ArticleProtein science : a publication of the Protein Society2002
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes.
Article in Protein science : a publication of the Protein Society, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 110 citations in OpenAlex.
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- A Brief History of Protein Sorting Prediction.The protein journal · 2019Review
- Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.Computational and structural biotechnology journal · 2017Review
- Systematic protein interactome analysis of glycosaminoglycans revealed YcbS as a novel bacterial virulence factor.Scientific reports · 2016Article
- Life at the border: adaptation of proteins to anisotropic membrane environment.Protein science : a publication of the Protein Society · 2014Review
- Fur is the master regulator of the extraintestinal pathogenic Escherichia coli response to serum.mBio · 2014Article
- Structural adaptations of proteins to different biological membranes.Biochimica et biophysica acta · 2013Article
- Charge asymmetry in the proteins of the outer membrane.Bioinformatics (Oxford, England) · 2013Article
- Article
- A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins.PloS one · 2013Article
- Review
- Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation.BMC bioinformatics · 2012Article
- Isolation of improved free fatty acid overproducing strains ofEnvironmental progress & sustainable energy · 2012Article
- Study on mechanisms of colonization of nitrogen-fixing PGPB, Klebsiella pneumoniae NG14 on the root surface of rice and the formation of biofilm.Current microbiology · 2011Article
- Outer membrane proteins can be simply identified using secondary structure element alignment.BMC bioinformatics · 2011Article
- OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.Nucleic acids research · 2011Article
- CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.BMC microbiology · 2010Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Many outer membrane proteins (OMPs) in Gram-negative bacteria possess known beta-barrel three-dimensional (3D) structures. These proteins, including channel-forming transmembrane porins, are diverse in sequence but exhibit common structural features. We here report computational analyses of six outer membrane proteins of known 3D structures with respect to (1) secondary structure, (2) hydropathy, and (3) amphipathicity. Using these characteristics, as well as the presence of an N-terminal targeting sequence, a program was developed allowing prediction of integral membrane beta-barrel proteins encoded within any completely sequenced prokaryotic genome. This program, termed the beta-barrel finder (BBF) program, was used to analyze the proteins encoded within the Escherichia coli genome. Out of 4290 sequences examined, 118 (2.8%) were retrieved. Of these, almost all known outer membrane proteins with established beta-barrel structures as well as many probable outer membrane proteins were identified. This program should be useful for predicting the occurrence of outer membrane proteins in bacteria with completely sequenced genomes.
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