Prediction of beta-barrel membrane proteins by searching for restricted domains

Prediction of β-barrel membrane proteins by searching for restricted domains

  • BACKGROUND: The identification of beta-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses. RESULTS: For the prediction of beta-barrel membrane proteins within prokaryotic proteomes a set of parameters was developed. We have focused on a procedure with a low false positive rate beside a procedure with lowest false prediction rate to obtain a high certainty for the predicted sequences. We demonstrate that the discrimination between beta-barrel membrane proteins and other proteins is improved by analyzing a length limited region. The developed set of parameters is applied to the proteome of E. coli and the results are compared to four other described procedures. CONCLUSION: Analyzing the beta-barrel membrane proteins revealed the presence of a defined membrane inserted beta-barrel region. This information can now be used to refine other prediction programs as well. So far, all tested programs fail to predict outer membrane proteins in the proteome of the prokaryote E. coli with high reliability. However, the reliability of the prediction is improved significantly by a combinatory approach of several programs. The consequences and usability of the developed scores are discussed.

Download full text files

Export metadata

Additional Services

Share in Twitter Search Google Scholar
Metadaten
Author:Oliver MirusGND, Enrico SchleiffORCiDGND
URN:urn:nbn:de:hebis:30:3-246504
DOI:https://doi.org/10.1186/1471-2105-6-254
ISSN:1471-2105
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/16225682
Parent Title (English):BMC bioinformatic
Publisher:BioMed Central
Place of publication:London
Document Type:Article
Language:English
Date of Publication (online):2012/06/11
Date of first Publication:2005/10/14
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2012/06/11
Volume:6
Issue:254
Page Number:13
HeBIS-PPN:306861623
Institutes:Biowissenschaften / Biowissenschaften
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Licence (German):License LogoCreative Commons - Namensnennung 3.0