I have a protein with two domain connected by short loop. depending on ligand and post-translational modification, it adopt open or close conformation. I want to design the loop residues so that I can shift the equilibrium towards close conformation. what is the best way/protocol to do that in Rosetta?
I think your best bet is to use constraints based on the closed conformation – either through RosettaScripts and the ConstraintGenerator machinery or through a constraint file. You can then do sequence design in FastRelax/FastDesign while minimizing the backbone of your loop.
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