%0 Journal Article
%T Prediction of protein-protein binding site by using core interface residue and support vector machine
%A Nan Li
%A Zhonghua Sun
%A Fan Jiang
%J BMC Bioinformatics
%D 2008
%I BioMed Central
%R 10.1186/1471-2105-9-553
%X In this work, we describe a binding site prediction method by designing a new residue neighbour profile and by selecting only the core-interface residues for SVM training. The residue neighbour profile includes both the sequential and the spatial neighbour residues of an interface residue, which is a more complete description of the physical and chemical characteristics surrounding the interface residue. The concept of core interface is applied in selecting the interface residues for training the SVM models, which is shown to result in better discrimination between the core interface and other residues.The best SVM model trained was tested on a test set of 50 randomly selected proteins. The sensitivity, specificity, and MCC for the prediction of the core interface residues were 60.6%, 53.4%, and 0.243, respectively. Our prediction results on this test set were compared with other three binding site prediction methods and found to perform better. Furthermore, our method was tested on the 101 unbound proteins from the protein-protein interaction benchmark v2.0. The sensitivity, specificity, and MCC of this test were 57.5%, 32.5%, and 0.168, respectively.By improving both the descriptions of the interface residues and their surrounding environment and the training strategy, better SVM models were obtained and shown to outperform previous methods. Our tests on the unbound protein structures suggest further improvement is possible.The functions of proteins rely on their interactions with various biological molecules including proteins, DNAs, RNAs and other small molecules. Among those interactions, one of the most important ones is the protein-protein interaction. Hence, the identification of protein binding site for protein-protein interaction becomes one of the basic questions in the research of protein functions. Several experimental methods such as X-ray crystallography, NMR, and site-directed mutagenesis [1] are well established in providing structural information o
%U http://www.biomedcentral.com/1471-2105/9/553