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