. 2004 Jun 18;4:8. doi: 10.1186/1472-6807-4-8

Table 2.

Performance of the density score function on 83 decoy sets grouped by their generation methods.

Protein (PDB code)	N	RMSD range (Å)	R_B1	log P_B1	log P_B10	F.E.(%)	C.C.	R.C.	R_exp	C.C._orig
4state_reduced

1ctf	630	1.32 – 9.07	7	-1.95	-2.8	88.9	0.98	0.99	1	0.95
1r69	675	0.88 – 8.31	7	-1.98	-2.83	87.4	0.96	0.98	1	0.88
1sn3	660	1.31 – 9.13	11	-1.78	-2.82	86.4	0.96	0.97	1	0.95
2cro	674	0.81 – 8.31	1	-2.82	-2.83	84.6	0.96	0.98	1	0.82
3icb	653	0.95 – 9.39	2	-2.51	-2.81	84.2	0.98	0.99	4	0.95
4pti	687	1.41 – 9.27	11	-1.8	-2.84	91.7	0.95	0.96	3	0.91
4rxn	677	1.36 – 8.14	3	-2.35	-2.83	84.2	0.98	0.98	1	0.95
Average	665	1.15 – 8.80		-2.17	-2.82	86.8	0.97	0.98		0.92

fisa

1fc2	500	3.11 – 10.58	115	-0.64	-0.98	6	0.95	0.67	399	0.91
1hdd-C	500	2.77 – 12.92	18	-1.44	-1.62	28	0.95	0.88	248	0.93
2cro	500	4.29 – 12.60	109	-0.66	-1.7	26	0.74	0.75	98	0.62
4icb	500	4.75 – 14.13	81	-0.79	-1.68	24	0.69	0.69	138	0.60
Average	500	3.73 – 12.56		-0.89	-1.5	21	0.83	0.75		0.77

fisa_casp3

1bg8-A	1,200	6.03 – 15.80	177	-0.83	-1.16	13.3	0.39	0.39	721	0.2
1bl0	971	3.63 – 18.17	44	-1.34	-2.03	57.7	0.74	0.73	129	0.7
1eh2	2,413	4.00 – 15.29	196	-1.09	-2.68	52.6	0.8	0.81	300	0.75
1jwe	1,407	7.79 – 20.87	345	-0.61	-0.72	4.2	-0.24	-0.23	1298	-0.23
l30	1,400	6.47 – 24.62	474	-0.47	-0.91	0	0.28	0.25	N/A	0.21
smd3	1,200	8.54 – 17.00	74	-1.21	-1.21	17.5	0.65	0.6	993	0.45
Average	1,432	6.08 – 18.63		-0.93	-1.45	24.2	0.43	0.42		0.35

lattice_ssfit

1beo	2,000	7.00 – 15.61	6	-2.52	-2.52	30.5	0.46	0.45	1069	0.07
1ctf	2,000	5.45 – 12.81	174	-1.06	-1.74	40	0.71	0.72	882	0.55
1dkt-A	2,000	6.69 – 14.05	74	-1.43	-2	34	0.42	0.4	1987	0.18
1fca	2,000	5.14 – 11.39	224	-0.95	-1.81	43	0.55	0.54	1287	0.35
1nkl	2,000	5.27 – 13.64	264	-0.88	-2.19	20	0.54	0.56	1103	0.33
1pgb	2,000	5.81 – 12.91	796	-0.4	-1.04	10	0.39	0.35	1840	0.27
1trl-A	2,000	5.38 – 12.52	480	-0.62	-1.63	14.5	0.41	0.39	1458	0.3
4icb	2,000	4.74 – 12.92	16	-2.1	-2.3	41	0.69	0.69	318	0.61
Average	2,000	5.68 – 13.23		-1.24	-1.9	29.1	0.52	0.51		0.33

