The Protein Design Project is the highlight of the senior undergraduate Protein and Nucleic Acid Structure course at the University of Guelph in Guelph, Ontario, Canada. In this project, students apply problem-solving skills while working in pairs to design a zinc finger protein intended to bind to a specific sequence of DNA and act as a possible therapeutic. Problem-solving skills are critical throughout the exercise as the students define what they want their protein to do and which design elements they will include to achieve their goals. The students then report the design of their proteins and the justification of their design elements. Manuscripts are prepared and submitted using a Web-based tool that handles the administration of submission, peer review, revision, grade assignment, and correspondence with authors. Through this process students gain direct experience with the process of scientific publishing using electronic submission, review, and revision, and learn valuable lessons regarding the emotional aspects of publishing in science.