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...