PHAR2821 Lecture 1: Drug Discovery 1C
Document Summary
(realistic) forms unless we have prior knowledge from e. g. pharmacophore models. The docking process as we normally think of it is a two step process that involves: Docking place the ligand in the binding cavity. Scoring evaluate the goodness of fit. Important to ask what level of precision is required. Are we trying to predict free energies of binding or are we satisfied with being able to rank two molecules in terms of likelihood of binding to the receptor. Glide xp docking higher precision because it includes more sampling of molecules and more correction terms. Docking is a reasonably good method to predict binding modes of compounds. Scoring functions are less impressive can still be improved. Identifies binding sites and assesses them energetically by calculating the potential energy of probes, i. e. water, hydrophobic, hydrogen bond donor and hydrogen bond acceptor.
