Skip Navigation



Bioinformatics Advance Access published online on July 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl366
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
22/17/2081    most recent
btl366v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Lin, K.
Right arrow Articles by Zhang, D.-Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lin, K.
Right arrow Articles by Zhang, D.-Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 The Author(s)
Received April 2, 2006
Revised June 5, 2006
Accepted July 2, 2006

Article

An initial strategy for comparing proteins at the domain architecture level

Kui Lin 1 *, Lei Zhu 1, and Da-Yong Zhang 1

1 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.
Kui Lin, E-mail: linkui{at}bnu.edu.cn


  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 (COGs) 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/.

Associate Editor: Christos Ouzounis
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
B. Lee and D. Lee
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W60 - W64.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. Rattei, P. Tischler, R. Arnold, F. Hamberger, J. Krebs, J. Krumsiek, B. Wachinger, V. Stumpflen, and W. Mewes
SIMAP structuring the network of protein similarities
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D289 - D292.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. E. Vinogradov
'Genome design' model and multicellular complexity: golden middle
Nucleic Acids Res., November 6, 2006; 34(20): 5906 - 5914.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.