	0.92
+C	0.68	0.8	0.8
+T	0.95	1.25	1.02
+G	1.0	1.31	1.2
+F	0.85	1.04	1.05
+R	1.18	1.39	1.21
+K	1.4	1.69	1.56
+L	1.3	1.46	1.67
+E	1.64	1.78	2.11
+P	1.71	1.8	2.12
+C	1.8	1.82	2.37
+D	1.74	1.81	2.4
+S	1.82	1.88	2.43
+N	1.43	1.62	1.98
+E	1.24	1.38	1.78
+E	1.24	1.4	1.75
+K	1.17	1.39	1.64
+R	0.95	1.09	1.33
+L	0.93	1.0	1.27
+K	0.96	1.1	1.28
+L	0.82	0.93	1.12
+A	0.7	0.73	0.92
+R	0.8	0.9	0.98
+A	0.81	0.95	1.0
+I	0.64	0.7	0.83
+Y	0.7	0.84	0.81
+R	0.88	1.11	1.0
+K	0.85	1.08	1.01
+Y	0.72	0.93	0.88
+I	0.79	1.06	0.9
+L	1.05	1.4	1.1
+D	1.22	1.59	1.26
+N	1.52	2.05	1.69
+N	1.45	2.04	1.9
+G	1.05	1.5	1.39
+I	0.82	1.18	1.14
+V	0.62	0.89	0.84
+S	0.76	1.17	0.89
+R	0.88	1.42	1.11
+Q	0.78	1.15	1.0
+T	0.79	1.26	0.95
+K	1.02	1.6	1.08
+P	1.18	1.8	1.24
+A	1.24	1.91	1.29
+T	0.99	1.52	1.04
+K	0.94	1.41	0.98
+S	1.18	1.72	1.23
+F	1.1	1.61	1.14
+I	0.88	1.24	0.9
+K	1.07	1.44	1.13
+G	1.23	1.65	1.38
+C	1.05	1.41	1.24
+I	1.02	1.29	1.16
+M	1.31	1.58	1.48
+K	1.36	1.6	1.68
+Q	1.19	1.65	1.56
+L	1.1	1.66	1.53
+I	1.0	1.14	1.48
+D	1.1	1.41	1.43
+P	1.13	1.52	1.32
+A	1.18	1.66	1.17
+M	0.91	1.26	0.92
+F	0.7	0.97	0.72
+D	0.88	1.26	0.83
+Q	0.88	1.32	0.8
+A	0.68	0.96	0.68
+Q	0.67	0.87	0.73
+T	0.86	1.17	0.81
+E	0.78	1.06	0.77
+I	0.61	0.79	0.72
+Q	0.78	1.0	0.88
+A	0.86	1.14	0.95
+T	0.74	1.0	0.92
+M	0.76	0.99	0.96
+E	0.96	1.24	1.2
+E	1.07	1.36	1.32
+N	0.98	1.24	1.26
+T	0.83	1.14	1.06
+Y	0.86	1.21	1.03
+P	1.02	1.31	1.14
+S	1.01	1.28	1.12
+F	0.94	1.4	1.08
+L	1.07	1.59	1.18
+K	1.22	1.65	1.29
+S	1.16	1.72	1.28
+D	1.41	2.13	1.5
+I	1.39	2.22	1.5
+Y	1.25	2.04	1.34
+L	1.74	2.31	1.52
+E	2.13	2.74	1.73
+Y	2.19	2.68	1.69
+T	2.35	2.74	1.72
+R	1.98	2.74	2.03
+T	2.66	3.5	3.06
+G	3.88	4.02	4.12
+S	4.7	5.34	4.6
+E	4.85	7.2	5.9
+S	5.44	9.55	7.82
+P	6.64	12.14	9.65
+K	8.33	14.3	11.41
+V	10.61	16.83	13.91

