Hi, Dear colleagues!
I am new to Rosetta and am now finding whether there is a solution to my problem using powerful Resetta.
I want to cut a loop which is responsible for the binding of A to B from protein A. I need to constrain this loop so it will maintain its bound conformation though it is now in the apo form.
The problems are:
1) I need to find a way to automatically constrain it either by using disulfide bond and cyclization;
2) The loop is disulfide-bonded to the rest of the protein and this disulfide bond may be responsible for maining a turn in its bound conformation;
Is there anyone that know how can achieve this using Rosetta?
Thanks in advance!