The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI

We present an evaluation of our protein-protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6-11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium-accuracy predictions. In the new scoring portion of the CAPRI exercise, we were able to attain at least one acceptable prediction for the three targets submitted and achieved three medium-accuracy predictions for Target 26. Scoring was performed using ZRANK, a new algorithm for reranking initial-stage docking predictions using a weighted energy function and no structural refinement. Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted.