Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis discriminant.
The conotoxin proteins are disulfide rich small peptides that target ion channels and G protein coupled receptors. And they provide promising application in treating some chronic pain, epilepsy, cardiovascular diseases, and so on. Conotoxins may be classified into 11 superfamilies: A, D, I1, I2, J, L, M, O, P, S, and T according to the disulfide connectivity, highly conserved N-terminal precursor sequence and similar mode of actions. Successful prediction mature conotoxin superfamily peptide has important signification for the biological and pharmacological functions of the toxins. In this study, a new algorithm of increment of diversity combined with modified Mahalanobis discriminant is presented to predict five superfamilies by using the pseudo amino acid composition. The results of jackknife cross-validation test show that the overall prediction sensitivity and specificity are 88% and 91%, respectively. The predictive algorithm is also used to predict three O-conotoxin families. The 72% sensitivity and 78% specificity are obtained. These results indicate that the conotoxin superfamily peptides correlate with their amino acid compositions.
Lin
Hao
H
Laboratory of Theoretical Biophysics, Department of Physics, College of Sciences and Technology, Inner Mongolia University, Hohhot 010021, PR China.
Li
Qian-Zhong
QZ
D000465:Algorithms; D000596:Amino Acids / Q000032:analysis* / Q000235:genetics; D000818:Animals; D020916:Conotoxins / Q000032:analysis / Q000145:classification* / Q000235:genetics*; D016002:Discriminant Analysis; D005810:Multigene Family; D011237:Predictive Value of Tests; D012908:Snails / Q000737:chemistry / Q000235:genetics
D000596:Amino Acids; D020916:Conotoxins