期刊
BIOINFORMATICS
卷 27, 期 7, 页码 939-945出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btr072
关键词
-
类别
资金
- RIKEN, Japan
Motivation: Clustering is commonly used to identify the best decoy among many generated in protein structure prediction when using energy alone is insufficient. Calculation of the pairwise distance matrix for a large decoy set is computationally expensive. Typically, only a reduced set of decoys using energy filtering is subjected to clustering analysis. A fast clustering method for a large decoy set would be beneficial to protein structure prediction and this still poses a challenge. Results: We propose a method using propagation of geometric constraints to accelerate exact clustering, without compromising the distance measure. Our method can be used with any metric distance. Metrics that are expensive to compute and have known cheap lower and upper bounds will benefit most from the method. We compared our method's accuracy against published results from the SPICKER clustering software on 40 large decoy sets from the I-TASSER protein folding engine. We also performed some additional speed comparisons on six targets from the 'semfold' decoy set. In our tests, our method chose a better decoy than the energy criterion in 25 out of 40 cases versus 20 for SPICKER. Our method also was shown to be consistently faster than another fast software performing exact clustering named Calibur. In some cases, our approach can even outperform the speed of an approximate method.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据