HADDOCK3

Introduction

HADDOCK, standing for High Ambiguity Driven protein-protein DOCKing, is a widely used computational tool for the integrative modeling of biomolecular interactions. Developed by researchers at Utrecht University in the BonvinLab for more than 20 years, it integrates various types of experimental data, biochemical, biophysical, bioinformatic prediction and knowledge to guide the docking process.

Installation

Simple installation of the latest release of HADDOCK3 (requires Python 3.10+):

pip install haddock3

For Python environment setup and installation instructions, see docs/pages/PYTHON.md.

For development installation or to install the latest unreleased version please refer to docs/pages/DEVELOPMENT.md

Usage

The most basic usage is:

haddock3 <configuration-file.toml>

Check the EXAMPLES page for more some usage examples and the User manual for a more detailed explanation of the configuration file.

Support

If you encounter any code-related issues, please open an issue.

If you have any other questions or need help, please contact us at ask.bioexcel.eu.

If you clone this repository and use haddock3 for your research, please support us by signing up in this form. This will allow us contact you when needed for haddock3-related issues, and also provide us a mean to demonstrate impact when reporting for grants - which grealty helps us to keep the project alive!

Useful resources

• haddock-restraints: Tool to generate restraints to be used in haddock3.
• haddock-runner: Tool to run large scale haddock3 simulations using multiple input molecules in different scenarios
• haddock-tools: Set of useful utility scripts developed over the years by the BonvinLab group members
• User manual: The online HADDOCK3 guide describing every aspects of the tool.
• Best practice guide (HADDOCK2.X series)
• The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot. 2024

Development

For development setup and guidelines, see docs/pages/DEVELOPMENT.md.

Contributing

See CONTRIBUTING.md

Cite us

If you used haddock3 for your research, please cite us:

• Research article: M. Giulini, V. Reys, J.M.C. Teixeira, B. Jiménez-García, R.V. Honorato, A. Kravchenko, X. Xu, R. Versini, A. Engel, S. Verhoeven, A.M.J.J. Bonvin, HADDOCK3: A modular and versatile platform for integrative modelling of biomolecular complexes Journal of Chemical Information and Modeling (2025). doi: 10.1021/acs.jcim.5c00969 [BioRxiv]

• Cite this repository: M.C. Teixeira, J., Vargas Honorato, R., Giulini, M., Bonvin, A., SarahAlidoost, Reys, V., Jimenez, B., Schulte, D., van Noort, C., Verhoeven, S., Vreede, B., SSchott, & Tsai, R. (2024). haddocking/haddock3: v3.0.0-beta.5 (Version 3.0.0-beta.5) [Computer software]. https://doi.org/10.5281/zenodo.10527751