ArticleBMC bioinformatics2005
Prediction of beta-barrel membrane proteins by searching for restricted domains.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- The Two TpsB-Like Proteins inJournal of bacteriology · 2021Article
- 50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification.Biological research · 2016Article
- The composition of the global and feature specific cyanobacterial core-genomes.Frontiers in microbiology · 2015Article
- Defining the core proteome of the chloroplast envelope membranes.Frontiers in plant science · 2013Article
- TMBB-DB: a transmembrane β-barrel proteome database.Bioinformatics (Oxford, England) · 2012Article
- Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions.Bioinformatics (Oxford, England) · 2012Article
- Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation.BMC bioinformatics · 2012Article
- Filling the gap, evolutionarily conserved Omp85 in plastids of chromalveolates.The Journal of biological chemistry · 2010Article
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Authors and funding
2 authors.
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Abstract
backgroundThe 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.
resultsFor 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.
conclusionAnalyzing 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.
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