A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC

• Published in: Journal of theoretical biology 2014-03, Vol.344, p.31-39
• Main Authors: Han, Guo-Sheng, Yu, Zu-Guo, Anh, Vo
• Format: Article
• Language: English
• Subjects: Algorithms; Amino acid classification; Amino Acids - chemistry; Amino Acids - classification; Animals; Chemistry, Physical; Computational Biology - methods; Databases, Protein; Feature extraction; Hilbert–Huang transform; Membrane protein type; Membrane Proteins - analysis; Membrane Proteins - chemistry; Support Vector Machine
• ISSN: 0022-5193; 1095-8541
• DOI: 10.1016/j.jtbi.2013.11.017

Membrane proteins play important roles in many biochemical processes and are also attractive targets of drug discovery for various diseases. The elucidation of membrane protein types provides clues for understanding the structure and function of proteins. Recently we developed a novel system for predicting protein subnuclear localizations. In this paper, we propose a simplified version of our system for predicting membrane protein types directly from primary protein structures, which incorporates amino acid classifications and physicochemical properties into a general form of pseudo-amino acid composition. In this simplified system, we will design a two-stage multi-class support vector machine combined with a two-step optimal feature selection process, which proves very effective in our experiments. The performance of the present method is evaluated on two benchmark datasets consisting of five types of membrane proteins. The overall accuracies of prediction for five types are 93.25% and 96.61% via the jackknife test and independent dataset test, respectively. These results indicate that our method is effective and valuable for predicting membrane protein types. A web server for the proposed method is available at http://www.juemengt.com/jcc/memty_page.php •We present a novel SVM method for predicting membrane protein types.•The SVM method is combined with a two-step optimal feature selection process.•The performance of the proposed method is evaluated on two benchmark datasets.•Our method provides better performance as compared to the existing approaches.