lmds

1b0n-B	497	2.45 – 6.03	70	-0.85	-0.85	2	0.14	0.16	468	0.15
1bba	500	2.78 – 8.91	162	-0.49	-0.72	0	0.39	0.24	300	0.5
1ctf	497	3.59 – 12.53	185	-0.43	-0.58	0	0.41	0.49	367	0.1
1dtk	215	4.32 – 12.58	90	-0.38	-0.93	14	0.63	0.55	121	0.53
1fc2	500	3.99 – 8.45	245	-0.31	-0.7	4	0.46	0.22	488	0.25
1igd	500	3.11 – 12.55	135	-0.57	-1.7	38	0.81	0.79	113	0.84
1shf-A	437	4.39 – 12.35	19	-1.36	-1.36	13.7	0.15	0.16	211	0.18
2cro	500	3.87 – 13.48	208	-0.38	-0.8	0	0.36	0.36	362	0.16
2ovo	347	4.38 – 13.38	15	-1.36	-1.5	23.1	0.56	0.59	162	0.45
4pti	343	4.94 – 13.18	119	-0.46	-1.28	14.6	0.67	0.52	250	0.63
unk	500	6.68 – 13.94	190	-0.42	-0.46	0	0.25	0.07	N/A	0.07
Average	440	4.05 – 11.58		-0.64	-0.99	9.9	0.44	0.38		0.35

semfold

1ctf	11,400	4.44 – 12.98	1,936	-0.77	-0.87	9.7	0.13	0.17	10252	0.05
1e68	11,360	2.98 – 12.53	6,388	-0.25	-0.27	14.5	0.19	0.13	2951	0.31
1eh2	11,440	5.32 – 15.07	1,068	-1.03	-1.41	21.9	0.24	0.21	3998	0.22
1khm	21,080	3.84 – 14.77	8,992	-0.37	-0.67	5.9	0.1	0.1	13444	0.07
1nkl	11,660	3.84 – 14.22	2,862	-0.61	-0.73	14.4	0.32	0.32	3992	0.32
1pgb	11,280	4.67 – 13.01	3,650	-0.49	-0.59	7.4	0.09	0.11	11274	0.06
Average	13,037	4.18 – 13.76		-0.59	-0.76	12.3	0.18	0.17		0.17

