Induced fit with replica exchange improves protein complex structure prediction
Fig 2
T-REMC improves low-resolution performance in global rigid-body and local flexible docking for two representative protein targets.
(A) Global rigid-body docking performance for protein targets 2CFH (trafficking protein particle complex subunits) [37] and 1XQS (HspB1 core domain complexed with Hsp70 ATPase domain) [38]. Plots show the Motif Updated Dock Score (REU) vs all-atom Cα rmsd (Å). Blue points denote the refined native structures. (B) Comparison of different residue selections for performing backbone moves. Performance of ReplicaDock 2.0 with four conditions: (1) 5.5 Å interface patch, (2) 8 Å interface patch (3) 5.5 Å interface patch + loops, (4) 8 Å interface patch + loops. The metric is 〈N5〉, the average number of near-native models in the five top-scoring structures. For reference, RosettaDock 4.0 performance is highlighted in gray. (C) Local flexible backbone docking performance. Motif Updated Dock Score (REU) vs Cα rmsd (Å) for two targets, 2CFH [37] and 1XQS [38]. Panels show ∼5,000 decoys generated by RosettaDock 4.0 (left) and ReplicaDock 2.0 (right, this work).