PRED-TMBB -- A Web Server for Predicting the Topology of xdf-barrel Outer Membrane Proteins

What you can do:
Predict the transmembrane strands and the topology of xdf-barrel outer membrane proteins of Gram-negative bacteria.
Highlights:
  • 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 xdf-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.
Keywords:
  • xdf-barrel outer membrane proteins
  • membrane proteins
  • Gram-negative bacteria
  • protein structure prediction
  • protein topology
Literature & Tutorials:
This record last updated: 05-11-2005
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