Rosetta

1a32	1,610	0.92 – 16.89	352	-0.66	-1.02	19.3	0.89	0.93	290	0.87
1aa3	1,865	3.02 – 12.77	390	-0.68	-0.77	3.8	0.57	0.6	1	0.66
1afi	1,824	2.24 – 15.14	26	-1.85	-2.22	42.8	0.92	0.94	201	0.95
1ail	1,807	1.97 – 14.69	95	-1.28	-1.77	59.8	0.92	0.93	49	0.91
1am3	1,898	1.36 – 11.63	245	-0.89	-1.92	39	0.69	0.75	1	0.81
1bq9	1,825	2.59 – 15.73	303	-0.78	-1.88	30.1	0.41	0.47	1	0.68
1bw6	1,900	1.89 – 12.30	11	-2.22	-2.5	27.9	0.75	0.74	1	0.84
1cc5	1,892	6.41 – 26.78	280	-0.83	-1.06	30.7	0.46	0.46	1891	0.36
1cei	1,897	4.57 – 16.34	185	-1.01	-2.8	51.1	0.82	0.84	255	0.75
1csp	1,809	3.89 – 17.92	361	-0.7	-1.03	7.7	0.49	0.47	1	0.58
1ctf	1,922	5.07 – 15.81	305	-0.8	-2.44	31.2	0.75	0.7	1	0.67
1dol	1,871	3.77 – 14.87	100	-1.27	-1.27	17.1	0.37	0.4	1	0.6
1gab	1,898	2.75 – 11.81	345	-0.74	-0.74	0.5	0.29	0.29	1	0.38
1hyp	1,893	4.64 – 15.63	337	-0.75	-1.62	20.6	0.19	0.26	55	0.42
1kjs	1,893	3.37 – 13.68	77	-1.39	-1.68	30.1	0.79	0.76	1	0.78
1lfb	1,893	2.47 – 14.93	198	-0.98	-1.65	27.5	0.73	0.74	1	0.81
1msi	1,894	5.84 – 14.52	107	-1.25	-1.58	32.7	0.47	0.49	1	0.59
1mzm	1,934	3.68 – 15.08	443	-0.64	-0.66	1	0.05	0.1	191	0.19
1nkl	1,898	2.73 – 12.74	208	-0.96	-1.41	24.2	0.58	0.54	1	0.58
1nre	1,893	1.80 – 17.11	300	-0.8	-1.5	37	0.7	0.75	1	0.82
1orc	1,883	2.88 – 15.08	343	-0.74	-1.09	20.2	0.57	0.57	2	0.65
1pgx	1,851	5.03 – 16.75	465	-0.6	-0.6	0	-0.19	-0.17	1261	-0.2
1pou	1,898	2.28 – 17.68	322	-0.77	-2.13	46.9	0.59	0.64	1	0.77
1ptq	1,885	5.42 – 12.23	368	-0.71	-1.29	11.7	0.12	0.09	1	0.41
1r69	1,733	2.26 – 12.58	218	-0.9	-1.03	30	0.73	0.76	1	0.74
1res	1,723	1.89 – 9.15	475	-0.56	-0.57	0	-0.13	0	334	-0.17
1sro	1,881	3.39 – 15.36	462	-0.61	-0.83	4.8	0.77	0.75	1	0.68
1tif	1,849	2.61 – 11.56	464	-0.6	-1.46	15.1	0.59	0.53	1	0.61
1tuc	1,894	4.49 – 16.85	37	-1.71	-2.16	35.9	0.66	0.66	1	0.69
1uba	1,899	4.07 – 11.62	346	-0.74	-1.22	31.6	0.39	0.41	1	0.51
1utg	1,897	3.36 – 16.50	535	-0.55	-0.73	18.5	0.51	0.5	1	0.65
1uxd	1,896	1.12 – 10.13	181	-1.02	-1.21	25.8	0.61	0.58	1	0.68
1vcc	1,857	3.85 – 16.90	64	-1.46	-3.27	41.5	0.76	0.78	1	0.6
1vif	1,896	4.78 – 15.18	233	-0.91	-1.03	6.9	0.76	0.76	1	0.76
2ezh	1,893	2.34 – 18.26	510	-0.57	-2.24	28.5	0.56	0.57	1	0.68
2fow	1,834	4.03 – 13.89	59	-1.49	-2.22	39.3	0.46	0.54	1	0.64
2fxb	1,800	7.46 – 19.02	58	-1.49	-2.3	47.8	0.75	0.75	1	0.48
2pdd	1,740	2.33 – 10.02	934	-0.27	-1.09	17.8	0.21	0.23	1	0.53
2ptl	1,835	2.21 – 15.45	16	-2.06	-2.22	38.2	0.86	0.86	1	0.78
5icb	1,870	2.98 – 13.68	527	-0.55	-2.49	30	0.59	0.62	1	0.7
5pti	1,853	4.88 – 15.31	586	-0.5	-1.28	8.6	0.24	0.2	1	0.6
Average	1,858	3.38 – 14.87		-0.96	-1.56	25.2	0.54	0.56		0.61

The PDB code, the number of decoy conformations (N), the RMSD range of the decoys relative to the experimentally determined conformation, the RMSD ranking of the best-scoring conformation, the log probability of selecting the best-scoring conformation (log P_B1), the log probability of selecting the lowest RMSD conformation in the top 10 best scoring conformations (log P_B10), the fraction enrichment of the 10% lowest RMSD conformations in the top 10% best scoring conformations (F.E.), the correlation coefficient between scores and RMSDs (C.C.), the Spearman's rank correlation coefficient between scores and RMSDs (R.C.), the ranking of the experimentally determined conformation relative to the decoy conformations based on density scores (R_exp), and the correlation coefficient calculated by the original formula used by Simons et. al. [27] (C.C._orig) are shown. In general, the density score function performs very well, with dependence on the properties of the decoy sets.