Prediction of protein-protein binding site by using core interface residue and support vector machine

Background: The prediction of protein-protein binding site can provide structural annotation to the protein interaction data from proteomics studies. This is very important for the biological application of the protein interaction data that is increasing rapidly. Moreover, methods for predicting protein interaction sites can also provide crucial information for improving the speed and accuracy of protein docking methods. Results: 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 b...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Nan Li, Zhonghua Sun, Fan Jiang
• Keywords: BMCBI 2008, Protein Interaction, Protein Interaction Data, Proteins