PRED-TMBB: a web server for predicting the topology of -barrel outer membrane proteins

P. G. Bagos, T. D. Liakopoulos, I. C. Spyropoulos, S. J. Hamodrakas
2004 Nucleic Acids Research  
The b-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different webbased predictors for a-helical membrane proteins, currently there is no freely available prediction method for b-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
more » ... -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 b-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.
doi:10.1093/nar/gkh417 pmid:15215419 pmcid:PMC441555 fatcat:roej5xoq6nee3adfbb273c75tu