PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides

BMC Bioinformatics

Table 4 Comparison of number of hits detected by different methods in recently deposited proteins solved by NMR in PDB (July 2012 to March 25, 2014)

Method	Positive hits	True positive hits	False positive hits	Calculated sensitivity (%) for STPs^a	Calculated precision (%) for STPs
PredSTP	23	21	2	91.30	91.30
PSI BLAST with e-value 0.01	13	12	1	52.17	92.30
PSI BLAST with e-value 0.1	21	17	4	73.90	80.95
PSI BLAST with e-value 0.5	52	17	35	73.90	32.69
Knoter1D	8	8	0	57.14	100

^aSensitivity for PredSTP and PSI BLAST was calculated based on total experimentally positive STPs (22 chains) in the NewNMR subset from PDB, while sensitivity for Knoter1D was calculated only for Knottins (knotted STPs)

ISSN: 1471-2105