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.

This workshop explores essential web-based methods for guiding drug discovery projects without a known protein structure. It examines SAR analysis through R-group profiling and matched molecular pairs (MMP) analysis, using MOEsaic to identify relationships within a chemical series. The session highlights computational strategies for extracting meaningful insights from structure-activity data to support informed decision-making in drug design. The workshop also introduces the CLE application as a powerful tool for streamlining the search of available reagent catalogs using multi-component chemical reactions. It demonstrates how to apply a reaction both as a query and as a transformation to efficiently enumerate all possible product combinations. The session covers methods for inspecting, filtering, and exporting reagents and products, including catalog IDs, for synthesis.