Teaching Structure-Based Drug Discovery Through Molecular Docking

This guide presents a structured molecular docking workflow aimed at enhancing the understanding of drug discovery in upper-level undergraduate and early graduate courses in chemistry and related fields. It outlines the rationale for integrating molecular recognition and protein structure concepts, which are often taught in isolation, thereby limiting students' ability to connect structural reasoning with predictive modeling. The module includes detailed learning objectives, such as interpreting enzyme-ligand interactions and validating docking protocols. The workflow consists of protein and ligand preparation, grid definition, and docking execution using AutoDock Vina. It emphasizes the importance of protocol validation through redocking and provides a critical reflection section for students to evaluate the limitations of rigid-receptor docking and the assumptions in scoring functions. The implementation guide specifies the required software and materials, making it adaptable for educational settings.