Induced fit with replica exchange improves protein complex structure prediction
Fig 3
Improvement in docking performance after full protocol for two representative targets.
(A,D) Interface score (REU) vs I-rmsd (Å), (B,E) Ligand-RMSD(Å) versus Receptor-RMSD(Å), and (C,F) Interface score (REU) vs fraction of native-like contacts post all-atom refinement for RosettaDock 4.0 [11] and ReplicaDock 2.0(this work) for two targets 2CFH and 1XQS. Relative to RosettaDock 4.0, ReplicaDock 2.0 samples decoys that score better, are closer to the native, have higher native-like contacts(fnat) and better CAPRI quality. However, backbone RMSDs (B,E) have not moved closer to the native but rather diverged away from it.