CABS-flex: server for fast simulation of protein structure fluctuations

Download models Download C^α trajectory

Status: Done started: 2018-Feb-11 07:50:35 UTC

Project Name	Lysozyme
Sequence	KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDITA SVNCAKKIVS DGNGMNAWVA WRNRCKGTDV QAWIRGCRL
Secondary structure	CCCCHHHHHH HHHHCCCCCC CCCCHHHHHH HHHHHHCCCC CCEEECCCCC EEECCCCEEC CCCCCCCCCC CCCCCCCCCC CCCCCCCCHH HHHHHHHHHC CCCCCCCCHH HHHHCCCCCC CCCCCCCCC
Movie from predicted structures	To download the movie, right click on the desired file format:
Estimated finish time	2018-Feb-11 11:26 UTC

Project Name	Lysozyme

Multimodel

Multimodel [PDB] Multimodel with superimposed input structure [PDB] Fluctuation data [TXT] Fluctuation plot [EPS]

Model 001

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 002

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 003

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 004

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 005

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 006

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 007

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 008

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 009

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 010

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 011

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Model 012

Model [PDB] Model with superimposed input structure [PDB] RMSD data [TXT] RMSD plot [EPS]

Project Name	Lysozyme

Clustering data

Cluster #	1	2	3	4	5	6	7	8	9	10	11	12
Cluster density	274.4	209.8	174.9	157.1	136.0	130.6	129.1	111.9	101.2	96.9	88.6	68.4
Cluster size	334	247	208	183	160	171	151	125	120	109	103	89
Average cluster RMSD	1.2	1.2	1.2	1.2	1.2	1.3	1.2	1.1	1.2	1.1	1.2	1.3

Read about clustering method.

C^α RMSD & GDT_TS to the input structure

#	1	2	3	4	5	6	7	8	9	10	11	12
RMSD	2.63	2.81	2.61	3.32	2.85	2.36	2.15	2.72	2.39	2.70	2.63	2.55
GDT_TS	0.66	0.68	0.68	0.65	0.64	0.71	0.73	0.67	0.71	0.69	0.67	0.73

The table contains RMSD and GDT_TS values (calculated on the Cα atoms) between the predicted models and the input structure. Note that GDT_TS metric is intended as a more accurate measurement than the more common RMSD.
Read more about the root-mean-square deviation (RMSD) measure
Read more about the global distance test (GDT, also written as GDT_TS to represent "total score") measure.

C^α RMSD between predicted models

#	1	2	3	4	5	6	7	8	9	10	11	12
1	0.00	2.42	2.23	2.25	2.13	2.00	2.17	2.24	2.25	2.08	2.16	2.04
2	2.42	0.00	3.43	2.09	1.79	3.02	2.75	3.04	3.12	3.15	2.76	2.96
3	2.23	3.43	0.00	3.27	2.93	1.63	2.25	2.80	2.34	2.46	2.73	2.09
4	2.25	2.09	3.27	0.00	2.08	2.90	2.85	2.85	3.00	2.61	2.59	2.62
5	2.13	1.79	2.93	2.08	0.00	2.45	2.65	2.97	2.85	2.98	2.76	2.73
6	2.00	3.02	1.63	2.90	2.45	0.00	1.90	2.73	2.19	2.32	2.40	2.14
7	2.17	2.75	2.25	2.85	2.65	1.90	0.00	2.57	1.89	2.43	2.23	2.02
8	2.24	3.04	2.80	2.85	2.97	2.73	2.57	0.00	2.38	2.20	2.12	2.10
9	2.25	3.12	2.34	3.00	2.85	2.19	1.89	2.38	0.00	2.06	2.32	1.84
10	2.08	3.15	2.46	2.61	2.98	2.32	2.43	2.20	2.06	0.00	1.86	1.96
11	2.16	2.76	2.73	2.59	2.76	2.40	2.23	2.12	2.32	1.86	0.00	2.10
12	2.04	2.96	2.09	2.62	2.73	2.14	2.02	2.10	1.84	1.96	2.10	0.00

The table contains RMSD values (calculated on the Cα atoms) between the predicted models.
Read more about the root-mean-square deviation (RMSD) measure.

C^α GDT_TS between predicted models

#	1	2	3	4	5	6	7	8	9	10	11	12
1	1.00	0.71	0.71	0.73	0.73	0.76	0.71	0.72	0.71	0.72	0.74	0.74
2	0.71	1.00	0.62	0.79	0.78	0.67	0.68	0.67	0.66	0.65	0.66	0.71
3	0.71	0.62	1.00	0.65	0.70	0.79	0.72	0.64	0.73	0.70	0.69	0.74
4	0.73	0.79	0.65	1.00	0.74	0.67	0.67	0.67	0.67	0.66	0.68	0.70
5	0.73	0.78	0.70	0.74	1.00	0.70	0.67	0.65	0.66	0.62	0.66	0.70
6	0.76	0.67	0.79	0.67	0.70	1.00	0.79	0.65	0.74	0.73	0.73	0.73
7	0.71	0.68	0.72	0.67	0.67	0.79	1.00	0.68	0.79	0.70	0.73	0.78
8	0.72	0.67	0.64	0.67	0.65	0.65	0.68	1.00	0.69	0.70	0.70	0.73
9	0.71	0.66	0.73	0.67	0.66	0.74	0.79	0.69	1.00	0.73	0.71	0.81
10	0.72	0.65	0.70	0.66	0.62	0.73	0.70	0.70	0.73	1.00	0.75	0.75
11	0.74	0.66	0.69	0.68	0.66	0.73	0.73	0.70	0.71	0.75	1.00	0.73
12	0.74	0.71	0.74	0.70	0.70	0.73	0.78	0.73	0.81	0.75	0.73	1.00

The table contains GDT_TS values (calculated on the Cα atoms) between the predicted models.
Read more about the global distance test (GDT, also written as GDT_TS to represent "total score") measure.

© Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw 2013