Directed induced-fit improves flexible protein docking performance.

(top) (a,b,c) ReplicaDock 2.0 without directed backbone sampling of putative interfaces i.e. unbiased moves, finds medium-quality structures (colors: green = high quality, red = moderate quality, yellow = acceptable quality, gray = incorrect) (bottom) (e,f,g) ReplicaDock 2.0 with directed backbone sampling of mobile residues improves protein docking and obtains high-quality structures. (d,h) Comparing with the Ras’ unbound structure (grey) superimposed over the bound (green), the docked structure loop (blue) has moved closer to the bound state (green) for the two cases respectively. With directed sampling, it is able to capture the backbone structure to sub-angstrom accuracy.