I'm having trouble docking a native ligand into the binding pocket of a metal-containing receptor. I find I need to add a hydrophobic constraint for a solvent-exposed phenyl ring. What might be the problem?

It's possible that the phenyl ring is not solvent-exposed in the crystal, but is interacting with a hydrophobic region on an adjacent chain. To see if this is the case, import the PDB structure, and choose Workspace → Crystal Mates to display the adjacent chains. If it is, you should include the adjacent chain when preparing the grids.

Keywords: Glide

Back to Search Results