atlas_1000_analysis/1dk8_A/1dk8_A_contacts.tsv

@@ -0,0 +1,148 @@
+seq	nb_chain	nb_ligand	nb_ion	nb_nucleotide	name_chain	name_ligand	name_ion	name_nucleotide
+G	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+P	0	0	1	0	-	-	A:SO4,502	-
+T	0	0	1	0	-	-	A:SO4,502	-
+P	0	0	0	0	-	-	-	-
+P	0	0	0	0	-	-	-	-
+Y	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+W	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+E	0	1	0	0	-	A:DTT,701	-	-
+S	0	1	0	0	-	A:DTT,701	-	-
+L	0	1	0	0	-	A:DTT,701	-	-
+H	0	1	0	0	-	A:DTT,701	-	-
+S	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+Q	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+G	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+S	0	0	1	0	-	-	A:SO4,504	-
+L	0	0	0	0	-	-	-	-
+F	0	0	0	0	-	-	-	-
+R	0	0	1	0	-	-	A:SO4,506	-
+T	0	0	1	0	-	-	A:SO4,506	-
+F	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+K	0	0	1	0	-	-	A:SO4,506	-
+Q	0	0	0	0	-	-	-	-
+E	0	0	0	0	-	-	-	-
+G	0	0	0	0	-	-	-	-
+C	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+F	0	0	0	0	-	-	-	-
+W	0	0	0	0	-	-	-	-
+F	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+C	0	0	0	0	-	-	-	-
+T	0	0	0	0	-	-	-	-
+G	0	0	0	0	-	-	-	-
+F	0	0	0	0	-	-	-	-
+R	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+E	0	0	0	0	-	-	-	-
+P	0	0	0	0	-	-	-	-
+C	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+N	0	0	0	0	-	-	-	-
+E	0	0	0	0	-	-	-	-
+E	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+R	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+R	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+Y	0	0	0	0	-	-	-	-
+R	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+Y	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+N	0	0	0	0	-	-	-	-
+N	0	0	0	0	-	-	-	-
+G	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+V	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+R	0	0	0	0	-	-	-	-
+Q	0	0	0	0	-	-	-	-
+T	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+P	0	1	0	0	-	A:GOL,605	-	-
+A	0	1	0	0	-	A:GOL,605	-	-
+T	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+S	0	1	0	0	-	A:GOL,605	-	-
+F	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+G	0	0	0	0	-	-	-	-
+C	0	1	0	0	-	A:GOL,603	-	-
+I	0	0	0	0	-	-	-	-
+M	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+Q	0	0	0	0	-	-	-	-
+L	0	1	0	0	-	A:GOL,603	-	-
+I	0	1	0	0	-	A:GOL,603	-	-
+D	0	1	0	0	-	A:GOL,603	-	-
+P	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+M	0	1	0	0	-	A:GOL,603	-	-
+F	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+Q	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+Q	0	0	0	0	-	-	-	-
+T	0	0	0	0	-	-	-	-
+E	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+Q	0	0	0	0	-	-	-	-
+A	0	0	0	0	-	-	-	-
+T	0	0	0	0	-	-	-	-
+M	0	0	0	0	-	-	-	-
+E	0	1	0	0	-	A:DTT,701	-	-
+E	0	0	0	0	-	-	-	-
+N	0	0	0	0	-	-	-	-
+T	0	0	0	0	-	-	-	-
+Y	0	0	0	0	-	-	-	-
+P	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+F	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+K	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+D	0	0	0	0	-	-	-	-
+I	0	0	0	0	-	-	-	-
+Y	0	0	0	0	-	-	-	-
+L	0	0	0	0	-	-	-	-
+E	0	0	0	0	-	-	-	-
+Y	0	0	0	0	-	-	-	-
+T	0	0	0	0	-	-	-	-
+R	0	1	0	0	-	A:GOL,604	-	-
+T	0	1	1	0	-	A:GOL,604	A:SO4,505	-
+G	0	1	1	0	-	A:GOL,604	A:SO4,505	-
+S	0	0	1	0	-	-	A:SO4,505	-
+E	0	0	0	0	-	-	-	-
+S	0	0	0	0	-	-	-	-
+P	0	1	0	0	-	A:GOL,601	-	-
+K	0	0	0	0	-	-	-	-
+V	0	0	0	0	-	-	-	-

