Molecular Modeling of Antibody-Combining Sites

Antibodies possess a vast repertoire of specificity and affinity. To understand the molecular basis of antibody function, we require high-resolution X-ray crystallographic structures and good solution structures of free and antigen-bound antibodies. The number of reported antibody structures grows each year. Yet the number of structures deposited with the Brookhaven Protein Database (PDB) (1 ) remains relatively small, with 43 deposited entries at the time of writing, when compared to the available sequence data. It is therefore important to develop an effective method of predicting the structure of antibody-combining sites. The validity of predicted structures can then be confirmed by mutagenesis in the combining site. The models can also provide valuable structural information to “humanize” antibodies for therapy effectively, to develop immunosensors, and even for the complete de novo design of new antibodies with different functions.