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

BMC Bioinformatics

Methodology Article

Ren-Xiang Yan¹  Ziding Zhang¹  Zhen Chen¹ 

[1] State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China;Bioinformatics Center, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China;

关键词: Receiver Operating Characteristic Curve;    Query Sequence;    Matthew Correlation Coefficient;    Test Protein;    Benchmark Experiment;   

DOI  :  10.1186/1471-2105-12-76

 received in 2010-08-02, accepted in 2011-03-17,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundOuter 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.ResultsBased 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Yan et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.