Predicting Protein Fold Types by the General Form of Chou's Pseudo Amino Acid Composition: Approached from Optimal Feature Extractions

Lei      Liu; Xiu-Zhen      Hu; Xing-Xing      Liu; Ying      Wang; Shao-Bo      Li

Abstract

Identification on protein folding types is always based on the 27-class folds dataset, which was provided by Ding & Dubchak in 2001. But with the avalanche of protein sequences, fold data is also expanding, so it will be the inevitable trend to improve the existing dataset and expand more folding types. In this paper, we construct a multi-class protein fold dataset, which contains 3,457 protein chains with sequence identity below 35% and could be classified into 76 fold types. It was 4 times larger than Ding & Dubchak's dataset. Furthermore, our work proposes a novel approach of support vector machine based on optimal features. By combining motif frequency, low-frequency power spectral density, amino acid composition, the predicted secondary structure and the values of auto-correlation function as feature parameters set, the method adopts criterion of the maximum correlation and the minimum redundancy to filter these features and obtain a 95-dimensions optimal feature subset. Based on the ensemble classification strategy, with 95-dimensions optimal feature as input parameters of support vector machine, we identify the 76-class protein folds and overall accuracy measures up to 44.92% by independent test. In addition, this method has been further used to identify upgraded 27-class protein folds, overall accuracy achieves 66.56%. At last, we also test our method on Ding & Dubchak's 27-class folds dataset and obtained better identification results than most of the previous reported results.

Keywords: Criterion of maximum relevance minimum redundancy, low-frequency power spectral density, motif frequency, optimal feature, protein fold, support vector machine, Mad Cow disease, Parkinson's disease, bioinformatics, Ding, &, Dubchak's dataset