title: PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins.
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.
authors.affiliation: Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15701, Greece. pbagos@biol.uoa.gr
authors.forename: Pantelis G
authors.initials: PG
authors.lastname: Bagos
authors.forename: Theodore D
authors.initials: TD
authors.lastname: Liakopoulos
authors.forename: Ioannis C
authors.initials: IC
authors.lastname: Spyropoulos
authors.forename: Stavros J
authors.initials: SJ
authors.lastname: Hamodrakas
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D003196:Computer Graphics; D006090:Gram-Negative Bacteria / Q000737:chemistry*; D020407:Internet; D008390:Markov Chains; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D001425:Bacterial Outer Membrane Proteins