ArticleBMC bioinformatics2011
Outer membrane proteins can be simply identified using secondary structure element alignment.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins.BMC bioinformatics · 2019Article
- Comparative Analysis of TM and Cytoplasmic β-barrel Conformations Using Joint Descriptor.Scientific reports · 2018Article
- Prediction of structural features and application to outer membrane protein identification.Scientific reports · 2015Article
- Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions.Bioinformatics (Oxford, England) · 2012Article
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3 authors.
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Abstract
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.
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