Bioinformatics Advance Access published online on July 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl366
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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.
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 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/.
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
Kui Lin, E-mail: linkui{at}bnu.edu.cn
Abstract 
function, and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures.
Associate Editor: Christos Ouzounis
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. Wichadakul, S. Numnark, and S. Ingsriswang d-Omix: a mixer of generic protein domain analysis tools Nucleic Acids Res., July 1, 2009; 37(suppl_2): W417 - W421. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|