How well does Glide deal with binding sites containing metal ions for docking?

Glide can dock ligands to metals in receptors. The GlideScore actually has a special reward term for the binding of negatively-charged and negative polar ligand atoms to net-positive metal centers. Interactions with metals were considered in the optimization of the GlideScore. The metal term has been primarily fit to systems where ligands interact with zinc and magnesium ions, with lesser contributions from systems where ligands interact with iron, calcium, copper, and manganese.

<> Starting in Suite 2009 (Glide 5.5), Glide has an option to incorporate Epik state penalties into the docking score. States appropriate for binding to metals can be generated by Epik, along with the penalty terms. This Epik feature is accesible via LigPrep, so you might want to use it when preparing your ligands for docking to receptors with active-site metals. These states do not normally have significant population at physiological pH, so they are not normally generated in a LigPrep run. Glide skips the "Metal only" ligand states if there is no metal in the active site, so we recommend generating these states when preparing a ligand database for general use.

Keywords: metal ions, docking, interactions with metals, active-site metals, Epik, metal-binding states, Glide

Back to Search Results