ArticleNucleic acids research2004
PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 182 papers.
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182 citing papers in PubMed, 363 citations in OpenAlex.
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- Topology and functional characterization of major outer membrane proteins of Treponema maltophilum and Treponema lecithinolyticum.Molecular oral microbiology · 2025Article
- A Survey of Current Status in AI-Based Topology Prediction of Transmembrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Loss of Lipooligosaccharide Synthesis inInternational journal of molecular sciences · 2024Article
- Oral administration of recombinant outer membrane protein A-based nanovaccine affords protection against Aeromonas hydrophila in zebrafish.World journal of microbiology & biotechnology · 2024Article
- Characterisation of Putative Outer Membrane Proteins fromMicroorganisms · 2024Article
- Protein Sorting Prediction.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Photocatalytic Reduction of Methylene Blue by Surface-Engineered RecombinantBioengineering (Basel, Switzerland) · 2023Article
- In Silico Analysis and Immune Response of YaeT Protein Against Riemerella anatipestifer in Ducks.Applied biochemistry and biotechnology · 2023Article
- Identification and characterisation of a major outer membrane protein from Methylacidiphilum fumariolicum SolV.Antonie van Leeuwenhoek · 2023Article
- Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.PLoS biology · 2023Article
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- LIC12254 Is a Leptospiral Protein That Interacts with Integrins via the RGD Motif.Tropical medicine and infectious disease · 2023Article
- A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni.PLoS neglected tropical diseases · 2023Article
122 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The beta-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for alpha-helical membrane proteins, currently there is no freely available prediction method for beta-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of beta-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane beta-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer.
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