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Open Access Highly Accessed Methodology article

Outer membrane proteins can be simply identified using secondary structure element alignment

Ren-Xiang Yan12, Zhen Chen12 and Ziding Zhang12*

Author Affiliations

1 State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China

2 Bioinformatics Center, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China

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BMC Bioinformatics 2011, 12:76  doi:10.1186/1471-2105-12-76

Published: 17 March 2011

Abstract

Background

Outer membrane proteins (OMPs) are frequently found in the outer membranes of gram-negative bacteria, mitochondria and chloroplasts and have been found to play diverse functional roles. Computational discrimination of OMPs from globular proteins and other types of membrane proteins is helpful to accelerate new genome annotation and drug discovery.

Results

Based on the observation that almost all OMPs consist of antiparallel β-strands in a barrel shape and that their secondary structure arrangements differ from those of other types of proteins, we propose a simple method called SSEA-OMP to identify OMPs using secondary structure element alignment. Through intensive benchmark experiments, the proposed SSEA-OMP method is better than some well-established OMP detection methods.

Conclusions

The major advantage of SSEA-OMP is its good prediction performance considering its simplicity. The web server implements the method is freely accessible at http://protein.cau.edu.cn/SSEA-OMP/index.html webcite.