Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility

Abstract

RosettaDock uses real‐space Monte Carlo minimization (MCM) on both rigid‐body and side‐chain degrees of freedom to identify the lowest free energy docked arrangement of 2 protein structures. An improved version of the method that uses gradient‐based minimization for off‐rotamer side‐chain optimization and includes information from unbound structures was used to create predictions for Rounds 4 and 5 of CAPRI. First, large numbers of independent MCM trajectories were carried out and the lowest free energy docked configurations identified. Second, new trajectories were started from these lowest energy structures to thoroughly sample the surrounding conformation space, and the lowest energy configurations were submitted as predictions. For all cases in which there were no significant backbone conformational changes, a small number of very low‐energy configurations were identified in the first, global search and subsequently found to be close to the center of the basin of attraction in the free energy landscape in the second, local search. Following the release of the experimental coordinates, it was found that the centers of these free energy minima were remarkably close to the native structures in not only the rigid‐body orientation but also the detailed conformations of the side‐chains. Out of 8 targets, the lowest energy models had interface root‐mean‐square deviations (RMSDs) less than 1.1 Å from the correct structures for 6 targets, and interface RMSDs less than 0.4 Å for 3 targets. The predictions were top submissions to CAPRI for Targets 11, 12, 14, 15, and 19. The close correspondence of the lowest free energy structures found in our searches to the experimental structures suggests that our free energy function is a reasonable representation of the physical chemistry, and that the real space search with full side‐chain flexibility to some extent solves the protein–protein docking problem in the absence of significant backbone conformational changes. On the other hand, the approach fails when there are significant backbone conformational changes as the steric complementarity of the 2 proteins cannot be modeled without incorporating backbone flexibility, and this is the major goal of our current work. Proteins 2005;60:187–194.