An assessment of catalytic residue 3D ensembles for the prediction of enzyme function

BMC Bioinformatics

Table 2 Classification performance for pose comparison

	Method	MCC	TP	FP	TN	FN
DIFF_SF	cu_ RMSD _N2 = 0.65 Å, 6 EC classes	0.19	61	58	417	159
	cu_ RMSD _N2 = 0.21 Å, cu_ S _GO = 0.88, CC, BP, MF	0.44	2	8	608	0
	cu_ RMSD _N2 = 0.21 Å, cu_ S _GO = 0.88, BP, MF	0.64	5	5	607	1
	cu_ RMSD _N2 = 0.50 Å, cu_ S _GO = 0.75, BP, MF	0.36	35	38	493	52
	cu_ RMSD _N2 = 0.21 Å, cu_ S _GO = 0.75, BP, MF	0.29	5	5	587	21
	cu_ RMSD _N2 = 0.91 Å, cu_ S _GO = 0.88, BP, MF	0.11	6	279	333	0
	cu_ RMSD _N2 = 0.91 Å, cu_ S _GO = 0.75, BP, MF	0.13	20	265	327	6
ALL_ENZ_SITES	cu_ RMSD _N2 = 0.37 Å, cu_ S _GO = 0.90, BP, MF	0.29	14	41	546	17
	cu_ RMSD _N2 = 0.99 Å, cu_ S _GO = 0.77, BP, MF	0.47	59	78	459	22
	cu_ RMSD = 0.85 Å, cu_ S _GO = 0.70, MF	0.57	167	73	325	53
	best of 10 cu_ RMSD _N2 = 1.10 Å, cu_ S _GO = 0.75, BP, MF	0.58	163	65	337	53

In all cases, the cut-offs for the comparison of poses (cu_ RMSD or cu_ RMSD _N2) and sets of GO terms (S _GO) are given under Method. The terms CC, BP, and MF indicate which combination of terms from the annotation domains were analyzed, respectively. The columns on the right give the MCC value and the number of TP, FP, TN, and FN cases, which resulted from a classification using these cut-offs. For the experiments labeled DIFF_SF, only poses for enzymes from different superfamilies were compared; for ALL_ENZ_SITES, sites from all entries of ENZ_SITES were compared

ISSN: 1471-2105