haddocking / haddock3

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 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 (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 for using either or ) . To install haddock3 with MPI support (required an OpenMPI installation - refer to the instructions in INSTALL.md use: In case you rather install the latest unreleased version use instead: For detailed instructions and installation of third-party software, please check INSTALL.md You might also want to check the following utilities: • : Tool to generate restraints to be used in . • : Tool to run large scale simulations using multiple input molecules in different scenarios • : Set of useful utility scripts developed over the years by the BonvinLab group members Usage The most basic usage is: For help on haddock3 usage: 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 for your research, please support us by signing up in this form. This will allow us contact you when needed for -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 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]](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 Useful resources • 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 Please check DEVELOPMENT for instructions on how to develop Code Documentation The code documentation is automatically built and hosted at bonvinlab.org/haddock3. To build it locally it is necessary to have some extra packages installed. You can install them using the following command: Then, to build the documentation, run the following commands: > Warning messages are expected, but the documentation should be built successfully. The rendered documentation will be available at . This will open a local webpage with the Contributing Check the CONTRIBUTING file for instructions on how to contribute with the project! -->