The Dive into Research module supports components of the modules leading up to it and is not really a standalone module but given the structure of this collection, makes the most sense to organize it as such.

PDBs (straight from the PDB) The folder name says it all, these are the PDBs you could easily fetch from the PDB but in this workflow it is helpful to have them in a shared folder and actually, AHB1 is a model and is not from a crystal structure so that one was pulled for Cao et al 2020 supplemental.

PDBs Original Binder Scaffolds with Viral Variants (minimized) The files in this folder are a key starting point for the workflows in this project. Students minimized these files in Foldit after making the mutations on the viral spike side of the complex to represent the viral variants of concern: beta and gamma (and the WT too). The collection includes these variants for the three binder scaffolds students investigated in this project: LCB1, LCB3, AHB1.

5.1 Cao et al 2020. Miniprotein binders This is a PDF version of the paper that the research project was based on.

5.2 Guide using FastDesign to compare and optimize your binder redesigns This is a shortcut to the PyRosetta Module guide but it is foundational to guiding students research so it is included in this module as well.

5.3 SARS-CoV2 minibinder redesign project Intro & Discussion slides This slide deck covers the rationale for the project and cites relevant components of the Cao et al 2020 paper and follow-up research that investigates linking binders into flexible trimers. The deck concludes with a set of open-ended discussion questions to support students thinking in expanding their work and connecting it to the larger scientific goals outside this project.

The goal of this form is to cull and organize the data we collectively generated in our summer together. This means the binder redesigns you made!

The form will prompt you to enter the information one of the designs you worked on. Some of these will be the universal designs. It’s okay if more than one person adds in this data but optimally, you would coordinate with your team so we don’t make overlapping efforts.

To be clear: You will be completing a form entry for each redesign that you want to submit for testing/assaying. You may submit as many entries as you like.