Protein-ligand interactions / Ligand optimization / Protein-ligand docking / Pharmacophore modeling / Template-based docking / High-throughput screening / Scaffold replacement / R-group exploration / Bioisosteric transformations / Ligand properties

This workshop presents common molecular modeling and design techniques for identifying, optimizing and prioritizing small-molecule drug candidates, using MOE. It covers structure preparation and pocket analysis followed by in situ modification. The workshop explains template-based docking (congeneric series) and pharmacophore-guide docking (preserving key interactions) to predict how small molecules bind to a protein target. It also covers advanced settings for achieving high-throughput docking for screening large databases. This workshop continues with a series of de novo fragment-based drug design applications. It focuses on scaffold hopping and fragment growing methods to generate novel compound ideas, optimize structures in the pocket, and score them. It also discusses the use of molecular descriptors and pharmacophore models to guide the drug design process. Finally, a method for generating closely related analogs through bioisosteric replacements is presented.