Learner-centered molecular modeling exercises in college science courses can be especially challenging for nonchemistry majors as students typically have a higher degree of anxiety and may not appreciate the relevance of the work. This article describes a learner-centered project given to allied health majors in a Biochemistry course. The project involved building molecular models of imagined protein binding sites for the drug thalidomide. By designing their own sites, students should have a better understanding of how proteins interact with other molecules and that small changes in the three-dimensional structure of the molecule have the potential to reduce interactions with the protein. Surveys suggested that students understood the purpose of the project and its relevance to their careers beyond the Biochemistry course. There was slightly less agreement as to whether this type of project made the material more comprehensible. Nevertheless, there was a significant improvement of final exam scores over previous classes. In addition, students expressed some anxiety over the project prior to and on its initiation. Anxiety was reduced and enthusiasm was greatly improved as the project progressed. Together these findings suggest that a molecular modeling exercise can be successfully introduced to allied health majors to provide spatial reasoning and critical thinking skills.