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

Proteins

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

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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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      Journal
      10.1002/prot.21747
      17803212

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