Prediction of the disulphide bridges in proteins using SVM

Authors:
Aiguo Du;Xiaohua Hu;Yi Pan
Affiliations:
Department of Computer Science, Georgia State University, 30303 Atlanta, GA, USA.;College of Information Science and Technology, Drexel University, 19104 Philadelphia, PA, USA.;Department of Computer Science, Georgia State University, 30303 Atlanta, GA, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2007

Citing 6
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Abstract

Disulphide bonds link distant portions of protein chains and provide strong structural constraints in the form of long-range interactions. Prediction and knowledge of disulphide bond connectivity is important in reducing the search space of protein conformation. In this research, we present an effective way to predict disulphide bridges by Support Vector Machine (SVM). The SVM encoding was based on experimental results on the binding motifs of protein disulphide isomerases. The physical-chemical characteristics of the flanking sequences and the linear distance between the concerned cysteine pairs were also included in the encoding. An overall pair wise accuracy of 92% was obtained for the SP39 dataset.