In docking with Glide, can I get the interaction between an electrophile and nucleophile?

While the GlideScore can account for favorable electrophile/nucleophile interactions through its electrostatic term, it doesn't have a specific scoring term for this type of interaction (as for H-bonds). Also, Glide does not model chemical changes in either the receptor or ligand that could occur upon binding.

We do have a covalent docking script that uses Prime, starting with Suite 2009. You specify the location on the receptor where binding occurs, provide a SMARTS pattern for the reactive group of the ligand, and the workflow will attach ligands to the receptor and sample their conformations. This script can be run from Applications → Prime → Covalent Docking.

If you want to follow the course of the nucleophilic attack through the transition state (if there is one), you can consider using QSite, in which you can place the ligand and selected receptor residues into the QM region, and treat the rest of the system with MM.

Keywords: bonding interaction, electrophile, neucleophile, Glide

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