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首页> 外文会议>Database and Expert Systems Applications; Lecture Notes in Computer Science; 4080 >3D Protein Structure Matching by Patch Signatures
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3D Protein Structure Matching by Patch Signatures

机译：通过补丁签名匹配3D蛋白质结构

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摘要

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.
机译：为了确定两种蛋白质之间的功能依赖性，它们都以3D结构表示，这是它们具有一个或多个匹配的称为拼块的结构区域的基本条件。由于蛋白质的3D结构庞大，复杂且不断发展，因此针对大型蛋白质数据库来确定给定蛋白质的补丁可能位置和大小在计算上非常昂贵且非常耗时。在本文中，我们解决了基于蛋白质空间的蛋白质结构表示方法，该区域中的载体形成了一个斑块。根据我们的预览工作，此处应用了名为补丁签名的补丁的紧凑表示形式。然后根据两个补丁的签名得出两个补丁的相似性度量。为了在大型蛋白质数据库中实现快速补丁匹配，提出了一种匹配和扩展策略。给定查询补丁，就会在匹配阶段生成一组称为k的小k大小匹配补丁。通过在扩展阶段放大k进一步过滤候选补丁。我们广泛的实验结果表明，对于这一生物学上至关重要但以前在计算上难以解决的问题，其性能令人鼓舞。

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