APR 30, 2026

Hands-On Workshop: Searching for the “Chemical Core” using Ligand-Based Virtual Screening with Phase

Traditional medicinal chemistry education often struggles to bridge the gap between 2D Lewis structures and the 3D reality of molecular recognition. This hands-on workshop introduces faculty to Schrödinger’s Phase panel as a pedagogical bridge for teaching students to decode the “molecular message.” Participants will learn how to guide students in abstracting a ligand into a 3D Pharmacophore Hypothesis, identifying essential hydrogen bond donors, acceptors, and hydrophobic regions to visualize how a protein “reads” a spatial map rather than a chemical name.

The session will explore the “Scaffold Hop,” a core industry concept used to overcome drug resistance and patent limitations. Attendees will learn to design classroom challenges where students perform virtual screening to identify bioisosteres—structurally diverse molecules that satisfy the same biological requirements. By analyzing the Phase Fitness Score, professors will help students understand how disparate chemical skeletons can achieve functional equivalence through precise 3D alignment.

Finally, the workshop focuses on model validation and critical auditing. Participants will learn to implement inquiry-based labs where students screen “blinded” libraries containing both known actives and inactive “decoys.” By utilizing ranking metrics to evaluate their model’s predictive power, students move beyond “pushing buttons” to performing rigorous, data-driven evaluation of in silico results. Attendees will leave with a complete framework for integrating modern virtual screening workflows into their chemistry and biochemistry curricula.

Learning Objectives:

• Decoding the “Molecular Message”: Feature Identification and Abstraction
• Mastering the “Scaffold Hop”: Exploring Chemical Diversity
• Evaluating “In Silico” Success: Validation and Enrichment

Interactive Demo | Slides