I'm completely new to Rosetta and I'm trying to get a feel for what is possible. I have a template pdb structure of a dimer and several query sequences, I'd like to thread these sequences in turn on to the relevant subunit of the structure and produce candidate structures. Is this kind of homology modelling of interactions possible in Rosetta? Does the software support threading on to the two subunits all at once or would I need to produce a structure for each subunit separately and then dock the subunits?
any pointers are appreciated...
If it's a symmetric homodimer, I think fold_and_dock will do you what you want.
If it's an asymmetric dimer, I think you'll need to fold them separately and then dock. (I could be wrong; the developers most likely to try these sorts of experiments don't frequent these boards.)