Protein structure, secondary, tertiary, ligand, binding pocket, binding affinity, interactions, therapeutic drug, drug target, ligand docking


Cell Biology | Molecular Biology | Science and Mathematics Education


We describe a series of engaging exercises in which students emulate the process that researchers use to efficiently develop new pharmaceutical drugs, that of rational drug design. The activities are taken from a three- to four-hour workshop regularly conducted with first-year college students and presented here to take place over three to four class periods. Although targeted at college students, these activities may be appropriate at the high school level as well, particularly in an AP Biology course. The exercises introduce students to the topics of bioinformatics and computer modeling, in the context of rational drug design, using free online resources such as databases and computer programs. Through the process of learning about computational drug design and drug optimization, students also learn content such as elements of protein structure and protein–ligand interactions. Based on our assessment, students enjoy the exercises, become more interested in bioinformatics and computer modeling, and demonstrate an increase in content knowledge relevant to the topics.


This article was originally published by the University of California Press on behalf of the National Association of Biology Teachers, and posted in ScholarWorks@GVSU by permission of The American Biology Teacher.

Original Citation

SZARECKA, A., & DOBSON, C. (2019). Protein Structure Analysis: Introducing Students to Rational Drug Design. The American Biology Teacher, 81(6), 423–429.