PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

The Biophysicist, 2021:

Suggested citation: Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte JW, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner BD, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp DW, Das R, Dunbrack RL, Schief W, Kuhlman B, Siegel JB, Gray JJ (2021) "PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design," The Biophysicist 2(1), 108-122 DOI: 10.35459/tbp.2019.000147

Abstract: Biomolecular structure drives function, and computational capabilities have progressed such that the prediction and computational design of biomolecular structures is increasingly feasible. Because computational biophysics attracts students from many different backgrounds and with different levels of resources, teaching the subject can be challenging. One strategy to teach diverse learners is with interactive multimedia material that promotes self-paced, active learning. We have created a hands-on education strategy with a set of fifteen modules that teach topics in biomolecular structure and design, from fundamentals of conformational sampling and energy evaluation to applications like protein docking, antibody design, and RNA structure prediction. Our modules are based on PyRosetta, a Python library that encapsulates all computational modules and methods in the Rosetta software package. The workshop-style modules are implemented as Jupyter Notebooks that can be executed in the Google Colaboratory, allowing learners access with just a web browser. The digital format of Jupyter Notebooks allows us to embed images, molecular visualization movies, and interactive coding exercises. This multimodal approach may better reach students from different disciplines and experience levels as well as attract more researchers from smaller labs and cognate backgrounds to leverage PyRosetta in their science and engineering research. All materials are freely available at