I wanted to carry out a ligand-based interface design of a protein-RNA-ligand complex, where my goal is to find out the affinity-reducing mutants of the protein towards the ligand. Currently, I am using a Rosetta script (attached), whose goal is to find out designs that improve the affinity towards the ligand. What I need is the exact opposite, but I couldn't find any relevant information about this in literature/Rosetta commons. Could you please suggest if there is any way to modify the xml file that I am currently using (attached a .txt file) to achieve my objective or it is not possible at all?
Also, is there any way to use the same affinity-enhancing Rosetta xml/protocol to consider in this case i.e. for finding affinity-reducing mutants?
If not, are there any protocols that have been developed by others to find-out affinity-reducing mutants? If someone has any similar protocol or a modified one that suits my objective, it would be really helpful if that can be shared with me.
Thank you very much. I look forward to hear from you.
With best regards