SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models.

ABSTRACT: High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering. When a crystallographic structure of a complex is unavailable, the structure must be predicted using computational tools. In this work, we illustrate a novel approach, named SnugDock, to predict high-resolution antibody-antigen complex structures by simultaneously structurally optimizing the antibody-antigen rigid-body positions, the relative orientation of the antibody light and heavy chains, and the conformations of the six complementarity determining region loops. This approach is especially useful when the crystal structure of the antibody is not available, requiring allowances for inaccuracies in an antibody homology model which

SUBMITTER: Sircar A 

PROVIDER: S-EPMC2800046 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature