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.
Please check the INSTALL file for instructions.
You might also want to check the following utilities:
haddock-restraints: Tool to generate restraints to be used inhaddock3.haddock-runner: Tool to run large scalehaddock3simulations using multiple input molecules in different scenarioshaddock-tools: Set of useful utility scripts developed over the years by the BonvinLab group members
The most basic usage is:
haddock3 <configuration-file.toml>Check the EXAMPLES page for more some usage examples and the MANUAL (coming soon!) for a more detailed explanation of the configuration file.
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!
If you used haddock3 for your research, please cite us:
- Research article: (coming soon!)
- 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
- User manual (coming soon!)
- Best practice guide
- The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot. 2024
🚧 Coming soon! We are currently working on the development guide 🚧
The code documentation is automatically built and hosted at bonvinlab.org/haddock3.
To build it locally (considering you have followed the installation instructions):
tox -e docsWarning messages are expected, but the documentation should be built successfully.
The rendered documentation will be available at haddock3-docs/index.html. This will open a local webpage with the
Check the CONTRIBUTING file for instructions on how to contribute with the project!
