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 1 The mean MCC and BDT raw scores and Z-scores obtained by FunFOLD are compared with those obtained by each CASP8 function prediction group.

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		Increase 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
FN407	25	0.768	0.689	0.778	0.702	0.010	0.013	1.105	1.099	1.137	1.134	0.734	0.487	0.699	0.526	0.266	0.513	0.301	0.474
FN293	19	0.742	0.684	0.789	0.748	0.050	0.064	1.016	1.022	1.164	1.254	0.318	0.128	0.285	0.172	0.682	0.872	0.715	0.828
FN202	23	0.670	0.578	0.797	0.754	0.130	0.176	0.845	0.801	1.158	1.259	0.004	0.001	0.006	0.004	0.996	0.999	0.994	0.996
FN417	26	0.485	0.387	0.747	0.702	0.260	0.315	0.335	0.165	1.066	1.134	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN034	23	0.488	0.387	0.810	0.762	0.320	0.375	0.249	0.086	1.200	1.283	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN209	11	0.465	0.376	0.779	0.694	0.310	0.319	0.230	0.163	1.200	1.207	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN163	23	0.438	0.426	0.717	0.668	0.280	0.242	0.209	0.281	1.017	1.066	0.000	0.002	0.000	0.002	1.000	0.998	1.000	0.998
FN057	24	0.405	0.393	0.769	0.718	0.360	0.326	0.084	0.138	1.118	1.184	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN450	25	0.358	0.286	0.755	0.715	0.400	0.429	0.073	-0.031	1.072	1.162	0.000	0.000	0.000	0.001	1.000	1.000	1.000	0.999
FN325	25	0.377	0.336	0.778	0.730	0.400	0.394	-0.003	-0.015	1.131	1.203	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN437	17	0.209	0.183	0.768	0.716	0.560	0.534	-0.564	-0.603	1.151	1.243	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN108	24	0.136	0.133	0.769	0.730	0.630	0.597	-0.682	-0.663	1.121	1.203	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN483	21	0.076	0.094	0.723	0.669	0.650	0.575	-0.736	-0.719	1.040	1.063	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN242	26	0.126	0.133	0.747	0.702	0.620	0.569	-0.744	-0.704	1.066	1.134	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN105	26	0.011	0.044	0.747	0.702	0.740	0.658	-1.069	-0.983	1.066	1.134	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000
FN086	24	0.024	0.068	0.781	0.728	0.760	0.660	-1.077	-0.933	1.151	1.222	0.000	0.000	0.000	0.000	1.000	1.000	1.000	1.000

The analysis is based on common subsets of all CASP8 function prediction 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 tables are sorted by the Mean MCC Z-score for groups with the best CASP8 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 (FN293 and FN105 were extended deadline server groups; no publicly available server could be found for FN293 at the time of writing; group FN202 now have a publicly available server which is comparable to their CASP8 performance [15]).

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ISSN: 1471-2105

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