SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Figure 2
Docking perturbation plots for blocking antibody 11k2 complexed with human monocyte chemoattractant protein (MCP)-1 (2BDN [33]).
(A) Standard rigid-body docking using RosettaDock starting with the antibody crystal structure. The red point represents the native crystal structure. (B) Standard rigid-body docking using RosettaDock with the lowest-energy RosettaAntibody model. (C) Docking with VL-VH optimization using the lowest-energy RosettaAntibody model. (D) Docking with VL-VH optimization with CDR minimization and CDR H3 perturbation using the lowest-energy RosettaAntibody model. (E) Docking with SnugDock (VL-VH optimization with CDR minimization and CDR H3+H2 perturbations) using the lowest-energy RosettaAntibody model. (F) Rigid-body docking using EnsembleDock with the ten lowest-energy RosettaAntibody models. (G) Docking using a combined protocol incorporating EnsembleDock and SnugDock with the ten lowest-energy RosettaAntibody models.