An initial strategy for comparing proteins at the domain architecture level
An initial strategy for comparing proteins at the domain architecture level
复制标题
在域架构水平上比较蛋白质的初始策略
DOI：
10.1093/bioinformatics/btl366
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发表时间：
2006-09-01
期刊：
影响因子：
5.8
通讯作者：
Zhang, Da-Yong
中科院分区：
文献类型：
--
作者：
Lin, Kui;Zhu, Lei;Zhang, Da-Yong
动机：理想情况下，只有表现出高度相似的结构域结构的蛋白质才应该作为同源物相互比较，或者被分类到单个家族中。通过结合三种不同的指标，Jaccard指数，Goodman-Kruskal y函数和结构域重复指数，到一个单一的相似性度量，我们提出了一种方法来比较蛋白质的结构域架构的基础上.使用真核生物蛋白质组（KOG）数据库对该方法进行的评估表明，它允许自动和有效地比较多结构域蛋白质，这通常是基于序列相似性测量的经典方法难以解决的。作为一个案例研究，PDZ和LRR_1结构域被用来证明如何蛋白质含有混杂结构域可以清楚地比较使用我们的方法。为了方便用户，我们建立了一个Web服务器，在其中实现了三个不同的查询接口，以比较不同的结构域结构或蛋白质与结构域，并从蛋白质的OrthopathologicGroupsofProteins数据库中识别给定KOG内结构域结构之间的关系。我们提出的方法适用于估计蛋白质结构域的相似性，特别是那些multiclomain蛋白质。可用性：http://cmb.bnu.edu.cn/pdart/联系人：linkui@bnu.edu. cn补充信息：补充数据可在生物信息学在线。
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 y 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 multiclomain proteins.Availability: http://cmb.bnu.edu.cn/pdart/ Contact: linkui@bnu.edu.cnSupplementary Information: Supplementary data are available at Bioinformatics online.