APR 28, 2026
Hands-on workshop: Teaching protein-ligand complementarity using Schrödinger’s Ligand Designer
Modern chemical education is shifting from the memorization of 2D structures to the mastery of 3D molecular recognition. This hands-on workshop introduces faculty to Schrödinger’s Ligand Designer, a powerful tool for bringing industry-standard drug discovery into the undergraduate classroom.
Participants will explore how to move beyond “Lock and Key” metaphors by using Interaction Maps and Real-time Scoring to quantify the “molecular handshake” between proteins and ligands. Through a guided “Modify and Measure” workflow, attendees will practice iterative lead optimization—interpreting steric clashes and growth-space visualizations to explain the thermodynamic drivers of binding affinity.
Finally, the session focuses on pedagogical integration, providing strategies for designing inquiry-based labs. Participants will learn to develop assessment tools, such as “Design Justification” reports, that challenge students to defend their chemical intuition with computational data. Attendees will leave with a ready-to-use framework for transforming static textbook concepts into dynamic, data-driven student experiences.
Learning Objectives:
- Visualize and Quantify Molecular Complementarity
- Execute Iterative Lead Optimization Workflows
- Integrate Computational “Inquiry-Based” Labs into Existing Curricula
Slides | Interactive Demo
Our Speakers
Kat Bay
Manager, Teaching with Schrödinger
Dr. Katherine Bay is a Senior Scientist responsible for leading the Teaching with Schrödinger program. She develops academic curricula that integrates Schrödinger’s molecular modeling tools into the classroom. Prior to joining Schrödinger in 2021, she was an Assistant Professor of Organic Chemistry where she designed her course as a flipped classroom model in response to the COVID-19 pandemic. She earned her Ph.D. in Organic Chemistry from the University of California, Los Angeles elucidating reactions using density functional theory.
Emma Kuczkowski
Senior Scientist I, Life Science Education, Schrödinger
Emma Kuczkowski, holding a MS degree in Chemistry from the State University of New York at Oswego, serves as a Scientist II on the Schrödinger Education team. With a background spanning education and commercial drug manufacturing, she brings her expertise to computational chemistry education. Since joining Schrödinger, she has played a pivotal role in crafting and delivering cutting-edge small molecule life science courses, notably the flagship course “Introduction to Molecular Modeling in Drug Discovery.” Her contributions extend to crafting various educational materials such as tutorials, reference sheets, videos, and workshops, all aimed at fostering deeper understanding and proficiency in applied molecular modeling.