Exploring potential discriminatory information embedded in PSSM to enhance protein structural class prediction accuracy

Abstract

Determining the structural class of a given protein can provide important information about its functionality and its general tertiary structure. In the last two decades, the protein structural class prediction problem has attracted tremendous attention and its prediction accuracy has been significantly improved. Features extracted from the Position Specific Scoring Matrix (PSSM) have played an important role to achieve this enhancement. However, this information has not been adequately explored since the protein structural class prediction accuracy relying on PSSM for feature extraction still remains limited. In this study, to explore this potential, we propose segmentation-based feature extraction technique based on the concepts of amino acids' distribution and auto covariance. By applying a Support Vector Machine (SVM) to our extracted features, we enhance protein structural class prediction accuracy up to 16% over similar studies found in the literature. We achieve over 90% and 80% prediction accuracies for 25PDB and 1189 benchmarks respectively by solely relying on the PSSM for feature extraction. © 2013 Springer-Verlag Berlin Heidelberg.