I am trying to generate models of a 281 aa long protein domain with Modeller. The problem is the low sequence identity with the templates (ranges between 30-40%) and an unaligned region, which is 46 aa long, but induces a conformation disorder spanning from residue 84 to 161 (77 aa long). So I though to build this fragment of the model with pyrosetta and optimize the structure. My questions:
1. I'm new to Rosetta, hence I'm not sure if what I am after is possible. (?)
2. If yes could you point me to the appropriate tutorials/scripts?
3. Is it easier to use PyRosetta for this task rather than Rosetta? (Unbiased opinions please)
I would greatly appreciate any advice.