Table of Contents
ISRN Computational Biology
Volume 2014, Article ID 581245, 11 pages
http://dx.doi.org/10.1155/2014/581245
Research Article

Application of Hybrid Functional Groups to Predict ATP Binding Proteins

Center for Bioinformatics & Computational Biology, Department of Biology, Jackson State University, Jackson, MS 39217, USA

Received 2 September 2013; Accepted 29 October 2013; Published 8 January 2014

Academic Editors: S.-A. Marashi and B. Oliva

Copyright © 2014 Andreas N. Mbah. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The ATP binding proteins exist as a hybrid of proteins with Walker A motif and universal stress proteins (USPs) having an alternative motif for binding ATP. There is an urgent need to find a reliable and comprehensive hybrid predictor for ATP binding proteins using whole sequence information. In this paper the open source LIBSVM toolbox was used to build a classifier at 10-fold cross-validation. The best hybrid model was the combination of amino acid and dipeptide composition with an accuracy of 84.57% and Mathews Correlation Coefficient (MCC) value of 0.693. This classifier proves to be better than many classical ATP binding protein predictors. The general trend observed is that combinations of descriptors performed better and improved the overall performances of individual descriptors, particularly when combined with amino acid composition. The work developed a comprehensive model for predicting ATP binding proteins irrespective of their functional motifs. This model provides a high probability of success for molecular biologists in predicting and selecting diverse groups of ATP binding proteins irrespective of their functional motifs.