The antigen-binding sites of antibodies are constructed principally from six 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 last loop (CDR3 of the heavy chain) are much more variable, and here we only distinguish among conformations of the portions of this region adjacent to the framework. Given the rapid growth in population of antibody structures in 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 assignment 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 structures, and (2) coordinates of examples that define each canonical structure of each loop.
All Science Journal Classification (ASJC) codes
- Electronic, Optical and Magnetic Materials
- Condensed Matter Physics