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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Predicting conotoxin superfamily and family by using pseudo amino acid composition and modified Mahalanobis
1Laboratory of Theoretical Biophysics, Department of Physics, College of Sciences and Technology, Inner Mongolia University, Hohhot 010021, PR China.
Abstract:
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.
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