TOP:: a new method for protein structure comparisons and similarity searches
TOP:: a new method for protein structure comparisons and similarity searches
复制标题
DOI：
10.1107/s0021889899012339
复制
发表时间：
2000-02-01
影响因子：
6.1
通讯作者：
Lu, GG
中科院分区：
文献类型：
--
作者：
Lu, GG
为了便于蛋白质的三维结构比较，开发了用于与数据库中的蛋白质结构进行比较和搜索相似性的软件。该程序识别两个蛋白质之间主链和侧链原子共享相似位置的残基。该软件的独特功能还包括通过基于互联网和网络的服务器为不同类型的用户进行数据库处理。所开发的方法和ifs友好的用户界面解决了蛋白质结构比较中经常出现的许多问题，例如检测结构等效残基、C-α原子重合引起的错位、循环序列排列、繁琐的重复访问、最新数据库的维护以及用户界面的不便。该程序还设计为与结构生物信息学中的其他工具配合，例如 3DB 浏览器软件 [Prilusky (1998)，Protein Data Bank Q. Newslett。 54, 3-4] 和 SCOP 数据库 [Murzin, Brenner, Hubbard & Chothia (1995)。 J.梅尔.生物。 247, 536-540]，方便分子建模和蛋白质结构分析。提出了“结构多样性”的相似性排名分数，以便根据蛋白质三维结构的比较来估计蛋白质之间的进化距离。该程序的功能已被用作多蛋白质结构比对自动化程序的一部分。本文对程序的算法和系统测试结果进行了介绍和讨论。
In order to facilitate the three-dimensional structure comparison of proteins, software for making comparisons and searching for similarities to protein structures in databases has been developed. The program identifies the residues that share similar positions of both main-chain and side-chain atoms between two proteins. The unique functions of the software also include database processing via Internet- and Web-based servers for different types of users. The developed method and ifs friendly user interface copes with many of the problems that frequently occur in protein structure comparisons, such as detecting structurally equivalent residues, misalignment caused by coincident match of C-alpha atoms, circular sequence permutations, tedious repetition of access, maintenance of the most recent database, and inconvenience of user interface. The program is also designed to cooperate with other tools in structural bioinformatics, such as the 3DB Browser software [Prilusky (1998), Protein Data Bank Q. Newslett. 54, 3-4] and the SCOP database [Murzin, Brenner, Hubbard & Chothia (1995). J. Mel. Biol. 247, 536-540], for convenient molecular modelling and protein structure analysis. A similarity ranking score of 'structure diversity' is proposed in order to estimate the evolutionary distance between proteins based on the comparisons of their three-dimensional structures. The function of the program has been utilized as a part of an automated program for multiple protein structure alignment. In this paper, the algorithm of the program and results of systematic tests are presented and discussed.