Anti-gen and Anti-body Informatics

Abstract

Antibodies bind their antigen using residues, which are part of the hypervariable loops. The properties of the antibody-antigen interaction site are primarily governed by the three dimensional structure of the CDR-loops (complementarity determining region). The mode of antibody binding corresponding antigen is conservation. Antibody structure is rearranged to recognize and bind antigen with at least moderate affinity. Different types of antibody combining sites have been studied such as: cavity or pocket (hapten), groove (peptide, DNA, carbohydrate) and planar (protein). Much effort has focused on characters of antibody structure, antibody-antigen binding sit and mutation on the affinity and specificity of the antibody. In functional studies on antibody-antigen complexes, a few residues are tight bound among a number of contact residues in antibody-antigen interface. The distance between antibody’s interface residue and antigen surface is the one of antigen-antibody binding characters. In this chapter, we set three type of interaction distance range between antibody residue and antigen surface. The residue belong to these distance range in antibody structure is predicted by MCQP, LDA, Decision Tree and SVM to study correlation between characters of antibody surface residue and antigen-antibody interaction.