An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several reports show that the visualization techniques employed to help students understand protein structure often lead to confusion and propagate further misconceptions. Here, we report on a lab exercise using computer-based modeling to support student proficiency in using and making models and understanding H-bonding and the hydrophobic effect in the context of protein folding. We analyzed student drawings and explanations of protein structure and found significant improvements from pre- to postlab, indicating that students improved their understanding of protein folding. Further, we report on how we systematically refined our laboratory materials based on student work.