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一种在结构域架构层面比较蛋白质的初始策略。

An initial strategy for comparing proteins at the domain architecture level.

作者信息

Lin Kui, Zhu Lei, Zhang Da-Yong

机构信息

MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China.

出版信息

Bioinformatics. 2006 Sep 1;22(17):2081-6. doi: 10.1093/bioinformatics/btl366. Epub 2006 Jul 12.

Abstract

MOTIVATION

Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal gamma function and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures.

RESULTS

Evaluation of the method using the eukaryotic orthologous groups of proteins (KOGs) database indicated that it allows the automatic and efficient comparison of multiple-domain proteins, which are usually refractory to classic approaches based on sequence similarity measures. As a case study, the PDZ and LRR_1 domains are used to demonstrate how proteins containing promiscuous domains can be clearly compared using our method. For the convenience of users, a web server was set up where three different query interfaces were implemented to compare different domain architectures or proteins with domain(s), and to identify the relationships among domain architectures within a given KOG from the Clusters of Orthologous Groups of Proteins database.

CONCLUSION

The approach we propose is suitable for estimating the similarity of domain architectures of proteins, especially those of multidomain proteins.

AVAILABILITY

http://cmb.bnu.edu.cn/pdart/.

摘要

动机

理想情况下,只有那些具有高度相似结构域架构的蛋白质才能作为同源物相互比较,或者被归类为同一个家族。通过将三种不同的指标,即杰卡德指数、古德曼-克鲁斯卡尔伽马函数和结构域重复指数,组合成一个单一的相似性度量,我们提出了一种基于蛋白质结构域架构来比较蛋白质的方法。

结果

使用真核生物直系同源蛋白质组(KOGs)数据库对该方法进行评估表明,它能够自动且高效地比较多结构域蛋白质,而这些蛋白质通常难以用基于序列相似性度量的经典方法进行处理。作为一个案例研究,使用PDZ和LRR_1结构域来展示如何使用我们的方法清晰地比较含有混杂结构域的蛋白质。为方便用户,搭建了一个网络服务器,其中实现了三个不同的查询界面,用于比较不同的结构域架构或带有结构域的蛋白质,并从直系同源蛋白质组数据库中识别给定KOG内结构域架构之间的关系。

结论

我们提出的方法适用于评估蛋白质结构域架构的相似性,尤其是多结构域蛋白质的结构域架构相似性。

可用性

http://cmb.bnu.edu.cn/pdart/

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