JUN 5, 2025

Educator’s Month: Powerful computational tools to help bring proteins to life for students

In this talk, Arthur Sikora will showcase two examples of how technology has brought biochemistry to life for his students. Special focus will be on sharing resources and dissemination of curricula that will support students learning in-silico.

One of the highlights of my career so far has been collaborating to develop and then teach a course-based undergraduate research experience (CURE) called the Biochemistry Authentic Scientific Inquiry Lab (BASIL). The BASIL CURE uses a combined computational and wet lab approach to study protein structures of unknown functions. Students experience research, many for the first and only time, as part of a course they must already take for their degree. Powerful computational tools are used to find homologs and students predict potential enzymatic substrates which are refined using molecular docking. In combination with wet lab experiments students work towards the elucidation of enzyme function. This curriculum is freely available at basilbiochem.org, and we can offer new adopters both synchronous support via virtual meetings and asynchronous support via Slack.

I am very lucky to also teach a course in our Honors college centered around protein modeling. This course focuses on a molecular story that groups of students explore using both virtual and 3D printed molecular models. Every year students discover and utilize innovative bioinformatic tools to enhance their molecular stories. From peptide docking simulations to alpha fold structure prediction, I always learn something new along the way. I explain strategies to get students into a creative space where they are free to direct the project and present several examples from recent years of especially unique and impactful proects.