Skip Navigation


Bioinformatics Advance Access originally published online on October 4, 2005
Bioinformatics 2005 21(23):4223-4229; doi:10.1093/bioinformatics/bti697
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/23/4223    most recent
bti697v1
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 ISI Web of Science
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 Search for citing articles in:
ISI Web of Science (13)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Park, K.-J.
Right arrow Articles by Suwa, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Park, K.-J.
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. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Discrimination of outer membrane proteins using support vector machines

Keun-Joon Park 1,2, M. Michael Gromiha 1,*, Paul Horton 1 and Makiko Suwa 1

1Computational 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
2Laboratory of Functional Analysis in silico, Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokane-dai Minato-ku, Tokyo 108–8639, Japan

*To whom correspondence should be addressed.

Motivation: Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important task both for dissecting outer membrane proteins (OMPs) from genomic sequences and for the successful prediction of their secondary and tertiary structures.

Results: We have developed a method based on support vector machines using amino acid composition and residue pair information. Our approach with amino acid composition has correctly predicted the OMPs with a cross-validated accuracy of 94% in a set of 208 proteins. Further, this method has successfully excluded 633 of 673 globular proteins and 191 of 206 {alpha}-helical membrane proteins. We obtained an overall accuracy of 92% for correctly picking up the OMPs from a dataset of 1087 proteins belonging to all different types of globular and membrane proteins. Furthermore, residue pair information improved the accuracy from 92 to 94%. This accuracy of discriminating OMPs is higher than that of other methods in the literature, which could be used for dissecting OMPs from genomic sequences.

Availability: Discrimination results are available at http://tmbeta-svm.cbrc.jp

Contact: michael-gromiha{at}aist.go.jp

Received on June 27, 2005; revised on September 27, 2005; accepted on September 27, 2005

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
M. M. Gromiha, Y. Yabuki, S. Kundu, S. Suharnan, and M. Suwa
TMBETA-GENOME: database for annotated {beta}-barrel membrane proteins in genomic sequences
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D314 - D316.
[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.