Protein structure prediction by all-atom free-energy refinement

BMC Structural Biology

Table 1 Results for high quality data sets

pdb	nres	<3	3–4	Δ_1best	Δ_1min	R	Δ_1cl	N	Z
1res	35	0.97	0.02	1.84	1.84	1	1.55	21	-2.68
1uxd	43	0.62	0.12	1.48	1.48	1	1.46	31	-2.38
2pdd	43	0.09	0.22	7.40	3.76	10	3.29	43	-2.98
1dv0	45	0.00	0.10	4.33	2.93	7	3.48	31	-1.70
1gab	47	0.37	0.23	2.51	2.51	1	2.23	46	-2.17
1vif	48	0.28	0.02	9.44	2.33	2	1.45	42	-2.56
1aa3	56	0.01	0.17	7.03	3.57	9	2.67	27	-2.88
1bw6	56	0.14	0.21	4.59	3.65	3	2.18	25	-2.94
1am3	57	0.30	0.09	7.85	3.32	14	7.12	18	-4.80
1pgx	57	0.12	0.18	7.97	2.92	7	5.75	28	-3.93
1r69	61	0.22	0.07	1.63	1.63	1	1.20	37	-4.76
1a32	65	0.23	0.08	1.65	1.65	1	1.01	38	-2.66
2ezh	65	0.01	0.17	5.76	3.17	4	3.18	28	-2.72
1nre	66	0.08	0.14	10.89	2.38	2	1.79	38	-3.36
1sro	66	0.00	0.14	3.78	3.78	1	3.61	36	-1.88
2fow	66	0.00	0.12	4.31	3.67	31	5.47	26	-1.62
1ctf	67	0.00	0.19	10.97	3.99	76	5.13	46	-4.38
1nkl	70	0.00	0.14	6.43	3.55	4	3.27	28	-3.83
1pou	70	0.01	0.10	3.90	3.90	1	2.71	30	-3.82
1mzm	71	0.00	0.16	3.96	3.96	1	2.75	39	-2.84
1afi	72	0.02	0.24	3.54	3.54	1	2.38	49	-3.23
1kjs	74	0.00	0.17	3.89	3.89	1	3.17	48	-1.32

Name, number of amino acids, fraction of decoys with less than 3 Å and between 3–4 Å C_αRMSD respectively, D deviation of the energetically lowest/lowest near-native decoy (Δ_1best/Δ_1min) and the rank of the latter (A rank of one indicates that the lowest energy decoy is near-native), Δ_1cl is the C_αRMSD of the largest cluster of the fifty best decoys, followed by the size of this cluster(N) and Z-score of the native decoys against the decoy set.

ISSN: 1472-6807