Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W164-W167; doi:10.1093/nar/gki367
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (100K) Freely available
Right arrow Screen PDF (125K) Freely available
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
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Gromiha, M. M.
Right arrow Articles by Suwa, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Gromiha, M. M.
Right arrow Articles by Suwa, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins

M. Michael Gromiha*, Shandar Ahmad1 and Makiko Suwa

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan 1Department of Biochemical Engineering and Science, Kyushu Institute of Technology Iizuka 820 8502, Fukuoka, Japan

*To whom correspondence should be addressed. Tel: +81 3 3599 8046; Fax: +81 3 3599 8081; Email: michael-gromiha{at}aist.go.jp

Received February 6, 2005. Revised February 28, 2005. Accepted February 28, 2005.

We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning ß-strand segments. The amino acid compositions of globular and outer membrane proteins have been systematically analyzed and a statistical method has been proposed for discriminating outer membrane proteins. The prediction of membrane spanning segments is mainly based on feed forward neural network and refined with ß-strand length. Our program takes the amino acid sequence as input and displays the type of the protein along with membrane-spanning ß-strand segments as a stretch of highlighted amino acid residues. Further, the probability of residues to be in transmembrane ß-strand has been provided with a coloring scheme. We observed that outer membrane proteins were discriminated with an accuracy of 89% and their membrane spanning ß-strand segments at an accuracy of 73% just from amino acid sequence information. The prediction server is available at http://psfs.cbrc.jp/tmbeta-net/.


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
 BioinformaticsHome page
A. Randall, J. Cheng, M. Sweredoski, and P. Baldi
TMBpro: secondary structure, {beta}-contact and tertiary structure prediction of transmembrane {beta}-barrel proteins
Bioinformatics, February 15, 2008; 24(4): 513 - 520.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Waldispuhl, B. Berger, P. Clote, and J.-M. Steyaert
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W189 - W193.
[Abstract] [Full Text] [PDF]

Home page
 Microbiol. Mol. Biol. Rev.Home page
M.-J. Han and S. Y. Lee
The Escherichia coli Proteome: Past, Present, and Future Prospects
Microbiol. Mol. Biol. Rev., June 1, 2006; 70(2): 362 - 439.
[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.