[Molecular modeling of immunological proteins by bioinformatics]

The antibody combining site is composed of six complementarity determining regions (CDRs), whose typical structures have been classified as "canonical structures" except CDR-H3, depending upon the segment lengths and the positions of specific amino acid residues in the segments. Using the method of structural bioinformatics, we have proposed a novel classification of the CDR-H3 structures, and revealed several remarkable relationships between their sequences and the loop conformations. Based upon the canonical structures and our new rules, structural models of antibodies have been built in order to understand the molecular basis of antigen recognition. Another new computational method of almost exhaustive conformational search is introduced for future applications.