%0 Journal Article
%T Application of Hybrid Functional Groups to Predict ATP Binding Proteins
%A Andreas N. Mbah
%J ISRN Computational Biology
%D 2014
%R 10.1155/2014/581245
%X 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. 1. Introduction Recent advances in the next generation sequencing and human genome projects have resulted in rapid increase of protein sequences, thus widening the protein sequence-structure gap [1, 2], leading to diverse protein functions from common family. Computation prediction tools for predicting protein structure and function are highly needed to narrow the widening gap [3]. The ATP binding proteins (ATP-BPs) are a diverse family of proteins in terms of amino acid sequences, function, and their three-dimensional structures. These proteins hydrolyze ATP to provide the energy necessary to drive biochemical reactions in the cell [4]. There are two distinct functional groups of ATP binding proteins. The first functional group has the Walker A motif [GXXXXGK (T/S) or G-4X-GK (T/S)] in their sequences for ATP binding [5]. Many members are transmembrane proteins and are responsible for transporting a wide variety of substrates across extra- and intracellular membranes [6]. The biochemical functions of ATP binding proteins are well exhibited within the ABC transporters group. In bacteria cell, ABC transporters pump substances such as sugars, vitamins, and metal ions into the cell, while in eukaryotes they transport molecules out of the cell [7]. They are also known to transport lipids and play a protective role to the developing fetus against xenobiotics [7]. ABC transporters are crucial in the development of multidrug
%U http://www.hindawi.com/journals/isrn.computational.biology/2014/581245/