Alignment-free local structural search by writhe decomposition.
Alignment-free local structural search by writhe decomposition.
复制标题
通过扭动分解进行无对齐局部结构搜索。
DOI：
10.1093/bioinformatics/btq127
复制
发表时间：
2010
期刊：
影响因子：
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通讯作者：
Brenner,StevenE
中科院分区：
文献类型：
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作者：
Zhi,Degui;Shatsky,Maxim;Brenner,StevenE
动机：蛋白质结构搜索的快速方法使生物学发现基于灵活定义的结构相似性，释放出越来越多的解决蛋白质结构的力量。投影方法显示出快速结构数据库搜索解决方案的发展前景。投影方法将结构映射到高维空间中的一个点，并通过测量投影点之间的距离来比较两个结构。这些方法提供了一个巨大的增加速度超过残留水平的结构比对方法。然而，目前的投影方法是不实用的，部分原因是他们无法识别局部similarity.Results：我们提出了一种新的基于投影的方法，可以快速检测全球以及局部结构相似性。局部结构搜索是由拓扑启发的扭动分解协议，产生少量的片段，同时确保类似的结构以类似的方式切割。在基准测试中，我们表明，我们的方法，作家，提高了准确性超过现有的投影方法在recognizingscopdomains的多域蛋白质，同时保持准确性与现有的投影方法在一个标准的单域基准test.Availability：源代码可在以下网站：http://compbio.berkeley.edu/proj/writher/Contact:dzhi@compbio.berkeley.eduSupplementary信息：补充数据可在Bioinformaticsonline。
Motivation:Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous increase in speed over residue-level structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities.Results:We propose a new projection-based approach that can rapidly detect global as well as local structural similarities. Local structural search is enabled by a topology-inspired writhe decomposition protocol that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In benchmark tests, we show that our method, writher, improves accuracy over existing projection methods in terms of recognizingscopdomains out of multi-domain proteins, while maintaining accuracy comparable with existing projection methods in a standard single-domain benchmark test.Availability:The source code is available at the following website: http://compbio.berkeley.edu/proj/writher/Contact:dzhi@compbio.berkeley.eduSupplementary information:Supplementary data are available atBioinformaticsonline.