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.
Are there any restraints on membrane protein to add to my default script? Or, do you have any suggestion to overcome the bias? Could I include a special "membrane environment" in the calculation?
Thank you for your time,
Dr. Marco Lolicato, PhD.
Università degli Studi di Milano
Dip. Biologia - Sez. Biochimica e Fisiologia delle Piante
Via Celoria, 26