Table 2.

Quality Comparison of the Decoys Generated by the 1^st-Order and 2^ND-Order CRF Models

	Size	C		Best	≤6Å	≤7Å	≤8Å	≤9Å	≤10Å	≤11Å	≤12Å
1aa2	108	α	O1	7.34	0	0	0.0350	0.245	1.05	4.27	13.5
			O2	7.31	0	0	0.0145	0.116	0.97	4.99	17.7
1beo	98	α	O1	6.42	0	0.0200	0.200	0.990	3.27	9.70	23.0
			O2	5.84	0.00963	0.0481	0.385	1.37	4.50	12.5	29.3
1ctfA	68	αβ	O1	3.70	2.41	7.18	16.2	31.4	51.7	77.2	95.9
			O2	3.67	6.62	22.3	47.1	64.7	78.9	94.8	99.5
1dktA	72	β	O1	6.15	0	0.100	0.870	3.81	12.5	33.4	62.8
			O2	5.07	0.121	1.48	5.94	16.2	34.3	59.3	82.6
1enhA	54	α	O1	2.32	22.4	32.4	44.7	61.2	85.4	98.5	100
			O2	2.21	69.3	72.0	77.7	87.1	97.4	99.9	100
1fc2C	43	α	O1	1.94	49.1	64.1	85.0	97.6	99.7	100	100
			O2	2.28	85.4	91.7	97.3	99.8	100	100	100
1fca	55	β	O1	4.99	0.145	1.3	6.00	19.9	49.7	85.5	99.3
			O2	4.96	0.207	2.65	13.5	36.3	68.2	94.0	99.8
1fgp	67	β	O1	7.40	0	0	0.035	0.46	4.21	20.2	54.2
			O2	5.94	0.00481	0.0433	0.582	4.25	18.2	48.2	81.8
1jer	110	β	O1	9.64	0	0	0	0	0.0050	0.120	0.910
			O2	10.2	0	0	0	0	0	0.185	1.11
1nkl	78	α	O1	3.64	5.91	14.1	25.1	45.2	66.6	86.8	97.7
			O2	3.06	20.3	30.1	44.2	65.3	84.0	96.7	99.8
1pgb	56	αβ	O1	3.15	22.3	45.0	65.1	81.0	93.0	98.6	99.9
			O2	2.60	63.2	85.8	93.9	97.7	99.5	99.9	100
1sro	76	β	O1	6.22	0	0.0700	0.525	2.75	10.0	27.1	54.7
			O2	5.39	0.0193	0.289	1.54	5.09	14.5	32.9	60.0
1trlA	62	α	O1	3.53	13.5	25.3	38.5	57.4	85.1	99.1	99.9
			O2	3.72	34.1	45.3	53.5	68.0	94.8	100	100
2croA	65	α	O1	2.80	16.8	31.4	47.9	63.3	79.9	93.0	99.6
			O2	2.58	35.4	52.9	67.4	79.3	88.9	95.6	99.9
2gb1A	56	β	O1	2.91	23.3	45.6	65.8	81.8	93.2	98.8	99.9
			O2	2.04	65.2	86.1	93.8	97.8	99.5	100	100
4icbA	76	α	O1	4.63	0.515	2.65	7.64	16.8	33.6	59.1	84.3
			O2	4.40	0.125	0.600	2.85	12.3	31.0	58.9	88.5
T052	98	β	O1	7.58	0	0	0.0100	0.0350	0.135	0.800	3.52
			O2	8.37	0	0	0	0.0251	0.296	1.78	6.58
T056	114	α	O1	7.78	0	0	0.0198	0.0842	0.510	2.26	7.07
			O2	7.57	0	0	0.00497	0.0944	1.07	3.83	8.38
T059	71	β	O1	6.30	0	0.0100	0.135	1.14	7.20	26.8	61.1
			O2	6.21	0	0.0245	0.421	3.85	17.4	45.1	77.3
T061	76	α	O1	5.36	0.01	0.37	2.89	10.7	27.0	50.9	77.6
			O2	6.04	0	0.282	4.73	19.9	40.5	62.7	82.6
T064	103	α	O1	7.23	0	0	0.035	0.2	0.91	2.79	7.30
			O2	7.47	0	0	0.0320	0.412	1.53	3.62	9.05
T074	98	α	O1	4.86	0.0150	0.235	1.23	4.00	10.4	22.0	41.0
			O2	4.22	0.0980	0.835	3.56	9.62	18.7	30.4	49.3

Columns 1–3 list the PDB code, protein size and the type of the test proteins. Columns “best” list the RMSD (Å) of the best decoys; the other columns list the percentage of decoys with RMSD smaller than a given threshold. “O1” and “O2” denote the 1^st-order and the 2^nd-order CRF models, respectively. In total, ∼20,000 decoys are generated for each protein without an energy function.