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HADDOCK3

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is a widely used computational tool for the integrative modeling of biomolecular interactions. The software integrates various types of experimental data, biochemical, biophysical, bioinformatic prediction and knowledge to guide the docking process.

HADDOCK, developed by researchers at BonvinLab at Utrecht University, is a flagship software in the EU H2020 BioExcel Center of Excellence for Biomolecular Research.

Available

Version Available modules Notes
2025.5.0 haddock3/2025.5.0-mpi MPI-enabled module available
2025.8.1 haddock3/2025.8.1-mpi MPI-enabled module available

License

HADDOCK3 is free and open-source software, licensed under the Apache License 2.0 Commercial entities should verify and secure a license for CNS if needed. For this, please contact the main developer Alexandre Bonvin for details.

Usage

Load HADDOCK3 module on LUMI as the following:

 module use  /appl/local/csc/modulefiles/
 module load  haddock3/2025.8.1-mpi

LUMI

It is easy to try out the software on LUMI. First, download tutorial inputs by cloning this repository in your scratch folder:

  git clone https://github.com/haddocking/haddock3.git

HADDOCK will automatically dispatch subjobs, within the slurm allocation, also spanning multiple nodes (second example). Note, that you need to create the batch job in and launch it from the correct subfolder (mentioned in each example batch script).

Match the Slurm and cfg requirements

Make sure that the number of cores (ncores) in the input.cfg script matches what you ask from SLURM with --ntasks-per-node=XX (or --nodes=YY times that for the mpi-job). For these examples you need to edit also the .cfg files!

#!/bin/bash
#SBATCH --account=project_xxxxxxxx
#SBATCH --partition=standard
#SBATCH --time=00:15:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
#SBATCH --job-name=haddock3job

module use  /appl/local/csc/modulefiles/
module load  haddock3/2025.8.1-mpi

# create this batch script file in and submit it from
# haddock3/examples/docking-protein-ligand
# and make sure the requested cores match the ncores in *.cfg file

haddock3 docking-protein-ligand-test.cfg

#!/bin/bash
#SBATCH --account=project_xxxxxxxx
#SBATCH --partition=standard
#SBATCH --time=02:00:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=128
#SBATCH --job-name=haddock3mpi

module use  /appl/local/csc/modulefiles/
module load  haddock3/2025.8.1-mpi

# create this batch script file in and submit it from
# haddock3/examples/docking-antibody-antigen
# and make sure the requested cores match the ncores in *.cfg file

# execute
haddock3 docking-antibody-antigen-CDR-accessible-clt-full-mpi.cfg

The first job should complete in a few minutes, while the second job should finish in an hour. The second job has multiple stages executed as separate job steps. You can monitor their progress e.g. with sacct -j <JOBID> -o jobid,alloc,elapsed,maxrss. In addition to these subjobs, the workflow has a final analysis stage which takes longer with increasing cores used in the computation. In practice, it will limit the reasonable amount of resources to 2 nodes for this case.

References

Cite your work with the following references:

  • 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
  • M.C. Teixeira, J., Vargas Honorato, R., Giulini, M., Bonvin, A., Alidoost, S., 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)

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