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loop design for Conformational bias

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loop design for Conformational bias


   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


Post Situation: 
Thu, 2019-05-09 21:22

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.




Fri, 2019-05-10 07:53