atlas_1000_analysis/1dk8_A/1dk8_A_corresp.tsv

@@ -0,0 +1,148 @@
+UnP_seq	PDB_seq	PDB_num	CIF_num	UnP_num	gap	hetatm	corrected	no_fullbb	no_ca
+G	G	111	1	1	0	0	0	0	0
+S	S	112	2	2	0	0	0	0	0
+A	A	113	3	3	0	0	0	0	0
+S	S	114	4	4	0	0	0	0	0
+P	P	115	5	5	0	0	0	0	0
+T	T	116	6	6	0	0	0	0	0
+P	P	117	7	7	0	0	0	0	0
+P	P	118	8	8	0	0	0	0	0
+Y	Y	119	9	9	0	0	0	0	0
+L	L	120	10	10	0	0	0	0	0
+K	K	121	11	11	0	0	0	0	0
+W	W	122	12	12	0	0	0	0	0
+A	A	123	13	13	0	0	0	0	0
+E	E	124	14	14	0	0	0	0	0
+S	S	125	15	15	0	0	0	0	0
+L	L	126	16	16	0	0	0	0	0
+H	H	127	17	17	0	0	0	0	0
+S	S	128	18	18	0	0	0	0	0
+L	L	129	19	19	0	0	0	0	0
+L	L	130	20	20	0	0	0	0	0
+D	D	131	21	21	0	0	0	0	0
+D	D	132	22	22	0	0	0	0	0
+Q	Q	133	23	23	0	0	0	0	0
+D	D	134	24	24	0	0	0	0	0
+G	G	135	25	25	0	0	0	0	0
+I	I	136	26	26	0	0	0	0	0
+S	S	137	27	27	0	0	0	0	0
+L	L	138	28	28	0	0	0	0	0
+F	F	139	29	29	0	0	0	0	0
+R	R	140	30	30	0	0	0	0	0
+T	T	141	31	31	0	0	0	0	0
+F	F	142	32	32	0	0	0	0	0
+L	L	143	33	33	0	0	0	0	0
+K	K	144	34	34	0	0	0	0	0
+Q	Q	145	35	35	0	0	0	0	0
+E	E	146	36	36	0	0	0	0	0
+G	G	147	37	37	0	0	0	0	0
+C	C	148	38	38	0	0	0	0	0
+A	A	149	39	39	0	0	0	0	0
+D	D	150	40	40	0	0	0	0	0
+L	L	151	41	41	0	0	0	0	0
+L	L	152	42	42	0	0	0	0	0
+D	D	153	43	43	0	0	0	0	0
+F	F	154	44	44	0	0	0	0	0
+W	W	155	45	45	0	0	0	0	0
+F	F	156	46	46	0	0	0	0	0
+A	A	157	47	47	0	0	0	0	0
+C	C	158	48	48	0	0	0	0	0
+T	T	159	49	49	0	0	0	0	0
+G	G	160	50	50	0	0	0	0	0
+F	F	161	51	51	0	0	0	0	0
+R	R	162	52	52	0	0	0	0	0
+K	K	163	53	53	0	0	0	0	0
+L	L	164	54	54	0	0	0	0	0
+E	E	165	55	55	0	0	0	0	0
+P	P	166	56	56	0	0	0	0	0
+C	C	167	57	57	0	0	0	0	0
+D	D	168	58	58	0	0	0	0	0
+S	S	169	59	59	0	0	0	0	0
+N	N	170	60	60	0	0	0	0	0
+E	E	171	61	61	0	0	0	0	0
+E	E	172	62	62	0	0	0	0	0
+K	K	173	63	63	0	0	0	0	0
+R	R	174	64	64	0	0	0	0	0
+L	L	175	65	65	0	0	0	0	0
+K	K	176	66	66	0	0	0	0	0
+L	L	177	67	67	0	0	0	0	0
+A	A	178	68	68	0	0	0	0	0
+R	R	179	69	69	0	0	0	0	0
+A	A	180	70	70	0	0	0	0	0
+I	I	181	71	71	0	0	0	0	0
+Y	Y	182	72	72	0	0	0	0	0
+R	R	183	73	73	0	0	0	0	0
