I predicted the transmembrane span of a list of proteins. Quite sure about what it predicted for the probability of transmembrane span is true, but I am also very much sure about what it predicted as an extracellular region is a cytoplasmic portion of that transmembrane protein.
So, how good or bad it would be to rely upon the results of TMHMM/Phobius for segments other than transmembrane helices?
Run TMHMM with proteins for which you know (experimental evidence) the structure (ideally homologs to the proteins of your interest) to assess the reliability of inside/TMhelix/outside predictions.
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If you are 'sure', as you write, i.e. you 'know', use the source of your knowledge to determine the inside/outside of the membrane protein instead of TMHMM.
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