Rescoring ensembles of protein-protein docking poses using consensus approaches

ABSTRACT Scoring is a challenging step in protein-protein docking, where typically thousands of solutions are generated. Successful scoring is more often based on physicochemical evaluation of the generated interfaces and/or statistical potentials that reproduce known interface properties. Another route is offered by consensus-based rescoring, where the set of solutions is used to build statistics in order to identify recurrent solutions. We explore several ways to perform consensus-based rescoring on the ZDOCK decoy set for Benchmark 4. We show that the information of the interface size is critical for successful rescoring. We combine consensus-based rescoring with the ZDOCK native scoring function and show that this improves the initial results.