A series of computer-based laboratory experiments have been developed to aid undergraduate students in appreciating the three-dimensional nature of chemistry and biochemistry. Both lower- and upper-division experiments have been developed. Students are introduced to the use of ChemDraw for the production of professional-quality molecular structures, Chem3D for visualizing molecules in three dimensions, and VMD for investigating protein structures and dynamics. Through a series of guided experiments, students explore important concepts in chemistry and biochemistry, such as stereochemistry, protein secondary structure, intermolecular interactions, molecular recognition, and protein dynamics. An overwhelmingly positive response to these experiments was received, with students reporting an enhanced appreciation of the nature and behavior of molecular and protein systems, and an improved understanding of lecture material.