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      The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.

      Proteins
      Algorithms, Cluster Analysis, Computational Biology, methods, Computer Simulation, Crystallography, X-Ray, Databases, Protein, Dimerization, Genomics, Ligands, Molecular Conformation, Protein Binding, Protein Conformation, Protein Interaction Mapping, Proteins, chemistry, Proteomics, Software

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          Abstract

          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. (c) 2007 Wiley-Liss, Inc.

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