Hello and welcome to the Protein Science 101 and Foldit module. This README file captures the components of this folder and recommends an order to review them. Further resources are in the PCR-IO YouTube playlist.
1.0 Protein Folding Basics This slide deck describes the basics of how proteins fold up and how Rosetta models and designs around those tenets. The deck is 14 slides long and takes about 15 minutes to talk through. The last slide has resources linked if students want to go deeper.
1.1 Foldit Teaching & Learning resource manual This guide walks students and instructors through the download and installation of Foldit, Foldit Education Mode, and Foldit Standalone with examples, resources, and embedded guides for using each of the software packages.
1.2 Foldit Standalone as a research tool: the bagel project example This slide deck describes how the Siegel Lab has integrated Foldit Standalone into a project that examines the structure-function relationship in enzymes. This slide deck might not be useful for many labs. It’s 17 slides long and takes about 20 minutes to present.
1.2.1 Repacking & Minimization This slide deck reviews content presented in the Protein Folding Basics deck and expands to include: sidechain energy favorability, protein folding energy landscape, Gibbs free energy, intra/intermolecular protein bond types, favorable side chain interactions. Author: .
1.2.2 Minimizing in Foldit This slide deck describes minimizing in broad strokes to explain this essential feature of Foldit Standalone. The deck is 7 slides long and takes about 10 minutes to talk through. The images are mostly pulled from the ones in the following guide.
1.2.3 Guide: Minimizing structures and making mutations in Foldit Standalone This guide goes step by step through the mechanics of minimization in Foldit Standalone. The first couple pages also textually cover the content in the complementary slide deck.
Other Foldit Standalone resources
- Folder with BglB structure files
- Guide with Foldit Standalone instructions for modeling mutations
- Database of BglB mutations
1.3 Foldit works as a research tool This slide deck is more or less a journal club style presentation of Seth Cooper’s 2010 paper on Foldit efficacy and really makes the case for human intuition as a powerful means to solve some protein folding problems. It’s 9 slides long and can take up to a half hour to present. Depending how deep you go on the figures.