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论文类型：期刊论文

发表时间：2012-02-05

发表刊物：Journal of Computational Chemistry

收录刊物：EI、Scopus

卷号：33

期号：4

页面范围：471-474

ISSN号：01928651

摘要：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. Alternatively, a compiled version of Durandal is also distributed with the nightly builds of the Phenix () crystallographic software suite (Adams et al., Acta Crystallogr Sect D 2010, 66, 213). Copyright ? 2011 Wiley Periodicals, Inc.