Comparison study of two kernel-based learning algorithms for predicting the distance range between antibody interface residues and antigen surface

Authors:
Yong Shi;Jia Wan;Xinyang Zhang;Gang Kou;Yi Peng;Yajun Guo
Affiliations:
Chinese Academy of Sciences Research Center on Fictitions Economy and Data Science, Beijing, China;Chinese Academy of Sciences Research Center on Fictitions Economy and Data Science, Beijing, China;Chinese Academy of Sciences Research Center on Fictitions Economy and Data Science, Beijing, China;College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA;College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE, USA;International Joint Cancer Institute, The Second Military Medical University, Shanghai, China
Venue:
International Journal of Computer Mathematics - Bioinformatics
Year:
2007

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Abstract

A number of kernel-based machine algorithms have recently been used to study protein-protein interaction in the field of bioinformatics. In this paper we develop a kernel-based machine algorithm called multiple criteria quadratic programming (MCQP) to predict the distance range between antibody interface residues and the antigen surface in antigen-antibody complex. Antibodies bind their antigen using residues, which are part of the hypervariable loops. In this paper we explore the interaction between antibody interface residues and antigen in the study of antibody functions. The distance between the antibody's interface residue and the antigen surface is one of the antigen-antibody binding characteristics used to observe the details of the antibody-antigen interaction surface. The results predicted by MCQP are compared with those predicted by the support vector machine (SVM). The MCQP algorithm classifies observations into distinct groups based on a number of criteria via a hyperplane. MCQP shows strong advantages for distances of 8 Å and 10 Å. However, SVM gives better results for a distance of 12 Å.