Bioinformatics Advance Access originally published online on July 12, 2006
Bioinformatics 2006 22(17):2081-2086; doi:10.1093/bioinformatics/btl366
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
An initial strategy for comparing proteins at the domain architecture level
MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University Beijing 100875, China
*To whom correspondence should be addressed.
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 
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/
Contact: linkui{at}bnu.edu.cn
Supplementary Information: Supplementary data are available at Bioinformatics online.
Received on April 2, 2006; revised on June 5, 2006; accepted on July 2, 2006
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