PyRosetta Interactive Labs

Protein design is an inherently complex topic with a steep learning curve. There is plenty of academic literature for those already versed in computational protein design methods, but there are no readily accessible resources for individuals with a background in biology/biochemistry who want to learn how to use these computational tools.

I developed a series of Jupyter Notebooks to help bridge this gap. These notebooks are configured for absolute beginners with no previous computational experience. Setup is straight forward with Anaconda, and I use PyRosetta, PyMOL, and ipywidgets to help build an intuition for core design concepts and algorithms that are routinely used in computational design of proteins. The notebooks walk through investigating protein structures, modeling protein backbones and side chains, and ultimately designing an enzyme from scratch.

Check out the repository here!