CovDock (Covalent Docking)
CovDock (Covalent Docking) begins with Glide docking to a receptor with the reactive residue trimmed to alanine. The receptor reactive residue is then added and sampled to form a covalent bond with the ligand in different poses. Covalent complexes are minimized using the Prime VSGB2.0 energy model to score the top covalent complexes. An apparent affinity score, based on the Glide score of pre-reactive and post-reactive poses, is also calculated to estimate binding energies for use in virtual screening.
Covalent Docking is a workflow that requires ConfGen, Glide, MacroModel, and Prime.