Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface.

ABSTRACT: Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antib

SUBMITTER: Yu CM 

PROVIDER: S-EPMC3310866 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature