3D Protein Structure Matching by Patch Signatures
3D Protein Structure Matching by Patch Signatures
复制标题
通过补丁签名进行 3D 蛋白质结构匹配
DOI：
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发表时间：
2006
期刊：
影响因子：
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通讯作者：
D. Song
中科院分区：
文献类型：
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作者：
Zi Huang;Xiaofang Zhou;Heng Tao Shen;D. Song
为了确定两个蛋白质之间的功能相关性，这两个蛋白质都表示为3D结构，这是一个必要条件，它们具有一个或多个匹配的结构区域，称为补丁。由于蛋白质的3D结构庞大、复杂且不断进化，根据大型蛋白质数据库识别给定蛋白质的可能位置和大小是计算昂贵且非常耗时的。在本文中，我们提出了一种基于向量空间的蛋白质结构表示方法，其中区域内的向量形成了一个补丁。在前人工作的基础上，本文采用了一种紧凑的补丁表示方法--补丁签名。然后根据两个面片的特征得到两个面片的相似性度量。为了在大型蛋白质数据库中实现快速的斑块匹配，提出了一种匹配扩展策略。在给定查询块的情况下，在匹配阶段生成一组小k大小的匹配块，称为候选块。在扩展阶段，通过放大k进一步过滤候选块。我们广泛的实验结果表明，对于这个生物学上关键但以前计算上禁止的问题，我们表现出了令人鼓舞的性能。
For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches. As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein against a large protein database. In this paper, we address a vector space based representation for protein structures, where a patch is formed by the vectors within the region. Based on our previews work, a compact representation of the patch named patch signature is applied here. A similarity measure of two patches is then derived based on their signatures. To achieve fast patch matching in large protein databases, a match-and-expand strategy is proposed. Given a query patch, a set of small k-sized matching patches, called candidate patches, is generated in match stage. The candidate patches are further filtered by enlarging k in expand stage. Our extensive experimental results demonstrate encouraging performances with respect to this biologically critical but previously computationally prohibitive problem.