Training resources

Google Colab allows you to run Python code directly in your browser. You can use this resource to run your first design scripts and explore available training material. All you will need is a Gmail account. 

Google colab introduction

Many of our computational design pipelines use tools developed and maintained by the RosettaCommons. You can learn more about these tools and tested them using the following Colab notebooks. To actually produce designs, you will have to use the lab's GPU station, or the VUB or VIB HPC clusters, because the free computing time provided by Google colab won't be sufficient. 

Pyrosetta notebooks

RFDiffusion

Here, we provide the interactive teaching material we have developed for the courses we teach. After going through the training material, you will:

• Be able to un AlphaFold and interpret the results. You will understand the significance of the parameters you can change and of the output confidence metrics - Module 1.
• Learn how to Rosetta molecular modelling suite through Google colab. You will use the ddG calculation tool in Rosetta to predict the effect of mutations on the stability of a monomeric protein or the binding energy of a protein-protein complex - Module 2.
• Generate new protein structures from scratch using Rosetta and parameteric equations. You will explore the relationship betweent the design parameters and the output 3D protein structure - Module 3.
• Use Rosetta in Colab notebooks to generate new sequences compatible with an input 3D backbone - Module 4.
• Apply a de novo design pipeline using RFDiffusion, ProteinMPNN and AlphaFold to design binders to a give protein target. In the provided demo, you will design binders to the RBD of the SarsCov2 virus completely de novo or by scaffolding the known RBD/human receptor interaction motif - Module 5.

The content of the course is available on GitHub and consist of slide decks and Colab notebooks. To use the training material, download the notebook below and copy it to a new folder on your Google Drive. Use the notebook to download the different training modules.