Reply To: How to design a stand-alone loop from a binding interface?

[Anonymous]

I’m not sure I understand the question.

You have the conformation of a loop. You want to create a short peptide that maintains the same conformation in solution.

Your question is, what can Rosetta do to help ensure the loop will maintain its conformation?

I guess the counter question is, what are you willing to do to the peptide? You mention cyclization. Did you want to test locations to anchor that disulfide and then test that it will maintain conformation?

I’m not aware of anyone working with cyclic peptides currently (and I’m not an expert on disulfides). There’s no hits for cyclic peptides in the codebase.

I think Rosetta is up to the task of modeling this peptide, but I don’t think we have any protocols already written to do it. In other words, I think you’d need to write a fair amount of code yourself. (You may want to try it in PyRosetta, on the theory that python is easier to write in than C++.)