Hi
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?
Thank you
Dhiraj
Category:
Post Situation:
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.
https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file
https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/constraint_generators/ConstraintGenerators