Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors

Table 3 Evaluation of the success rate (ACC) of predicting IFR ensemble

PDB ID	Subfamily	Organism	TP	TN	FP	FN	ACC
1FY8	Trypsin	Bos taurus	44	244	0	0	1
3TGI	Trypsin	Bos taurus	42	239	5	0	0.98
1TPA	Trypsin	Bos taurus	44	240	1	3	0.98
3BTK	Trypsin	Bos taurus	43	241	1	4	0.98
3TPI	Trypsin	Bos taurus	43	242	1	2	0.98
2PTC	Trypsin	Bos taurus	44	241	0	3	0.98
2TGP	Trypsin	Bos taurus	45	240	0	3	0.98
4TPI	Trypsin	Bos taurus	44	239	1	4	0.98
2TPI	Trypsin	Bos taurus	44	241	1	2	0.98
1BZX	Trypsin	Bos taurus	43	242	2	1	0.98
1BRB	Trypsin	Rattus novergicus	41	236	2	2	0.98
1FAK	Coagulation factor VIII	Homo sapiens	44	247	6	0	0.97
1CBW	Chymotrypsin	Bos taurus	44	238	5	1	0.97
1MTN	Chymotrypsin	Bos taurus	45	239	1	3	0.98
2KAI	Kallikrein	Bos taurus	57	224	0	4	0.98
1EAW	Matriptase MTSP1	Homo sapiens	42	241	4	1	0.98

The true positives (TP) are IFR residues present in both the native and the rigid body docked complexes. The true negatives (TN) are solvent exposed residues both in native and in in silico complexes. The false positives (FP) are present in the rigid body docked IFR but absent in natural complexes, and the false negatives (FN) are not buried in native complexes but appear in the IFR in generated in silico complexes.

ISSN: 1472-6807