Vorolign-fast structural alignment using Voronoi contacts
Vorolign-fast structural alignment using Voronoi contacts
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DOI：
10.1093/bioinformatics/btl294
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发表时间：
2007-01-15
期刊：
影响因子：
5.8
通讯作者：
Zimmer, Ralf
中科院分区：
文献类型：
--
作者：
Birzele, Fabian;Gewehr, Jan E.;Zimmer, Ralf
介绍了一种快速、灵活的蛋白质结构比对方法Vorolign。该方法使用双动态规划比对蛋白质结构，并基于蛋白质结构中它们相应的Voronoi接触的进化保守性来测量两个残基的相似性。这种相似性函数允许比对蛋白质结构，即使在存在结构灵活性的情况下。多个结构比对是从一组使用一致性为基础的，渐进的多个比对strategy.Results：Vorolign的性能进行评估，为不同的应用程序的蛋白质结构比较，包括自动家庭检测以及成对和多个结构比对。Vorolign准确地检测一组困难的靶结构上的SCOP分类的蛋白质的正确家族、超家族或折叠。针对> 4000个蛋白质的数据库的扫描平均每个靶标花费1分钟。Vorolign在计算成对和多重比对中的性能与其他成对和多重蛋白质结构比对方法相当。
Vorolign, a fast and flexible structural alignment method for two or more protein structures is introduced. The method aligns protein structures using double dynamic programming and measures the similarity of two residues based on the evolutionary conservation of their corresponding Voronoi-contacts in the protein structure. This similarity function allows aligning protein structures even in cases where structural flexibilities exist. Multiple structural alignments are generated from a set of pairwise alignments using a consistency-based, progressive multiple alignment strategy.Results: The performance of Vorolign is evaluated for different applications of protein structure comparison, including automatic family detection as well as pairwise and multiple structure alignment. Vorolign accurately detects the correct family, superfamily or fold of a protein with respect to the SCOP classification on a set of difficult target structures. A scan against a database of > 4000 proteins takes on average 1 min per target. The performance of Vorolign in calculating pairwise and multiple alignments is found to be comparable with other pairwise and multiple protein structure alignment methods.