Rapid 3D protein structure database searching using information retrieval techniques
Rapid 3D protein structure database searching using information retrieval techniques
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DOI：
10.1093/bioinformatics/bth036
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发表时间：
2004-05-01
期刊：
影响因子：
5.8
通讯作者：
Tan, KL
中科院分区：
文献类型：
--
作者：
Aung, Z;Tan, KL
动机：随着当今三维 (3D) 蛋白质结构数据库的大小快速增长，将 3D 查询结构与数据库中的每个结构进行比较的详尽数据库搜索变得效率低下。我们提出了一种名为“ProtDex2”的快速 3D 蛋白质结构检索系统，其中我们采用信息检索系统中使用的技术来执行快速数据库搜索，而无需访问数据库中的每个 3D 结构。检索过程基于数据库中所有 3D 蛋白质结构的二级结构元素 (SSE) 之间关系的特征向量构建的倒排索引。 ProtDex2 较其前身系统 ProtDex 在速度和准确性方面都有显着改进。 结果：实验结果表明，ProtDex2 比两种著名的蛋白质结构比较方法 DALI 和 CE 快得多，但不牺牲比较的准确性。与类似的基于 SSE 的方法（即 TopScan）相比，ProtDex2 速度更快且准确度相当。
Motivation: As the sizes of three-dimensional (3D) protein structure databases are growing rapidly nowadays, exhaustive database searching, in which a 3D query structure is compared to each and every structure in the database, becomes inefficient. We propose a rapid 3D protein structure retrieval system named 'ProtDex2', in which we adopt the techniques used in information retrieval systems in order to perform rapid database searching without having access to every 3D structure in the database. The retrieval process is based on the inverted-file index constructed on the feature vectors of the relationships between the secondary structure elements (SSEs) of all the 3D protein structures in the database. ProtDex2 is a significant improvement, both in terms of speed and accuracy, upon its predecessor system, ProtDex.Results: The experimental results show that ProtDex2 is very much faster than two well-known protein structure comparison methods, DALI and CE, yet not sacrificing on the accuracy of the comparison. When comparing with a similar SSE-based method, namely TopScan, ProtDex2 is much faster with comparable degree of accuracy.