Table 7.

Evaluation of the Pep-3D-Search's searching capability.

Mutation	Input sequence	TP/PE
		IT = 5000	IT = 10000	IT = 15000	IT = 20000	IT = 25000	IT = 30000
No	ESKQKINGNKDMKVLVAAYCQ	19/21	19/21	19/21	19/21	21/21	20/21
10%	ESKQRINGNKDMKVLPAAYCQ	19/21	15/21	19/21	18/21	15/21	19/21
15%	ESNQKINGNKSMKVLVAAMCQ	16/21	20/21	18/21	16/21	16/21	17/21
20%	ENKQKIDGNKDCKVLVPAYCQ	18/21	15/21	15/21	15/21	18/21	15/21
25%	ESKDRINGNCDMKVHVAAYAQ	17/21	10/21	15/21	10/21	10/21	10/21
30%	ASKQKLRGNKNMKVLCACYCQ	14/21	12/21	14/21	15/21	15/21	14/21

In the test case, the target path of 21 residues in length on the surface of the protein 1g9m (chain G) is E351 S347 K343 Q344 K348 I272 N234 G237 N94 K97 D99 M100 K487 V489 L226 V488 A224 A219 Y217 C218 Q246.

TP: number of true positives; PE: number of residues in the predicted epitope; IT: iteration number of Pep-3D-Search.