- Article -
| In Silico Biology 7, 0025 (2007); ©2007, Bioinformation Systems e.V. |
Prediction of neurotoxins based on their function and source
Sudipto Saha and Gajendra P. S. Raghava*
Bioinformatics Centre, Institute of Microbial Technology, Sector-39A, Chandigarh, India
URL: http://www.imtech.res.in/raghava/
* Corresponding author
Email: raghava@imtech.res.in
Edited by E. Wingender; received December 14, 2006; revised February 22, 2007, and March 23, 2007; accepted March 25, 2007; published April 06, 2007
Abstract
We have developed a method NTXpred for predicting neurotoxins and classifying them based on their function and origin. The dataset used in this study consists of 582 non-redundant, experimentally annotated neurotoxins obtained from Swiss-Prot. A number of modules have been developed for predicting neurotoxins using residue composition based on feed-forwarded neural network (FNN), recurrent neural network (RNN), support vector machine (SVM) and achieved maximum accuracy of 84.19%, 92.75%, 97.72% respectively. In addition, SVM modules have been developed for classifying neurotoxins based on their source (e.g., eubacteria, cnidarians, molluscs, arthropods have been and chordate) using amino acid composition and dipeptide composition and achieved maximum overall accuracy of 78.94% and 88.07% respectively. The overall accuracy increased to 92.10%, when the evolutionary information obtained from PSIBLAST was combined with SVM module of source classification. We have also developed SVM modules for classifying neurotoxins based on functions using amino acid, dipeptide composition and achieved overall accuracy of 83.11%, 91.10% respectively. The overall accuracy of function classification improved to 95.11%, when PSIBLAST output was combined with SVM module. All the modules developed in this study were evaluated using five-fold cross-validation technique. The NTXpred is available at www.imtech.res.in/raghava/ntxpred/ and mirror site at http://bioinformatics.uams.edu/mirror/ntxpred.
Keywords: NTXpred, prediction of neurotoxins, Webserver, blockers of ion channels