LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone

BMC Bioinformatics

Table 5 Performance and information on each of the CASP8 targets.

Target	Target PDB id	Number of residues	Ligand	Chemical Class	Sen (%)	Prec (%)	MCC	Ratio(%)^§
T0391	3d89	157	FES	Metal	44.44	80.00	0.58	5.73
T0406	3di5	167	NI		100.00	100.00	1.00	1.80
T0407	3e38	363	ZN ZN ZN		88.89	66.67	0.76	2.48
T0410	3d3l	541	FE		12.50	6.90	0.06	2.96
T0425	3czx	181	ZN		33.33	100.00	0.57	4.97
T0426	3da2	283	ZN		33.33	18.75	0.22	3.18
T0440	3dcp	275	FE ZN FE		100.00	42.86	0.64	3.27
T0444	2vux	326	FE		75.00	8.82	0.24	1.23
T0453	3ded	91	CA CA CA		25.00	33.33	0.26	4.40
T0457	3dev	320	MG		100.00	19.05	0.43	1.25
T0461	3dh1	189	ZN		100.00	27.27	0.51	1.59
T0470	3djb	223	MG		100.00	26.67	0.50	1.79
T0476	2k5c	108	ZN		100.00	100.00	1.00	3.70
T0478	3d19	283	MG FE		71.43	100.00	0.84	2.47
T0480	2k4x	55	ZN		75.00	75.00	0.73	7.27
T0487	3f73	685	MG		25.00	5.00	0.10	0.58
Average					61.50	50.65		2.79
T0394	3dcy	275	PO4	Non-metal	33.33	57.14	0.42	4.36
T0396	396	105	FAD		13.04	75.00	0.26	21.90
T0422	3d8b	357	ADP		41.18	38.89	0.37	4.76
T0430	3dlz	357	AMP		14.29	37.50	0.20	5.88
T0431	3dax	491	HEM		10.53	18.18	0.11	3.87
T0450	3da1	561	FAD		41.03	27.59	0.28	6.95
T0477	3dkp	242	ADP MG		60.00	50.00	0.53	4.13
T0483	3dls	335	ADP MG		39.13	42.86	0.37	6.87
T0485	3dlc	218	SAM		5.26	100.00	0.22	8.72
T0490	3dme	369	FAD		29.41	35.71	0.26	9.21
T0508	3dou	197	SAM		36.84	70.00	0.47	9.64
Average					29.46	50.26		7.84

^§It stands for the ratio of the number of ligand sites to the total number of residues of the protein chain.

ISSN: 1471-2105