Dear Theresa, Use as many prediction softwares as possible. First I would go for transmembrane topology prediction, try at least tmhmm, dgpred or topcons to see if they agree on the number of tm's that will be indicative of the fold. Topcons, octopus, will tell you if there is any re-entrant loop, sometimes present in ion channels. With this information you should be able to test if the template is suitable for your target. Membrane protein sequence conservation is so so. In my case, I built my model using modeller, but I refined my alignment with secondary structure prediction software (predictprotein), topology information (topcons), and evolutionary information (evfold/evcouplings), and I reached an optimal solution confirmed 1 year later by the hi-res structure.
Hope it helps, ask for more details. Alex On May 22, 2014 9:49 PM, "Theresa Hsu" <[email protected]> wrote: > Dear all > > I am working with a membrane protein without known structure. The closest > protein in PDB has 10% sequence identity/25% similarity to my protein. > > What is the best method and software to do homology modeling while I try > to get the crystal? Is the ligand binding site prediction reliable? There > is no available experimental data on this protein except to sugest it is > some type of ion transport. > > Thank you. > > Theresa >
