Molecular docking is a foundational method in drug discovery, encompassing key concepts such as ligand–target interactions and binding affinity. Teaching docking to a multidisciplinary audience, however, presents a pedagogical challenge as students from chemistry, biology, computer science, and clinical backgrounds often approach the topic with different expectations and varying levels of familiarity with computational chemistry. Designing a learning experience that balances accessibility with scientific rigor requires a workflow that is computationally straightforward while remains conceptually a learning experience.

This talk presents a scaffolded workflow for introducing target identification and molecular docking that can be used for Drug Discovery course where audience is multidisciplinary. The approach emphasizes conceptual understanding while using accessible and free computational tools, including SwissTargetPrediction, SwissDock (with AutoDock Vina), and PyMOL. By starting with intuitive graphical user interfaces and gradually introducing core computational principles, docking is framed not merely as a software exercise, but as a shared scientific language that connects disciplines and fosters collaborative thinking. We will share our workflow with the audience as a takeaway.

In our workflow, students engage in a ligand-based drug discovery exercise. They begin by selecting a FDA-approved drug and identifying potential biological targets through literature research and SwissTargetPrediction. After critically evaluating candidate targets, they retrieve ligand-bound crystal structures from the Protein Data Bank and use PyMOL to visualize protein–ligand interactions and characterize binding pockets. Students then perform docking using SwissDock with AutoDock Vina and conclude by analyzing docking poses, scoring functions, and key binding interactions.

By integrating biological reasoning, structural analysis, and computational modeling within a cohesive framework, this approach promotes both technical competency and critical interpretation skills, enabling students from diverse backgrounds to meaningfully engage docking’s role in drug discovery.

Speaker:

Samra Khan
Ph.D. Candiate
University of Windsor