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

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W400-4. doi: 10.1093/nar/gkh417.

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.

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry*
  • Computer Graphics
  • Gram-Negative Bacteria / chemistry*
  • Internet
  • Markov Chains
  • Protein Structure, Secondary
  • Sequence Analysis, Protein
  • Software*
  • User-Computer Interface

Substances

  • Bacterial Outer Membrane Proteins