CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein–protein docking decoys

Authors

  • Satoshi Omori,

    1. Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
    Search for more papers by this author
    • Satoshi Omori's current address is Graduate School of Nanobioscience, Yokohama City University.

  • Akio Kitao

    Corresponding author
    1. Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
    2. Japan Science and Technology Agency, Core Research for Evolutionary Science and Technology, Tokyo, Japan
    • Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
    Search for more papers by this author

Abstract

We propose a fast clustering and reranking method, CyClus, for protein–protein docking decoys. This method enables comprehensive clustering of whole decoys generated by rigid-body docking using cylindrical approximation of the protein–proteininterface and hierarchical clustering procedures. We demonstrate the clustering and reranking of 54,000 decoy structures generated by ZDOCK for each complex within a few minutes. After parameter tuning for the test set in ZDOCK benchmark 2.0 with the ZDOCK and ZRANK scoring functions, blind tests for the incremental data in ZDOCK benchmark 3.0 and 4.0 were conducted. CyClus successfully generated smaller subsets of decoys containing near-native decoys. For example, the number of decoys required to create subsets containing near-native decoys with 80% probability was reduced from 22% to 50% of the number required in the original ZDOCK. Although specific ZDOCK and ZRANK results were demonstrated, the CyClus algorithm was designed to be more general and can be applied to a wide range of decoys and scoring functions by adjusting just two parameters, p and T. CyClus results were also compared to those from ClusPro. Proteins 2013; © 2012 Wiley Periodicals, Inc.

Ancillary