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Performance of ZDOCK in CAPRI rounds 20-26.

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      Abstract

      We report the performance of our approaches for protein-protein docking and interface analysis in CAPRI rounds 20-26. At the core of our pipeline was the ZDOCK program for rigid-body protein-protein docking. We then reranked the ZDOCK predictions using the ZRANK or IRAD scoring functions, pruned and analyzed energy landscapes using clustering, and analyzed the docking results using our interface prediction approach RCF. When possible, we used biological information from the literature to apply constraints to the search space during or after the ZDOCK runs. For approximately half of the standard docking challenges we made at least one prediction that was acceptable or better. For the scoring challenges we made acceptable or better predictions for all but one target. This indicates that our scoring functions are generally able to select the correct binding mode.

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      Author and article information

      Affiliations
      [1 ] Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605..
      Journal
      Proteins
      Proteins
      Wiley-Blackwell
      1097-0134
      0887-3585
      Dec 2013
      : 81
      : 12
      24123140
      10.1002/prot.24432
      3975700
      NIHMS531505

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