Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges

ABSTRACT In addition to protein–protein docking, this CAPRI edition included new challenges, like protein–water and protein–sugar interactions, or the prediction of binding affinities and ΔΔG changes upon mutation. Regarding the standard protein–protein docking cases, our approach, mostly based on the pyDock scheme, submitted correct models as predictors and as scorers for 67% and 57% of the evaluated targets, respectively. In this edition, available information on known interface residues hardly made any difference for our predictions. In one of the targets, the inclusion of available experimental small‐angle X‐ray scattering (SAXS) data using our pyDockSAXS approach slightly improved the predictions. In addition to the standard protein–protein docking assessment, new challenges were proposed. One of the new problems was predicting the position of the interface water molecules, for which we submitted models with 20% and 43% of the water‐mediated native contacts predicted as predictors and scorers, respectively. Another new problem was the prediction of protein–carbohydrate binding, where our submitted model was very close to being acceptable. A set of targets were related to the prediction of binding affinities, in which our pyDock scheme was able to discriminate between natural and designed complexes with area under the curve = 83%. It was also proposed to estimate the effect of point mutations on binding affinity. Our approach, based on machine learning methods, showed high rates of correctly classified mutations for all cases. The overall results were highly rewarding, and show that the field is ready to move forward and face new interesting challenges in interactomics. Proteins 2013; 81:2192–2200. © 2013 Wiley Periodicals, Inc.