Durandal: Fast exact clustering of protein decoys

Authors

  • Francois Berenger,

    1. Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Search for more papers by this author
  • Rojan Shrestha,

    1. Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Search for more papers by this author
  • Yong Zhou,

    1. Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Current affiliation:
    1. Software School of Dalian University of Technology, Economy and Technology Development Area, Dalian 116620, People's Republic of China
    Search for more papers by this author
  • David Simoncini,

    1. Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Search for more papers by this author
  • Kam Y. J. Zhang

    Corresponding author
    1. Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    • Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
    Search for more papers by this author
    • Fax: (048) 467 8790


Abstract

In protein folding, clustering is commonly used as one way to identify the best decoy produced. Initializing the pairwise distance matrix for a large decoy set is computationally expensive. We have proposed a fast method that works even on large decoy sets. This method is implemented in a software called Durandal. Durandal has been shown to be consistently faster than other software performing fast exact clustering. In some cases, Durandal can even outperform the speed of an approximate method. Durandal uses the triangular inequality to accelerate exact clustering, without compromising the distance function. Recently, we have further enhanced the performance of Durandal by incorporating a Quaternion-based characteristic polynomial method that has increased the speed of Durandal between 13% and 27% compared with the previous version. Durandal source code is available under the GNU General Public License at http://www.riken.jp/zhangiru/software/durandal_released_qcp.tgz. Alternatively, a compiled version of Durandal is also distributed with the nightly builds of the Phenix (http://www.phenix-online.org/) crystallographic software suite (Adams et al., Acta Crystallogr Sect D 2010, 66, 213). © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

Ancillary