Protein & Peptide Letters

Prof. Ben M. Dunn  
Department of Biochemistry and Molecular Biology
University of Florida
College of Medicine
P.O. Box 100245
Gainesville, FL
USA
Email: bdunn@ufl.edu

Back

Predicting Protein-Protein Interactions by Combing Various Sequence- Derived Features into the General Form of Chou’s Pseudo Amino Acid Composition

Author(s): Xiao-Wei Zhao, Zhi-Qiang Ma, Ming-Hao Yin.

Abstract:

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.

Keywords: Protein-protein interactions, principal component analysis (PCA), support vector machine (SVM), protein sequences, prediction

Order Reprints Order Eprints Rights & PermissionsPrintExport

Article Details

VOLUME: 19
ISSUE: 5
Year: 2012
Page: [492 - 500]
Pages: 9
DOI: 10.2174/092986612800191080