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

Table 3 Prediction performance of LIBRA*

Target	PDB	Length	Sites	LIBRA Rank-1				LIBRA Rank-2
Target	PDB	Length	Sites	Prediction	TP	Model	MCC	Prediction	TP	Model	MCC
T0652	4HG0	292	11	7	1	N	0.08	8	7	N	0.74
T0657	2LUL	154	5	4	4	Y	0.89	4	0	N	0
T0659	4ESN	72	3	3	3	Y	1	3	0	N	0
T0675	2LV2	74	8	4	4	Y	0.69	4	4	N	0.69
T0686	4HQL	242	5	3	3	Y	0.77	3	3	Y	0.77
T0696	4RT5	111	6	7	0	N	0	5	0	N	0
T0697	4RIT	483	6	14	0	N	0	5	0	N	0
T0706	4RCK	217	5	3	0	N	0	8	1	N	0.14
T0720	4IC1	202	8	4	4	Y	0.7	5	0	N	0
T0721	4FK1	301	29	24	23	N	0.86	23	2	N	0.01
T0726	4FGM	589	7	6	6	N	0.92	10	0	N	0
T0737	3TD7	292	21	10	10	N	0.67	6	0	N	0
T0744	2YMV	329	19	12	12	Y	0.78	2	2	Y	0.64

*LIBRA prediction was based on the input of the PDBs of the target proteins. “Sites” is the number of ligand-binding sites recorded in PDB files of the target protein. “Y” in “Model” indicates that the prediction was made based on binding pockets in the PDB of the target protein as the template. “N” when the PDB of the target protein was not used in prediction

ISSN: 1471-2105