In trying to understand the numerous rosetta options I wanted to see if anyone could give some guidance on how to go about the following.
I have two proteins A and B that I need to dock where the interface between the two proteins is known from sequence homology of an already solved PDB structure for proteins C and B.
On Protein A I can do the low resolution model with the appropriate constraints and then do the high resolution docking. When the high resolution model is constructed I am under the assumption that the backbone of Protein A will not be adjusted. Once I have a high resolution docking model of Protein A and Protein B is there a particular Rosetta process that can be used to see how the docking would change the overall structure of Protein A. On another interface of Protein A it has a couple loops that could change/move based on docking with Protein B. Not sure how to have Rosetta explore finding a model with overall minimal energy where loops or other regions Protein A may change based on the docking.