Tutorials, cheat sheets, and other resources for computational methods for protein design.
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README.md
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README.md

protein-design-tutorials

This is a collection for all of the tutorials/resources for learning to use Rosetta and the other computational methods we use in our work. Please feel free to edit and update if you see old or incorrect info, even if you are new to the lab (sometimes new people bring the best insights on what is needed!) Note: Most of the documents in this repository are written in Markdown - here is a quick guide if you are new to it.

Contents

intro_to_sherlock.md - A quick-start guide for lab members new to or just getting started on Sherlock.

Remodel

We've assembled some cheat sheets, references, and tutorials for learning to use RosettaRemodel as a command line executable here in this repo. They're not meant to replace the documentation kept at RosettaCommons, which is already very well developed, some of which we have linked to below. The goal here is to just help you get started in the lab ASAP.

In this repository
remodel_overview.md - An introduction to RosettaRemodel, how it works, and some basic knowledge that will be useful in learning to use it. Start here if you are new to to Remodel!
remodel_flags.md - A newbie-friendly list of the most commonly used flags in RosettaRemodel.
remodel_bugs.md - A kind of Stack Overflow for RosettaRemodel. Adding bugs and fixes to this list will hopefully save everyone time in the long run!
de_novo_design/ - A step-by-step tutorial for de novo protein design using Rosetta fragment sampling.

External Resources
RosettaRemodel Docs
Old Remodel Docs & Tutorial
Rosetta 3 Forums
Remodel Flags & Options
General Remodel Tutorial
Stanford Rosetta Workshop
Loop Modeling Tutorial
Disulfide Design Tutorial

Pyrosetta

TODO Andres