I'm trying to predict secondary structure of a transmembrane protein. I've used the following tools/servers : PsiPred, Jpred, ProfSec (PhdSec), porter and spritz. I've got different results for predictions (in some case enough marked). How can optimize results and find a consensus?
I'm wondering if prepare a dataset using only homologs and perfom an analysis by a support vector machine.
Do you have a good reason to predict only TMHs instead the whole domain/protein? Anyway, you'll not find a consensus. Too many different methods. Besides that, only I-TASSER can possibly get better results than PsiPred server.
@Jarretinha: could you give us a reference for your statement about I-TASSER?