Based on the official HADDOCK3 Antibody-antigen modelling tutorial.

This tutorial aims to illustrate the process of protein-protein docking, step by step, using HADDOCK3 with the BioExcel Building Blocks library (biobb). The particular systems used in this tutorial are the Interleukin-1β (IL-1β) antigen (PDB code 4I1B) and the gevokizumab antibody (PDB code 4G6K). The complex is also available under the PDB code 4G6M.

• biobb_io: Tools to fetch biomolecular data from public databases.
• biobb_pdb_tools: Swiss army knife for manipulating and editing PDB files.
• biobb_haddock: Module collection to compute information-driven flexible protein-protein docking.

• jupyter: Free software, open standards, and web services for interactive computing across all programming languages.
• nglview: Jupyter/IPython widget to interactively view molecular structures and trajectories in notebooks.

git clone https://github.com/bioexcel/biobb_wf_haddock.git
cd biobb_wf_haddock
conda env create -f conda_env/environment.yml
conda activate biobb_wf_haddock
jupyter-notebook biobb_wf_haddock/notebooks/biobb_wf_haddock.ipynb

Click here to execute tutorial in Binder

Click here to open tutorial in Google Colab

2026.1 Release

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU Horizon Europe 101093290, EU H2020 823830, EU H2020 675728).

• (c) 2015-2026 Barcelona Supercomputing Center
• (c) 2015-2026 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.