I have a scenario where a protein is composed of two domains (its actually two chains, but I can make it a single chain) for Rosetta's purposes.
There is a binding pocket at the interface of these domains, and it is known that the domains "spread open" slightly upon ligand binding. I am trying to figure out how to compose a ligand docking simulation that (a) allows domain translational and rotational flexibilty, and (b) backbone perterbations and side chain optimizations, when the ligand is bound.
I have been able to do (b) with the attchached RosettaScripts XML, however, I can't figure out how to allow a domain to have "free" translation annd rotation flexibility to allow for the simulation to separate the two domains upon binding the ligand.
Does anyone have any pointers on how to simulate ligand docking while allowign two domains to move/rotate as a domain entity?
Unfortunaltey, there are no known ligand bound crystal structures, otherwise I would start with that PDB pose.