Recognizing that undergraduate students can benefit from analysis of 3D protein structure and function, we have developed a multiweek, inquiry-based molecular visualization project for Biochemistry I students. This project uses a virtual model of cyclooxygenase-1 (COX-1) to guide students through multiple levels of protein structure analysis. The first assignment explores primary structure by generating and examining a protein sequence alignment. Subsequent assignments introduce 3D visualization software to explore secondary, tertiary, and quaternary structure. Students design an inhibitor, based on scrutiny of the enzyme active site, and evaluate the fit of the molecule using computed binding energies. In the last assignment, students introduce a point mutation to model the active site of the related COX-2 enzyme and analyze the impact of the mutation on inhibitor binding. With this project we aim to increase knowledge about, and confidence in using, online databases and computational tools. Here, we share results of our mixed methods pre- and postsurvey demonstrating student gains in knowledge about, and confidence using, online databases and computational tools.