SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Figure 6
Predicted models of the complex of west Nile virus envelope protein DIII with neutralizing E16 antibody Fab (1ZTX [39]).
(A) Lowest-energy prediction (medium accuracy) generated by EnsembleDock-plus-SnugDock simulations ranked by all-atom score of the entire complex. (B) Lowest-energy prediction (acceptable accuracy) generated by EnsembleDock-plus-SnugDock simulations ranked by the intermolecular components of the all-atom score. The light (deep blue) and heavy (yellow) chain framework of the docked antibody is superposed on the corresponding residues of the crystal complex. Predicted orientation of the antigen, green; light and heavy chain CDRs, orange and cyan respectively; CDR H3 loop and antigen in the crystal structure, red; residues at the interface, transparent spheres.