SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
Figure 3
Summary of docking performance.
The bar plots show the number of correctly docked targets out of fifteen targets for different docking algorithms. (A) Docking performance considering the lowest-energy decoy. (B) Docking performance considering the most native-like prediction in the ten lowest-energy decoys. (C) Docking performance based on the presence of docking energy funnels. Crystal indicates standard rigid-body docking using crystal structures. RosettaAntibody indicates standard rigid-body docking using RosettaDock starting with the lowest-energy RosettaAntibody homology model. VL-VH indicates docking with VL-VH optimization. VL-VH+CDR H3 indicates docking with VL-VH optimization with CDR minimization and CDR H3 perturbation. SnugDock indicates docking using SnugDock. Rigid Body Ensemble indicates rigid-body docking using EnsembleDock with the ten lowest-energy RosettaAntibody homology models. Snug+Ensemble indicates docking using the EnsembleDock-plus-SnugDock combined protocol with the ten lowest-energy RosettaAntibody homology models.