# `haddock3`
[](https://doi.org/10.5281/zenodo.10527751)
[](https://research-software-directory.org/software/haddock3)
[](https://fair-software.eu)
[](https://www.bestpractices.dev/projects/8844)
[](https://pepy.tech/project/haddock3)
[](https://github.com/haddocking/haddock3/actions/workflows/ci.yml)
[](https://github.com/haddocking/haddock3/actions/workflows/pages.yml)
[](https://github.com/haddocking/haddock3/actions/workflows/github-code-scanning/codeql)
[](https://app.codacy.com/gh/haddocking/haddock3/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
[](https://app.codacy.com/gh/haddocking/haddock3/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
## Introduction
HADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**ing, is a widely used computational tool for the integrative modeling of biomolecular interactions. Developed by researchers at [Utrecht University](https://uu.nl) in the [BonvinLab](https://bonvinlab.org) 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](https://pypi.org/project/haddock3/) of HADDOCK3 (assuming you have a Python version 3.9 to 3.13 installed and the rights to install the software - if not refer to the instructions in [INSTALL.md](docs/INSTALL.md) for using either `venv` or `conda`) .
```bash
pip install haddock3
```
To install haddock3 with MPI support (required an OpenMPI installation - refer
to the instructions in [INSTALL.md](docs/INSTALL.md) use:
```bash
pip install 'haddock3[mpi]'
```
In case you rather install the latest unreleased version use instead:
```bash
git clone https://github.com/haddocking/haddock3.git
cd haddock3
pip install .
```
For detailed instructions and installation of third-party software, please check [INSTALL.md](docs/INSTALL.md)
You might also want to check the following utilities:
- [`haddock-restraints`](https://github.com/haddocking/haddock-restraints): Tool to generate restraints to be used in `haddock3`.
- [`haddock-runner`](https://github.com/haddocking/haddock-runner): Tool to run large scale `haddock3` simulations using multiple input molecules in different scenarios
- [`haddock-tools`](https://github.com/haddocking/haddock-tools): Set of useful utility scripts developed over the years by the BonvinLab group members
## Usage
The most basic usage is:
```bash
haddock3 <configuration-file.toml>
```
For help on haddock3 usage:
```bash
$ haddock3 -h
usage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe
positional arguments:
recipe The input recipe file path
optional arguments:
-h, --help show this help message and exit
--restart RESTART Restart the run from a given step. Previous folders from the selected step onwards will be deleted.
--extend-run EXTEND_RUN
Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.
--setup Only setup the run, do not execute
--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
-v, --version show version
```
Check the [EXAMPLES](https://github.com/haddocking/haddock3/blob/main/examples/README.md) page for more some usage examples and the [User manual](https://www.bonvinlab.org/haddock3-user-manual) for a more detailed explanation of the configuration file.
## Support
If you encounter any code-related issues, [please open an issue](https://github.com/haddocking/haddock3/issues/new/choose).
If you have any other questions or need help, please contact us at [ask.bioexcel.eu](https://ask.bioexcel.eu/).
If you clone this repository and use `haddock3` for your research, please support us by signing up in [this form](https://forms.gle/LCUHiYHh1hE9rd8L6). 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!
## 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*](https://pubs.acs.org/doi/10.1021/acs.jcim.5c00969) Journal of Chemical Information and Modeling (2025). doi: 10.1021/acs.jcim.5c00969 [[BioRxiv]](https://www.biorxiv.org/content/10.1101/2025.04.30.651432v1)
- **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](https://doi.org/10.5281/zenodo.10527751)
## Useful resources
- [User manual](https://www.bonvinlab.org/haddock3-user-manual): The online HADDOCK3 guide describing every aspects of the tool.
- [Best practice guide](https://www.bonvinlab.org/software/bpg/) (HADDOCK2.X series)
- [The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot. 2024](https://www.nature.com/articles/s41596-024-01011-0)
## Development
Please check [DEVELOPMENT](https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md) for instructions on how to develop `haddock3`
### Code Documentation
The code documentation is automatically built and hosted at [bonvinlab.org/haddock3](https://www.bonvinlab.org/haddock3/).
To build it locally it is necessary to have some extra packages installed. You can install them using the following command:
```bash
pip install -e '.[docs]'
```
Then, to build the documentation, run the following commands:
```bash
sphinx-apidoc -f -e -o docs/ src/haddock -d 1
sphinx-build -b html docs haddock3-docs
```
> Warning 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
### Contributing
Check the [CONTRIBUTING](CONTRIBUTING.md) file for instructions on how to contribute with the project!
<!-- ---
Happy HADDOCking!
