A novel protein structural classes prediction method based on predicted secondary structure

Knowledge of structural classes plays an important role in understanding protein folding patterns. In this paper, features based on the predicted secondary structure sequence and the corresponding E-H sequence are extracted. Then, an 11-dimensional feature vector is selected based on a wrapper feature selection algorithm and a support vector machine (SVM). Among the 11 selected features, 4 novel features are newly designed to model the differences between alpha/beta class and alpha + beta class, and other 7 rational features are proposed by previous researchers. To examine the performance of our method, a total of 5 datasets are used to design and test the proposed method. The results show that competitive prediction accuracies can be achieved by the proposed method compared to existing methods (SCPRED, RKS-PPSC and MODAS), and 4 new features are demonstrated essential to differentiate alpha/beta and alpha + beta classes. Standalone version of the proposed method is written in JAVA language and it can be downloaded from http://web.xidian.edu.cn/slzhang/paper.html. (C) 2012 Elsevier Masson SAS. All rights reserved.