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Bioinformatics Advance Access published online on November 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti126
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 24, 2004
Revised September 8, 2004
Accepted October 20, 2004

Article

A simple statistical method for discriminating outer membrane proteins with better accuracy

M. Michael Gromiha 1* and Makiko Suwa 1

1 Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi Frontier Building 17F, 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan

* To whom correspondence should be addressed.
M. Michael Gromiha, E-mail: michael-gromiha{at}aist.go.jp


  Abstract

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

Results: We have systematically analyzed the amino acid composition of globular proteins from different structural classes and outer membrane proteins. We found that the residues, Glu, His, Ile, Cys, Gln, Asn and Ser show a significant difference between globular and outer membrane proteins. Based on this information, we have devised a statistical method for discriminating outer membrane proteins from other globular and membrane proteins. Our approach correctly picked up the outer membrane proteins with an accuracy of 89% for the training set of 337 proteins. On the other hand, our method has correctly excluded the globular proteins at an accuracy of 79% in a non-redundant dataset of 674 proteins. Furthermore, the present method is able to correctly exclude {alpha}-helical membrane proteins up to an accuracy of 80%. These accuracy levels are comparable to other methods in the literature and this is a simple method, which could be used for dissecting outer membrane proteins from genomic sequences. The influence of protein size, structural class and specific residues for discrimination is discussed.

Availability: A program for the discrimination method is available upon request from the corresponding author. The datasets used in this work are available at http://www.cbrc.jp/~gromiha/omp/dataset.html.


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