<img src="https://www.bonvinlab.org/images/bio-haddock.png" alt="haddock" width="50px"> -->
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"description": "# `haddock3`\n\n\n\n[](https://doi.org/10.5281/zenodo.10527751)\n[](https://research-software-directory.org/software/haddock3)\n[](https://fair-software.eu)\n[](https://www.bestpractices.dev/projects/8844)\n\n[](https://pepy.tech/project/haddock3)\n\n\n\n[](https://github.com/haddocking/haddock3/actions/workflows/ci.yml)\n[](https://github.com/haddocking/haddock3/actions/workflows/pages.yml)\n[](https://github.com/haddocking/haddock3/actions/workflows/github-code-scanning/codeql)\n[](https://app.codacy.com/gh/haddocking/haddock3/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)\n[](https://app.codacy.com/gh/haddocking/haddock3/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)\n\n## Introduction\n\nHADDOCK, standing for **H**igh **A**mbiguity **D**riven protein-protein **DOCK**ing, is a widely used computational tool for the integrative modeling of biomolecular interactions. Developed by researchers at [Utrecht University](https://uu.nl) in the [BonvinLab](https://bonvinlab.org) for more than 20 years, it integrates various types of experimental data, biochemical, biophysical, bioinformatic prediction and knowledge to guide the docking process.\n\n## Installation\n\nSimple installation of the [latest release](https://pypi.org/project/haddock3/) of HADDOCK3 (assuming you have a Python version 3.9 to 3.13 installed and the rights to install the software - if not refer to the instructions in [INSTALL.md](docs/INSTALL.md) for using either `venv` or `conda`) .\n\n```bash\npip install haddock3\n```\n\nTo install haddock3 with MPI support (required an OpenMPI installation - refer\nto the instructions in [INSTALL.md](docs/INSTALL.md) use:\n\n```bash\npip install 'haddock3[mpi]'\n```\n\nIn case you rather install the latest unreleased version use instead:\n\n```bash\ngit clone https://github.com/haddocking/haddock3.git\ncd haddock3\npip install .\n```\n\nFor detailed instructions and installation of third-party software, please check [INSTALL.md](docs/INSTALL.md)\n\nYou might also want to check the following utilities:\n\n- [`haddock-restraints`](https://github.com/haddocking/haddock-restraints): Tool to generate restraints to be used in `haddock3`.\n- [`haddock-runner`](https://github.com/haddocking/haddock-runner): Tool to run large scale `haddock3` simulations using multiple input molecules in different scenarios\n- [`haddock-tools`](https://github.com/haddocking/haddock-tools): Set of useful utility scripts developed over the years by the BonvinLab group members\n\n## Usage\n\nThe most basic usage is:\n\n```bash\nhaddock3 <configuration-file.toml>\n```\n\nFor help on haddock3 usage:\n\n```bash\n$ haddock3 -h\nusage: haddock3 [-h] [--restart RESTART] [--extend-run EXTEND_RUN] [--setup] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-v] recipe\n\npositional arguments:\n recipe The input recipe file path\n\noptional arguments:\n -h, --help show this help message and exit\n --restart RESTART Restart the run from a given step. Previous folders from the selected step onwards will be deleted.\n --extend-run EXTEND_RUN\n Start a run from a run directory previously prepared with the `haddock3-copy` CLI. Provide the run directory created with `haddock3-copy` CLI.\n --setup Only setup the run, do not execute\n --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}\n -v, --version show version\n```\n\nCheck the [EXAMPLES](https://github.com/haddocking/haddock3/blob/main/examples/README.md) page for more some usage examples and the [User manual](https://www.bonvinlab.org/haddock3-user-manual) for a more detailed explanation of the configuration file.\n\n## Support\n\nIf you encounter any code-related issues, [please open an issue](https://github.com/haddocking/haddock3/issues/new/choose).\n\nIf you have any other questions or need help, please contact us at [ask.bioexcel.eu](https://ask.bioexcel.eu/).\n\nIf you clone this repository and use `haddock3` for your research, please support us by signing up in [this form](https://forms.gle/LCUHiYHh1hE9rd8L6). 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!\n\n## Cite us\n\nIf you used `haddock3` for your research, please cite us:\n\n- **Research article**: M. Giulini, V. Reys, J.M.C. Teixeira, B. Jim\u00e9nez-Garc\u00eda, 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*](https://pubs.acs.org/doi/10.1021/acs.jcim.5c00969) Journal of Chemical Information and Modeling (2025). doi: 10.1021/acs.jcim.5c00969 [[BioRxiv]](https://www.biorxiv.org/content/10.1101/2025.04.30.651432v1)\n \n- **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](https://doi.org/10.5281/zenodo.10527751)\n\n## Useful resources\n\n- [User manual](https://www.bonvinlab.org/haddock3-user-manual): The online HADDOCK3 guide describing every aspects of the tool.\n- [Best practice guide](https://www.bonvinlab.org/software/bpg/) (HADDOCK2.X series)\n- [The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot. 2024](https://www.nature.com/articles/s41596-024-01011-0)\n\n## Development\n\nPlease check [DEVELOPMENT](https://github.com/haddocking/haddock3/blob/main/DEVELOPMENT.md) for instructions on how to develop `haddock3`\n\n### Code Documentation\n\nThe code documentation is automatically built and hosted at [bonvinlab.org/haddock3](https://www.bonvinlab.org/haddock3/).\n\nTo build it locally it is necessary to have some extra packages installed. 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