Kind of a newbie to Rosetta. My protein has two structured domains connected by a short non-floppy loop (6 residues). One of the domains can have the structure accurately solved by comparative modelling. The other doesn't have related templates available, but I do have co-evolutionary information to probably obtain a nice structure via ab initio modelling. I am looking for the best way to do a hybrid approach to solve the whole structure of this protein. I am considering these options:
1. Model the two domains separately, then dock them and build the short loop.
2. Model the first domain with comparative method. Perform "ab initio" modeling of the whole sequence, but use the structure of the first domain as constraint (is that possible?). This way seems more interesting because the presence of one domain would affect the folding of the other...
I believe this is a common situation to find... can anyone help me to figure it out how this is usually done?
I really appreciate any comment on that!