Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins

Background: Recognition of binding sites in proteins is a direct computational approach to the characterization of proteins in terms of biological and biochemical function. Residue preferences have been widely used in many studies but the results are often not satisfactory. Although different amino acid compositions among the interaction sites of different complexes have been observed, such differences have not been integrated into the prediction process. Furthermore, the evolution information has not been exploited to achieve a more powerful propensity. Result: In this study, the residue interface propensities of four kinds of complexes (homopermanent complexes, homo-transient complexes, hetero-permanent complexes and heterotransient complexes) are investigated. These propensities, combined with sequence profiles and accessible surface areas, are inputted to the support vector machine for the prediction of protein binding sites. Such propensities are further improved by taking evolut...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan
• Keywords: BMCBI 2007, Interface Propensities, Propensities, Residue Interface Propensities