Hello! I have a small molecule that I would like to dock to a receptor site. The receptor site, however, includes nucleobases from RNA and amino acids from protein. I know some of the bases are important in establishing pi-pi stacking and some of the amino acid side chains are important in establishing H-bonds and electrostatics. Is there a workflow from HADDOCK that would support this docking job?
Dear user,
Of course, HADDOCK can handle such kind of scenario.
I would suggest to attribute the same chain to both the protein and the RNA, just make sure the residue ids are unique.
You can then get inspired by either the binding site protocol or the shape-restraints docking one to perform such kind of docking scenario.
Cheers,
Victor