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.
Highlights
Recent advances in the generation sequencing and human genome projects have resulted in rapid increase of protein sequences, widening the protein sequencestructure gap [1, 2], leading to diverse protein functions from common family
The general trend shows that combinations of descriptors perform better and improved the overall performances of individual descriptors, when combined with amino acid composition. This model provides a high probability of success for molecular biologists in predicting and selecting diverse motif groups of ATP binding proteins
The general assumption here is that every protein that binds to ATP molecule either universal stress proteins (USPs) or those having Walker A motif will have some common features embedded in their sequences
Summary
Recent advances in the generation sequencing and human genome projects have resulted in rapid increase of protein sequences, widening the protein sequencestructure gap [1, 2], leading to diverse protein functions from common family. 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]. The biochemical functions of ATP binding proteins are well exhibited within the ABC transporters group. 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 known to transport lipids and play a protective role to the developing fetus against xenobiotics [7]. One model called hydrophobic vacuum cleaner states that, in P-glycoprotein, the drugs are bound indiscriminately from the lipid phase based on their hydrophobicity [9]
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