Hello,
I’m working with a membrane-bound enzyme that has two types of substrate, a small-molecule and a lipid. From collaborators we have a structure from a fuller simulation of the protein and lipid, but some initial attempts to get the small-molecule ligand position with Haddock have been running into trouble where it ends up in what is known to be the lipid’s binding site. Since the web server lists a type of molecule to dock as ‘protein or protein-ligand’, is there a way to try docking the small molecule (ligand2) to the combined structure of the lipid and enzyme (protein-ligand1), or do I need to try incorporating this information less directly, e.g. by manually excluding the ligand1 binding site in the list of passive residues?
Best,
Hugh