On 8/9/12 7:53 AM, Marco Lolicato wrote: > I've already had a look into the forum but I didn't find the answer. > I would like to model a chimera protein where the two segments are > deposited into the Protein DataBank. One of the two proteins is a > membrane protein. > I used the default values with really interesting results, but I guess I > have a problem in modeling the soluble portion of the chimera: in fact, > in the model, it appear in the same orientation of the transmembrane > helices of the membrane portion. It seems that the soluble portion > itself can insert in the membrane.
Models generated in Modeller will always resemble the template, so you can definitely model membrane proteins, provided you have a membrane protein template - you don't need to do anything special. If the model does *not* look like the template, your alignment is probably incorrect (it sounds here as if you have aligned the soluble portion with the transmembrane portion by mistake).
Ben Webb, Modeller Caretaker