Automatic classification of the conformations of the loops of antibodies

The antigen-binding sites of antibodies are constructed principally from si x loops, the CDRs (complementarity-determining regions). For five of these loops the main-chain conformations follow the "canonical structure" model, according to which the mainchains of these loops have a small, discrete and limited repertoire of conformations. The observed conformations of the las t loop (CDR3 of the heavy chain) are much more variable, and here we only d istinguish among conformations of the portions of this region adjacent to t he framework. Given the rapid growth in population of antibody structures i n the protein data bank, it would be useful to have an automatic method for identifying the canonical structures of a new structure. We have written a program that takes as input the structure of an antibody and reports the a ssignment of canonical structures to its loops. The program uses (1) a set of known antibody structures and the definitions of the CDRs in all these s tructures, and (2) coordinates of examples that define each canonical struc ture of each loop.