Dear BB, I have a structure of a protein domain that binds to a peptide ligand containing either a lysine or an arginine. There are homologs in the PDB with the peptide in complex both with lysine and arginine. I would like to model both alternative ligands bound to the new domain. It looks like there is a slightly narrowed binding site in my new struture for the end of a lysine side chain, so I'm speculating that the preference will be for lysine over arginine, but I'd like to do something like an energy minimisation and see whether either there is a lower energy complex for the ligand with lysine, or if the arginine moves to an alternate binding site - there is a possible alternate site. Can anybody suggest a quick and easy (idiots) way of doing this?
Many thanks. Again, Ed
