Multiple flexible structure alignment using partial order graphs
Multiple flexible structure alignment using partial order graphs
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DOI：
10.1093/bioinformatics/bti353
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发表时间：
2005-05-15
期刊：
影响因子：
5.8
通讯作者：
Godzik, A
中科院分区：
文献类型：
--
作者：
Ye, YZ;Godzik, A
动机：现有的蛋白质结构比较不能描述结构差异和结构的灵活性，因为它们专注于识别一个共同的不变核心，而忽略了这个核心之外的结构部分。结果：提出了一种新的蛋白质多重结构比对方法POSA（PartialOrderStructureAlignment），该方法利用多重结构比对的偏序图表示方法，并将其应用于蛋白质的结构比对。POSA有两个独特的功能：（1）识别和分类仅在输入结构的子集中保守的区域，和（2）允许蛋白质结构中的内部重排。POSA在结构灵活性存在的情况下优于其他程序，并通过可视化多个结构对齐的马赛克性质提供了新的见解。POSA是研究不同结构家族中蛋白质结构变异的理想工具。
Motivation: Existing comparisons of protein structures are not able to describe structural divergence and flexibility in the structures being compared because they focus on identifying a common invariant core and ignore parts of the structures outside this core. Understanding the structural divergence and flexibility is critical for studying the evolution of functions and specificities of proteins.Results: A new method of multiple protein structure alignment, POSA (Partial Order Structure Alignment), was developed using a partial order graph representation of multiple alignments. POSA has two unique features: (1) identifies and classifies regions that are conserved only in a subset of input structures and (2) allows internal rearrangements in protein structures. POSA outperforms other programs in the cases where structural flexibilities exist and provides new insights by visualizing the mosaic nature of multiple structural alignments. POSA is an ideal tool for studying the variation of protein structures within diverse structural families.