Protein-protein Docking tutorial using HADDOCK with the BioExcel Building Blocks (biobb)

Based on the official HADDOCK3 Antibody-antigen modelling tutorial.

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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.

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Settings

Biobb modules used

• 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.

Auxiliary libraries used

• 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.

Conda Installation and Launch

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_aa.ipynb

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Tutorial

Click here to view tutorial in Read the Docs

Click here to execute tutorial in Binder

Click here to open tutorial in Google Colab

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Version

2025.1

Copyright & Licensing

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) 2015-2025 Barcelona Supercomputing Center
• (c) 2015-2025 Institute for Research in Biomedicine

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