Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

Aloy, Patrick; Oliva, Baldo

doi:10.1186/1472-6807-9-71

Table 6 Correlation between RMSD and residue-position Zscores

From: Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

Target Set									C(ΔZ_AE_min)		C_L(Z_AE_min)		C(ΔScZE_min)		C_L(ScZE_min)
	Average	P/N	Average	P/N	Average	P/N	Average	P/N	Average	P/N	Average	P/N	Average	P/N	Average	P/N
1bbh	0.7 ± 0.1	124/34	0.7 ± 0.1	82/76	0.7 ± 0.1	135/23	0.7 ± 0.1	109/49	0.7 ± 0.1	112/46	0.6 ± 0.1	37/121	0.6 ± 0.1	92/66	0.7 ± 0.1	56/102
1c2r	0.7 ± 0.1	87/22	0.6 ± 0.2	25/84	0.7 ± 0.1	62/47	0.6 ± 0.2	23/36	0.5 ± 0.2	10/99	0.6 ± 0.2	13/96	0.5 ± 0.2	6/103	0.5 ± 0.2	5/104
1cau	0.6 ± 0.2	22/16	0.7 ± 0.2	28/10	0.5 ± 0.2	4/34	0.7 ± 0.2	28/10	0.6 ± 0.2	11/27	0.7 ± 0.2	26/12	0.5 ± 0.2	7/31	0.6 ± 0.2	19/19
1cew	0.8 ± 0.0	1/11	0.5 ± 0.3	3/9	0.6 ± 0.0	1/11	0.8 ± 0.0	1/11	0.6 ± 0	1/11	0.5 ± 0.4	2/10	0.0 ± 0.0	0/12	0.8 ± 0.0	1/11
1cid	0.7 ± 0.1	56/27	0.8 ± 0.2	52/31	0.7 ± 0.1	60/23	0.7 ± 0.1	59/24	0.8 ± 0.1	77/6	0.7 ± 0.2	28/55	0.8 ± 0.1	80/3	0.7 ± 0.2	28/55
1dxt	0.6 ± 0.1	44/106	0.7 ± 0.1	89/61	0.6 ± 0.1	79/71	0.7 ± 0.1	111/39	0.5 ± 0.2	6/144	0.7 ± 0.2	46/104	0.5 ± 0.2	8/142	0.7 ± 0.1	56/94
1eaf	0.5 ± 0.2	10/50	0.6 ± 0.2	18/42	0.6 ± 0.2	15/45	0.5 ± 0.1	22/38	0.4 ± 0.2	3/57	0.6 ± 0.2	17/43	0.4 ± 0.2	3/57	0.6 ± 0.1	28/32
1gky	0.6 ± 0.2	12/17	0.7 ± 0.2	14/5	0.5 ± 0.2	5/14	0.6 ± 0.2	14/5	0.6 ± 0.2	13/6	0.6 ± 0.2	10/9	0.6 ± 0.2	13/6	0.7 ± 0.2	12/7
1lga	0.5 ± 0.2	12/95	0.5 ± 0.2	10/97	0.5 ± 0.2	9/98	0.5 ± 0.2	5/102	0.6 ± 0.0	1/106	0.5 ± 0.2	8/99	0.4 ± 0.3	2/105	0.4 ± 0.3	3/104
1mdc	0.7 ± 0.1	59/56	0.7 ± 0.2	42/73	0.7 ± 0.1	68/47	0.7 ± 0.2	47/68	0.6 ± 0.1	39/76	0.6 ± 0.1	28/87	0.6 ± 0.2	16/99	0.6 ± 0.2	18/97
1mup	0.7 ± 0.1	60/74	0.7 ± 0.1	73/61	0.7 ± 0.1	68/66	0.7 ± 0.1	77/57	0.7 ± 0.1	99/35	0.7 ± 0.1	59/75	0.7 ± 0.1	112/22	0.7 ± 0.1	53/81
1onc	0.7 ± 0.2	53/69	0.6 ± 0.2	29/93	0.7 ± 0.2	59/63	0.7 ± 0.2	38/84	0.7 ± 0.1	102/20	0.7 ± 0.2	43/79	0.7 ± 0.1	86/36	0.7 ± 0.1	40/82
2afn	0.6 ± 0.1	80/39	0.6 ± 0.1	73/46	0.6 ± 0.1	22/97	0.6 ± 0.1	71/48	0.5 ± 0.1	25/94	0.5 ± 0.2	18/103	0.5 ± 0.2	9/110	0.5 ± 0.1	17/102
2cmd	0.7 ± 0.1	101/128	0.6 ± 0.1	112/117	0.6 ± 0.1	93/136	0.6 ± 0.1	103/126	0.6 ± 0.1	102/127	0.6 ± 0.1	50/179	0.6 ± 0.1	42/187	0.6 ± 0.1	58/171
2fbj	0.6 ± 0.2	12/89	0.6 ± 0.1	24/77	0.6 ± 0.2	7/94	0.6 ± 0.2	13/88	0.6 ± 0.1	32/69	0.6 ± 0.2	11/90	0.6 ± 0.1	40/61	0.6 ± 0.1	19/82
2mta	0.6 ± 0.1	47/111	0.7 ± 0.1	48/110	0.7 ± 0.1	75/83	0.7 ± 0.2	32/126	0.7 ± 0.1	104/54	0.7 ± 0.1	73/85	0.7 ± 0.1	130/28	0.6 ± 0.2	40/118
2pna	0.7 ± 0.1	41/97	0.7 ± 0.1	73/65	0.7 ± 0.2	37/101	0.7 ± 0.1	71/67	0.0 ± 0.0	0/138	0.7 ± 0.2	67/71	0.6 ± 0.2	12/126	0.7 ± 0.2	59/79
2sim	0.5 ± 0.2	4/90	0.4 ± 0.3	3/91	0.0 ± 0.0	0/94	0.6 ± 0.0	1/93	0.4 ± 0.3	2/92	0.6 ± 0.0	1/93	0.4 ± 0.3	2/92	0.0 ± 0.0	0/94
4sbv	0.5 ± 0.4	2/2	0.4 ± 0.3	2/2	0.4 ± 0.3	2/2	0.4 ± 0.3	2/2	0.0 ± 0.0	0/4	0.0 ± 0.0	0/4	0.0 ± 0.0	0/4	0.0 ± 0.0	0/4
8i1b	0.4 ± 0.3	2/135	0.6 ± 0.2	11/126	0.5 ± 0.2	5/132	0.6 ± 0.2	13/124	0.6 ± 0.1	43/94	0.5 ± 0.1	18/119	0.5 ± 0.1	23/114	0.6 ± 0.2	13/124

Pearson correlation between RMSD of Cα atoms and residue-position Zscores of structure-models in MOULDER decoy set. In the first column is shown the code of the native protein used to generate the decoys of a model/target set. Next columns show: i) the average of Pearson correlation (Average) of those models with RMSD from the native structure smaller than 7Å and using only correlations higher than 0.5; and ii) the ratio P/N, being P the number of models with correlation larger than 0.5 and N those with correlation smaller than or equal to 0.5 among models with RMSD larger than 7Å. Residue-position Zscores are: Sc, ScZE_min, , Z_AE_min and the differences of Sc and ScZE_min of the decoy conformers with respect to their native structure (ΔSc and ΔScZE_min). Pearson correlations between Cα RMSDs and Zscores are denoted as C(Zscore) - in even columns -, while correlation of Cα RMSDs and Zscores normalized by length are indicated as C_L(Zscore) - in odd columns -.

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ISSN: 1472-6807

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