+K	K	184	74	74	0	0	0	0	0
+Y	Y	185	75	75	0	0	0	0	0
+I	I	186	76	76	0	0	0	0	0
+L	L	187	77	77	0	0	0	0	0
+D	D	188	78	78	0	0	0	0	0
+N	N	189	79	79	0	0	0	0	0
+N	N	190	80	80	0	0	0	0	0
+G	G	191	81	81	0	0	0	0	0
+I	I	192	82	82	0	0	0	0	0
+V	V	193	83	83	0	0	0	0	0
+S	S	194	84	84	0	0	0	0	0
+R	R	195	85	85	0	0	0	0	0
+Q	Q	196	86	86	0	0	0	0	0
+T	T	197	87	87	0	0	0	0	0
+K	K	198	88	88	0	0	0	0	0
+P	P	199	89	89	0	0	0	0	0
+A	A	200	90	90	0	0	0	0	0
+T	T	201	91	91	0	0	0	0	0
+K	K	202	92	92	0	0	0	0	0
+S	S	203	93	93	0	0	0	0	0
+F	F	204	94	94	0	0	0	0	0
+I	I	205	95	95	0	0	0	0	0
+K	K	206	96	96	0	0	0	0	0
+G	G	207	97	97	0	0	0	0	0
+C	C	208	98	98	0	0	0	0	0
+I	I	209	99	99	0	0	0	0	0
+M	M	210	100	100	0	0	0	0	0
+K	K	211	101	101	0	0	0	0	0
+Q	Q	212	102	102	0	0	0	0	0
+L	L	213	103	103	0	0	0	0	0
+I	I	214	104	104	0	0	0	0	0
+D	D	215	105	105	0	0	0	0	0
+P	P	216	106	106	0	0	0	0	0
+A	A	217	107	107	0	0	0	0	0
+M	M	218	108	108	0	0	0	0	0
+F	F	219	109	109	0	0	0	0	0
+D	D	220	110	110	0	0	0	0	0
+Q	Q	221	111	111	0	0	0	0	0
+A	A	222	112	112	0	0	0	0	0
+Q	Q	223	113	113	0	0	0	0	0
+T	T	224	114	114	0	0	0	0	0
+E	E	225	115	115	0	0	0	0	0
+I	I	226	116	116	0	0	0	0	0
+Q	Q	227	117	117	0	0	0	0	0
+A	A	228	118	118	0	0	0	0	0
+T	T	229	119	119	0	0	0	0	0
+M	M	230	120	120	0	0	0	0	0
+E	E	231	121	121	0	0	0	0	0
+E	E	232	122	122	0	0	0	0	0
+N	N	233	123	123	0	0	0	0	0
+T	T	234	124	124	0	0	0	0	0
+Y	Y	235	125	125	0	0	0	0	0
+P	P	236	126	126	0	0	0	0	0
+S	S	237	127	127	0	0	0	0	0
+F	F	238	128	128	0	0	0	0	0
+L	L	239	129	129	0	0	0	0	0
+K	K	240	130	130	0	0	0	0	0
+S	S	241	131	131	0	0	0	0	0
+D	D	242	132	132	0	0	0	0	0
+I	I	243	133	133	0	0	0	0	0
+Y	Y	244	134	134	0	0	0	0	0
+L	L	245	135	135	0	0	0	0	0
+E	E	246	136	136	0	0	0	0	0
+Y	Y	247	137	137	0	0	0	0	0
+T	T	248	138	138	0	0	0	0	0
+R	R	249	139	139	0	0	0	0	0
+T	T	250	140	140	0	0	0	0	0
+G	G	251	141	141	0	0	0	0	0
+S	S	252	142	142	0	0	0	0	0
+E	E	253	143	143	0	0	0	0	0
+S	S	254	144	144	0	0	0	0	0
+P	P	255	145	145	0	0	0	0	0
+K	K	256	146	146	0	0	0	0	0
+V	V	257	147	147	0	0	0	0	0

