SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Figure 5
Structural details of the monoclonal antibody Fab D44.1 complexed with lysozyme (1MLC [38]).
(A) The interface region of the lowest-energy RosettaAntibody homology model for target 1MLB complexed with the crystal structure of lysozyme (1LZA). (B) The interface region of the most native-like prediction in the ten lowest-energy docking predictions on docking with standard rigid-body RosettaDock. (C) The interface region of the most native-like prediction in the ten lowest-energy docking predictions on docking with SnugDock. (D) Superposition of the structures shown in (B) and (C) viewed facing the binding region from the antigen's side. Conformations of the antigen in the crystal structure, green; predicted by standard rigid-body RosettaDock, red; and that predicted by SnugDock, grey; heavy and light chains, shades of blue and yellow respectively. Sticks indicate the labeled residues that have relieved the steric clash present in the starting structure due to the flexibility allowed by SnugDock. Transparent spheres indicate the interface region of the predicted conformation of the antigen. The light and heavy chain frameworks of the predicted complexes are superposed on the corresponding residues of the antibody in the crystal structure.