Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts

Table 3 List of all domains with reconstruction accuracy below 0.5 TM-score

CASP	Domain	L	Type	H	E	N_c	TM-score	RMSD	GDT-TS	Energy
8	T0393-D2	99	TBM	74	0	50	0.29	10.6	27.8	0.0
8	T0405-D1	72	FM	58	0	67	0.42	7.2	45.5	0.0
8	T0443-D1	66	FM	41	0	42	0.45	6.6	50.0	0.0
8	T0443-D3	66	TBM	35	6	67	0.41	5.9	48.1	0.5
8	T0454-D2	140	TBM	94	0	141	0.49	6.6	40.0	1.0
8	T0470-D2	77	TBM	45	0	71	0.34	7.7	35.7	0.0
8	T0482-D1	67	FM	17	32	119	0.40	8.0	44.0	5.9
9	T0548-D2	60	TBM	43	0	45	0.42	7.4	49.6	0.2
9	T0553-D2	71	FM	46	0	59	0.49	4.6	52.8	0.0
9	T0575-D2	127	TBM	100	0	128	0.45	6.4	37.0	2.5
9	T0589-D2	82	TBM	58	0	74	0.48	5.2	48.8	0.0
9	T0598-D1	127	TBM	64	11	141	0.48	6.5	41.9	1.0
9	T0616-D1	97	FM	41	0	84	0.32	12.3	28.6	0.7
9	T0617-D1	136	TBM	96	8	143	0.49	11.8	43.2	8.1
9	T0629-D2	159	FM	0	4	31	0.16	25.2	12.1	0.0
9	T0637-D1	135	FM	109	0	75	0.33	16.1	24.4	0.3
9	T0639-D1	124	FM	76	4	133	0.36	8.3	30.9	2.7
10	T0680-D1	96	TBM	79	0	108	0.36	7.2	33.9	7.7
10	T0685-D1	72	TBM	54	0	42	0.27	8.5	31.3	0.0
10	T0693-D1	100	FM	47	12	101	0.38	14.7	34.5	1.3
10	T0724-D1	119	TBM	38	40	133	0.30	13.3	26.3	1.4
10	T0732-D2	91	TBM	48	0	91	0.44	5.8	46.2	1.5
10	T0741-D1	125	FM	0	73	218	0.45	17.1	39.0	5.8
10	T0756-D2	86	FM	45	0	15	0.25	12.0	25.9	0.0
11	T0820-D1	90	FM	65	0	72	0.40	7.3	41.9	0.0
11	T0821-D1	255	TBM	195	0	378	0.46	8.6	26.9	35.6
11	T0831-D1	155	TBM	114	0	141	0.44	15.8	34.8	1.5
11	T0836-D1	204	FM	157	0	198	0.38	12.9	22.8	7.2

The models were reconstructed with contacts only. L, H, E, and N_c refer to length of the protein, number of helical residues, strand residues, and number of native contacts in the native structures, respectively. TM-score, RMSD, and GDT-TS of the best-of-20 models for each domain are presented. The last column (Energy) is the sum of the distance deviation from 8 Å for all the contacts supplied as distance restraints

ISSN: 1471-2105