FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

Roche, Daniel B; Tetchner, Stuart J; McGuffin, Liam J

doi:10.1186/1471-2105-12-160

BMC Bioinformatics

Table 9 The mean MCC and BDT raw scores and Z-scores obtained by FunFOLD are compared with those obtained by the top CASP9 function prediction groups for the extended binding sites analysis.

From: FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

Group ID	N	Mean score for group		Mean score for FunFOLD		Difference in mean score		Mean Z-score for group		Mean Z-score for FunFOLD		P-value (raw score)		P-value (Z-score)		1 - p-value (raw score)		1 - p-value (Z-score)
		MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT	MCC	BDT
FN035	20	0.714	0.637	0.577	0.508	-0.137	-0.129	0.684	0.647	0.078	0.080	0.866	0.955	0.890	0.947	0.134	0.045	0.110	0.053
FN096	24	0.678	0.596	0.546	0.473	-0.132	-0.123	0.590	0.547	0.038	0.054	0.957	0.948	0.948	0.941	0.043	0.052	0.052	0.059
FN339	24	0.648	0.576	0.546	0.473	-0.102	-0.103	0.468	0.487	0.038	0.054	0.941	0.926	0.885	0.934	0.059	0.034	0.115	0.105
FN242	23	0.649	0.557	0.545	0.475	-0.104	-0.082	0.456	0.333	0.008	0.044	0.975	0.851	0.975	0.851	0.025	0.074	0.025	0.066
FN315	21	0.681	0.512	0.582	0.473	-0.099	-0.039	0.403	0.077	0.068	0.054	0.831	0.450	0.763	0.450	0.169	0.149	0.237	0.149
FN104	22	0.666	0.573	0.555	0.484	-0.112	-0.089	0.275	0.186	-0.012	-0.016	0.912	0.778	0.808	0.778	0.088	0.141	0.192	0.222
FN110	22	0.657	0.618	0.588	0.508	-0.070	-0.111	0.274	0.488	0.117	0.102	0.684	0.895	0.500	0.895	0.316	0.384	0.500	0.550
FN094	23	0.575	0.473	0.571	0.494	-0.004	0.021	-0.013	-0.104	0.113	0.112	0.301	0.112	0.233	0.112	0.699	0.375	0.767	0.500
FN114	23	0.576	0.478	0.539	0.472	-0.037	-0.006	-0.076	-0.198	-0.010	-0.002	0.662	0.277	0.404	0.277	0.388	0.835	0.596	0.888
FN113	22	0.575	0.516	0.565	0.493	-0.010	-0.023	-0.109	-0.027	0.067	0.056	0.377	0.500	0.266	0.500	0.623	0.419	0.734	0.581
FN236	24	0.535	0.444	0.546	0.473	-0.011	0.029	-0.121	-0.265	0.038	0.054	0.463	0.152	0.320	0.152	0.537	0.610	0.680	0.723
FN452	22	0.589	0.508	0.560	0.488	-0.028	-0.020	-0.166	-0.135	0.007	0.032	0.639	0.419	0.448	0.419	0.361	0.755	0.552	0.848
FN017	23	0.471	0.430	0.571	0.494	0.100	0.063	-0.442	-0.285	0.113	0.112	0.040	0.037	0.024	0.037	0.960	0.960	0.976	0.963
FN425	23	0.429	0.345	0.545	0.471	0.116	0.126	-0.523	-0.599	-0.011	0.011	0.049	0.012	0.049	0.012	0.951	0.984	0.951	0.941
FN072	23	0.474	0.423	0.571	0.494	0.097	0.071	-0.528	-0.376	0.113	0.112	0.024	0.059	0.019	0.059	0.976	0.957	0.981	0.970
FN057	23	0.475	0.419	0.571	0.494	0.096	0.075	-0.540	-0.386	0.113	0.112	0.022	0.030	0.012	0.030	0.978	0.978	0.988	0.990
FN415	23	0.457	0.416	0.571	0.494	0.114	0.078	-0.556	-0.426	0.113	0.112	0.022	0.022	0.012	0.010	0.978	0.992	0.988	0.988

The analysis is based on common subsets of all CASP9 targets, with a minimum of 10 predictions in common. N, size of the common subset used in the comparison; MCC, Matthews Correlation Coefficient; BDT, the Binding Site Distance Test Score [36].P-value, the p-value for the paired Wilcoxon signed rank sum test using the raw scores; P-value (Z-score), the p-value for the paired Wilcoxon signed rank sum test using the Z-scores; 1 - p-value, 1 minus the p-value for the paired Wilcoxon signed rank sum test using the raw scores; 1-p-value (Z-score), 1 minus the p-value for the paired Wilcoxon signed rank sum test using the Z-scores. The table is sorted by the Mean MCC Z-score for groups with the best CASP9 groups at the top. The highest mean scores, mean Z-scores, significant p-values and significant 1-p-values are indicated in bold. Server groups are underlined.

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