This course introduces some popular molecular graphics systems that allow for the visualization, animation, editing, and publication-quality imagery of proteins. It focuses on hands-on experience in the classroom and builds solid skills in visually investigating the 3D molecular structures of proteins and their interactions with each other and with ligands such as substrates and drugs. The course also explores the importance of protein sequence and structure alignment programs in revealing evolutionary relationships between proteins. Finally, it emphasizes the use of computational tools for predicting the effects of amino acid substitutions on protein structure and function as well as classifying mutations as deleterious or benign.