atlas_1000_analysis/1dk8_A/1dk8_A_gyrate.tsv

@@ -0,0 +1,1001 @@
+time	gyr_R1	gyr_R2	gyr_R3
+0.1	18.41	18.64	18.51
+0.2	18.71	18.53	18.72
+0.3	18.57	17.88	18.75
+0.4	18.48	18.28	18.72
+0.5	18.31	18.63	18.6
+0.6	18.71	18.46	18.91
+0.7	18.73	18.56	18.87
+0.8	18.65	18.93	18.72
+0.9	18.37	18.69	18.36
+1.0	18.79	18.47	18.32
+1.1	18.84	18.69	18.52
+1.2	18.61	18.7	18.39
+1.3	18.48	18.7	18.16
+1.4	18.05	18.64	18.33
+1.5	18.25	18.78	18.74
+1.6	18.39	18.97	18.79
+1.7	18.38	18.82	18.56
+1.8	18.24	18.76	18.54
+1.9	18.78	18.94	18.45
+2.0	18.69	18.71	18.65
+2.1	18.55	18.88	18.61
+2.2	18.62	18.85	18.77
+2.3	18.67	18.86	18.51
+2.4	18.52	18.98	18.51
+2.5	18.6	19.08	18.64
+2.6	18.35	18.97	18.47
+2.7	18.52	19.11	18.57
+2.8	18.57	19.08	18.53
+2.9	18.25	19.17	18.54
+3.0	18.2	19.27	18.73
+3.1	18.12	18.57	18.5
+3.2	18.13	18.86	18.38
+3.3	17.99	19.11	18.04
+3.4	17.92	19.13	18.24
+3.5	17.7	19.2	18.1
+3.6	17.59	18.88	18.37
+3.7	17.98	18.97	18.74
+3.8	18.07	18.93	18.45
+3.9	17.75	18.89	18.42
+4.0	17.94	18.93	18.34
+4.1	17.88	18.73	18.35
+4.2	17.86	18.94	18.6
+4.3	17.36	18.79	18.68
+4.4	17.7	18.66	18.76
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+95.3	17.44	18.53	17.34
+95.4	17.55	18.39	17.45
+95.5	17.54	18.27	17.26
+95.6	17.54	17.86	17.62
+95.7	17.54	17.79	17.34
+95.8	17.4	17.69	17.55
+95.9	17.47	17.66	17.74
+96.0	17.41	17.63	17.84
+96.1	17.66	17.48	17.84
+96.2	17.48	17.75	17.66
+96.3	17.54	17.66	17.84
+96.4	17.32	17.71	17.84
+96.5	17.26	17.98	17.84
+96.6	17.42	17.91	17.98
+96.7	17.65	18.03	17.73
+96.8	17.57	18.03	17.98
+96.9	17.75	17.97	17.65
+97.0	17.77	17.97	17.67
+97.1	17.36	17.99	17.66
+97.2	17.68	18.12	17.87
+97.3	17.51	17.9	17.88
+97.4	17.73	17.89	17.69
+97.5	17.48	17.69	17.78
+97.6	17.61	18.0	17.87
+97.7	17.8	17.96	18.16
+97.8	17.64	18.18	18.16
+97.9	17.82	18.54	18.03
+98.0	17.67	18.3	17.94
+98.1	17.57	18.09	17.77
+98.2	17.55	18.13	17.63
+98.3	17.37	18.11	17.64
+98.4	17.59	18.37	18.01
+98.5	17.49	17.78	17.86
+98.6	17.29	18.16	17.88
+98.7	17.31	18.07	18.02
+98.8	17.43	17.97	18.15
+98.9	17.4	18.01	18.11
+99.0	17.49	18.1	17.84
+99.1	17.34	18.12	17.76
+99.2	17.59	18.07	17.7
+99.3	17.81	17.94	17.47
+99.4	17.78	17.6	17.9
+99.5	17.72	17.85	18.04
+99.6	17.55	17.69	17.79
+99.7	17.56	17.54	17.64
+99.8	17.65	17.65	17.85
+99.9	17.43	17.75	18.15
+100.0	17.39	18.05	17.87

atlas_1000_analysis/1dk8_A/1dk8_A_pLDDT.tsv

@@ -0,0 +1,148 @@
+seq	pLDDT
+G	45.12
+S	61.68
+A	66.15
+S	74.46
+P	82.86
+T	83.51
+P	88.13
+P	91.51
+Y	92.59
+L	93.72
+K	95.02
+W	96.78
+A	96.23
+E	96.69
+S	97.96
+L	98.33
+H	97.92
+S	97.76
+L	98.32
+L	98.28
+D	97.13
+D	96.9
+Q	96.67
+D	95.61
+G	97.39
+I	98.38
+S	98.17
+L	98.07
+F	98.66
+R	98.65
+T	98.43
+F	98.6
+L	98.62
+K	98.51
+Q	98.0
+E	97.08
+G	97.79
+C	98.14
+A	98.57
+D	98.72
+L	98.79
+L	98.81
+D	98.75
+F	98.86
+W	98.76
+F	98.68
+A	98.58
+C	98.52
+T	97.55
+G	97.41
+F	97.9
+R	96.81
+K	94.63
+L	92.52
+E	86.76
+P	85.11
+C	88.67
+D	87.94
+S	89.52
+N	90.3
+E	92.26
+E	93.95
+K	94.61
+R	96.28
+L	96.68
+K	97.57
+L	97.86
+A	98.38
+R	98.46
+A	98.6
+I	98.72
+Y	98.73
+R	98.5
+K	98.52
+Y	98.7
+I	98.58
+L	98.11
+D	97.35
+N	96.24
+N	97.32
+G	98.0
+I	98.42
+V	98.76
+S	98.59
+R	98.46
+Q	98.46
+T	98.7
+K	98.6
+P	98.5
+A	98.59
+T	98.74
+K	98.75
+S	98.55
+F	98.65
+I	98.65
+K	98.48
+G	98.42
+C	98.07
+I	98.12
+M	97.69
+K	97.76
+Q	95.8
+L	94.37
+I	95.73
+D	95.63
+P	96.02
+A	97.34
+M	98.14
+F	98.7
+D	98.65
+Q	98.79
+A	98.8
+Q	98.82
+T	98.81
+E	98.82
+I	98.82
+Q	98.79
+A	98.72
+T	98.44
+M	98.68
+E	98.63
+E	98.29
+N	97.79
+T	98.23
+Y	98.7
+P	98.52
+S	98.47
+F	98.57
+L	98.14
+K	97.58
+S	97.86
+D	96.57
+I	96.09
+Y	96.38
+L	95.23
+E	93.26
+Y	90.81
+T	89.77
+R	86.75
+T	80.7
+G	65.6
+S	61.09
+E	55.62
+S	50.12
+P	48.15
+K	41.09
+V	36.17

