A study on the effect of using physico-chemical features in protein secondary structure prediction

Abstract

Protein structure prediction is a powerful tool in today’s drug design industry as well as in the molecular modeling stage of x-ray crystallography research. This paper proposes a redefined encoding scheme based on the combination of Chou-Fasman parameters, physico-chemical parameters and position specific scoring matrix for protein secondary structure prediction. A new method of calculating the reliability index based on the number of votes and the SVM decision value is also proposed and it has been shown to assist design of better filters. The proposed features are then tested on the RS126 and CB513 datasets and shown to give better cross-validation results compared to the existing techniq..