Workshop

Welcome to the workshop, we're happy to have you. In this workshop you can do antibody-antigen docking using HADDOCK3, de novo binding-protein design using RFdiffusion and de novo nanobody design using RFantibody. You can choose what you want to do!

You can start with either:

• 1.0 Binding-protein design, RFdiffusion
  • 2.0 Alphafold3
• 3.0 Antibody-Antigen docking, HADDOCK3
• 4.0 Nanobody design, RFantibody

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Install

To follow this workshops workflow, install the following, onto your laptop or computer:

• PyMOL.
• MobaXterm home edition.
  • Log in using the instructions laying around.

Setup

1.0 Folder creation

Lets create your own folder:

mkdir <your_name>

Note

Please change the <your_name> to your own name!

2.0 Moving into the folder

Then move into your freshly made folder by running:

cd <your_name>

Note

Please change the <your_name> to your own name!

3.0 Download files

We will download the files by cloning the github repository onto alice: This will generate a new folder you can can work in with all the files you need.

git clone https://github.com/Sir-Corgi/workshop.git

Note

You can move around the directory using:

• cd (change directory).
  • Followed by either the directory you want to enter.
  • Followed by .. (double dot) to go back one directory.
• ls (look in a directory).
  • Followed by either the directory you want to look into.
  • Followed by .. (double dot) to see one directory back.

Warning

Please check the box in the bottom left corner that says "Follow terminal folder". This will allow you to click and open files using the mouse.

5.0 Move into folder

Run the following, to get into the workshops folder containing everything you need to follow the workshop:

cd workshop
ls

Now you can chose to follow one of the modules I have prepared for you!

• Binding-protein design, RFdiffusion: please follow these instructions.
  • Alphafold3
• Antibody-Antigen docking, HADDOCK3: please follow these instructions.
• Nanobody design, RFantibody: please follow these instructions.

Have fun, and dont hesitate to ask questions!

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Acknowledgment

If you found this workshop helpful or used any of its materials in your own work, research, or teaching, please consider acknowledging it. A simple note like the following goes a long way:

“This work is based on materials from a workshop by Jesper (Sir-Corgi).”

For a full list of tools and citations used in this workshop, see CITATIONS.md.

Contact

For questions or feedback, contact me at j.e.buis@umail.leidenuniv.nl.