I am a new Rosetta (3.5) user and I would like to study the effects of some point mutations on a monomeric transmembrane protein.
Can ddg_monomer properly predict the change in stability induced by point mutations in transmembrane proteins? If yes, should I specify a particular score function file using -ddg:minimization_scorefunction option? I would like to study mutations in both, the transmembrane (membrane-facing and not) and the extracellular region of the protein, should I treat them separately?
If ddg_monomer can not properly predict the change in stability in transmembrane proteins, is there any other rosetta application that I can use for this purpose?
I have to parametrize some cofactors/ligands before I can start to study these mutations so I would like to know if it's really worth it.
Thank very much you for your time.