Communicating an understanding of the forces and factors that determine a protein's structure is an important goal of many biology and biochemistry courses at a variety of levels. Many educators use computer software that allows visualization of these complex molecules for this purpose. Although visualization is in wide use and has been associated with student learning, it is quite challenging to develop visualizations that allow students to interactively observe the effects of altered amino acid sequence on protein structure. A software simulation, the protein investigator (PI), has been developed to specifically facilitate this type of exploration. When using the PI, students enter or edit an amino acid sequence; the software then simulates its folding in two dimensions using the major forces involved in protein structure. This study explores freshman undergraduate students' use of visualization and simulation when learning about protein structure. It also evaluates some of the learning outcomes from these two approaches. Our results show that simulation leads to similar learning outcomes as visualization. Because simulation allows a more interactive exploration, a combination of the two approaches may be an effective approach to introducing the basic principles of protein structure.Keywords: Undergraduate, protein structure, visualization, simulation, evaluation.Proteins are a major component of all cells and are responsible for carrying out many of the functions of living organisms. A protein's function is determined primarily by its structure, which is largely determined by its amino acid sequence; this process is mediated by a variety of covalent and noncovalent interactions between the amino acids. Mutations can act by causing changes in the amino acid sequence of proteins that can lead to alterations in function, which may have effects on phenotype. An understanding of these issues is an essential part of understanding modern molecular biology and is a key component of biology and biochemistry courses from high school through graduate school, albeit at different levels of precision.Many methods have been developed to teach students about protein structure and the forces that govern it. These include two-dimensional presentations in textbooks and slides; physical models (for example, [1, 2]); audio feedback [3]; and, quite frequently, computer-aided visualization (for an extensive library of examples, see molviz.org). Visualization typically takes the form of twodimensional displays, where interactive controls allow the user to explore and experience the three-dimensional structure of the protein under study. A large number of software programs have been developed for this purpose (including [4,5], and www.jmol.org); these have been received positively by students [3,4] and their use has been correlated with increased understanding of key elements of protein biochemistry [1,6].One important use of these visualizations is to have students develop hypotheses about the interactions they observe and the possi...