ArticleBioinformatics (Oxford, England)2012
TMBB-DB: a transmembrane β-barrel proteome database.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 21 citations in OpenAlex.
- General features of transmembrane beta barrels from a large database.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Colicin E1 opens its hinge to plug TolC.eLife · 2022Article
- OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins.Frontiers in bioinformatics · 2021Article
- ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank.Database : the journal of biological databases and curation · 2019Article
- Article
- High-resolution structure prediction ofProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes.BMC microbiology · 2016Article
- FmvB: A Francisella tularensis Magnesium-Responsive Outer Membrane Protein that Plays a Role in Virulence.PloS one · 2016Article
- The Borrelia afzelii outer membrane protein BAPKO_0422 binds human factor-H and is predicted to form a membrane-spanning β-barrel.Bioscience reports · 2015Article
- All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.Nucleic acids research · 2014Article
- Identification of Protective Antigens for Vaccination against Systemic Salmonellosis.Frontiers in immunology · 2014Review
- The Treponema pallidum Outer Membrane.Current topics in microbiology and immunologyReview
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
motivationWe previously reported the development of a highly accurate statistical algorithm for identifying β-barrel outer membrane proteins or transmembrane β-barrels (TMBBs), from genomic sequence data of Gram-negative bacteria (Freeman,T.C. and Wimley,W.C. (2010) Bioinformatics, 26, 1965-1974). We have now applied this identification algorithm to all available Gram-negative bacterial genomes (over 600 chromosomes) and have constructed a publicly available, searchable, up-to-date, database of all proteins in these genomes.
resultsFor each protein in the database, there is information on (i) β-barrel membrane protein probability for identification of β-barrels, (ii) β-strand and β-hairpin propensity for structure and topology prediction, (iii) signal sequence score because most TMBBs are secreted through the inner membrane translocon and, thus, have a signal sequence, and (iv) transmembrane α-helix predictions, for reducing false positive predictions. This information is sufficient for the accurate identification of most β-barrel membrane proteins in these genomes. In the database there are nearly 50 000 predicted TMBBs (out of 1.9 million total putative proteins). Of those, more than 15 000 are 'hypothetical' or 'putative' proteins, not previously identified as TMBBs. This wealth of genomic information is not available anywhere else. AVAILABILITY: The TMBB genomic database is available at http://beta-barrel.tulane.edu/. CONTACT: wwimley@tulane.edu.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.