Research shows that computer animations are especially helpful in fields such as chemistry and in this mixed-methods study, we investigate the educational effectiveness of Bio-Organic Reaction Animations (BioORA), a 3-D software, in four undergraduate biochemistry classes at different universities. Statistically significant findings indicate that students performed better on a quiz completed after a lesson with BioORA than after a lesson with regular teaching methods in three out of four classes. Ratings on several survey items completed after experiencing BioORA, including items related to interest, value, and ability, were higher in two classes. Surveys and one-on-one interviews reveal instructor and student experiences with the software as well as the utility of various software features, which can be adopted in other programs. Instructors and students provide suggestions to maximize BioORA's benefits as an educational tool and findings suggest the importance of multiple forms of information to enhance student understanding and reach students with various learning preferences.