Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database

Table 2 Ligand-binding sites predictions of CASP10/11 targets proteins†

Target	PDB	Ligand	Type	Sites*	Prediction	TP	Precision	Recall	MCC
T0652	4HG0	AMP	Non-metal	11	17	6	0.35	0.55	0.41
T0657	2LUL	ZN	Metal	5	9	4	0.44	0.8	0.58
T0659	4ESN	ZN	Metal	3	No-hit
T0675	2LV2	ZN	Metal	8	9	8	0.89	1	0.94
T0686	4HQL	MG	Metal	5	6	3	0.5	0.6	0.54
T0696	4RT5	NA	Metal	6	3	1	0.33	0.17	0.21
T0697	4RIT	TRS	Non-metal	6	11	0	0	0	0
T0706	4RCK	MG	Metal	5	3	3	1	0.6	0.77
T0720	4IC1	MN/SF4	Metal	14	No-hit
T0721	4FK1	FAD	Non-metal	29	3	3	1	0.1	0.31
T0726	4FGM	ZN	Metal	7	No-hit
T0737	3TD7	FAD	Non-metal	21	13	12	0.92	0.57	0.71
T0744	2YMV	FNR	Non-metal	19	4	4	1	0.21	0.45

† Target 762 to 854 were taken from CASP11 whose protein-ligand interactions were well characterized in the crystal structures
*“Sites” is the number of ligand-binding sites recorded in PDB files of the target protein

ISSN: 1471-2105