atlas_1000_analysis/1dk8_A/README.txt

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+These trajectories and corresponding analysis were downloaded from the ATLAS database (https://www.dsimb.inserm.fr/ATLAS).
+
+ATLAS gathers standardized molecular dynamics simulations of protein structures accompanied by their analysis in the form of interactive diagrams and trajectory visualization. All the raw trajectories as well as the results of analysis are available for download.
+
+
+ • ARCHIVE CONTENT •
+Protein structure and trajectory files:
+     - PDB_Name.pdb: Protein structure in PDB format used to launch the molecular dynamics (after energy minimisation and equilibrations).
+     - PDB_Name_corresp.tsv: Correspondence between the author residue number (PDB file / CIF file) and the new numbering (starting from 1).
+     - PDB_Name_R{1,2,3}.tpr: File containing the starting structure of the simulation, the molecular topology and all the simulation parameters.
+     - PDB_Name_R{1,2,3}.xtc: MD trajectory without solvent molecules. Each trajectory is of 100 ns with frames saved every 100 ps (1,000 frames in total).
+
+Results of MD simulation analysis:
+     - PDB_Name_Bfactor.tsv: Experimental B-factor values of the initial PDB structure (in Ų).
+     - PDB_Name_RMSF.tsv: RMSF values for the 3 MD replicates (in Å).
+     - PDB_Name_Neq.tsv: Local deformability index Neq for the 3 MD replicates.
+     - PDB_Name_RMSD.tsv: RMSD values for the 3 MD replicates (in Å / ns).
+     - PDB_Name_gyr.tsv: Gyration radius values for the 3 MD replicates (in Å / ns).
+     - PDB_Name_contacts.tsv: Residue-level interactions co-crystallized with the protein of interest (chain, ligands, ions and nucleotides within 6 Å threshold of the α-carbon of the residue).
+     - PDB_Name_pLDDT.tsv: AlphaFold2 pLDDT. pLDDT is the per-residue prediction confidence metric, not a flexibility measurement.
+
+See the ATLAS about page (https://www.dsimb.inserm.fr/ATLAS/about.html) for details.
+
+ • MOLECULAR DYNAMICS PARAMETERS •
+Download the ATLAS GROMACS molecular dynamics parameters (.mdp) and force-field files (CHARMM36m) with https://www.dsimb.inserm.fr/ATLAS/data/download/ATLAS_parameters.zip or using the REST API with `curl -X 'GET' 'https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters' -o MD_parameters.zip`
+
+
+ • LICENSE •
+The ATLAS database is released under a Creative Commons Attribution-NonCommercial 4.0 International license (CC-BY-NC). This license is one of the Creative Commons licenses and allows users to share and adapt the dataset if they give credit to the copyright holder and do not use the dataset for any commercial purposes. See https://creativecommons.org/licenses/by-nc/4.0/ for details.
+Please contact us for commercial use.
+
+
+ • CONTACTS •
+For scientific collaboration, please contact:
+      Tatiana GALOCHKINA, Associate Professor, Université Paris Cité
+      tatiana.galochkina (at) u-paris.fr
+  or
+      Jean-Christophe GELLY, Professor, Université Paris Cité
+      jean-christophe.gelly (at) u-paris.fr 
+

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