Efficacy of different protein descriptors in predicting protein functional families

The performance of these descriptor-sets were ranked by Matthews correlation coefficient (MCC), and categorized into two groups based on their performance. While there is no overwhelmingly favourable choice of descriptor-sets, certain trends were found. The combination-sets tend to give slightly but consistently higher MCC values and thus overall best performance such that three out of four combination-sets show slightly better performance compared to one out of six individual descriptor-sets.Our study suggests that currently used descriptor-sets are generally useful for classifying proteins and the prediction performance may be enhanced by exploring combinations of descriptors.Sequence-derived structural and physicochemical descriptors have frequently been used in machine learning prediction of protein structural and functional classes [1-5], protein-protein interactions [6-9], subcellular locations [10-16], peptides containing specific properties[17,18], microarray data [19] and protein secondary structure prediction [20]. These descriptors serve to represent and distinguish proteins or peptides of different structural, functional and interaction profiles by exploring their distinguished features in compositions, correlations, and distributions of the constituent amino acids and their structural and physicochemical properties [2,8,21,22]. There is thus a need to comparatively evaluate the effectiveness of these descriptor-sets for predicting different functional problems by using the same machine learning method and parameter optimization algorithm. Moreover, it is of interest to examine whether combined use of these descriptor-sets help to improve predictive performance.This work is intended to evaluate the effectiveness of a total of six individual descriptor-sets and four combination-sets (Table 1) in the prediction of several protein functional families by using support vector machine (SVM). Six sets of individual descriptors and three combination-sets have be