HADDOCK

High Ambiguity Driven biomolecular DOCKing

based on biochemical and/or biophysical information.

Structure + Binformatic/Biophysical Data => Complex

Version: 2.5 (December 2024) (changes)

Authors: Alexandre Bonvin and members of the computational structural biology group, Utrecht University

Contact:

Bijvoet Center for Biomolecular Research
Padualaan 8, 3584 CH Utrecht, the Netherlands
Email: a.m.j.j.bonvin@uu.nl
Phone: +31-30-2533859 Fax: +31-30-2537623

HADDOCK is one of the flagship software in the EU H2020 BioExcel Center of Excellence for Biomolecular Research

Note that as of December 2024 we are only distributing the 2.5 version of HADDOCK, which is the Python3 port of HADDOCK2.4. The functionalities are the same as the 2.4 version (the online manual has not changed). The web server is still called HADDOCK2.4, but run in backgroun the 2.5 version.

HADDOCK2.4/5 manual: https://www.bonvinlab.org/software/haddock2.4/manual

HADDOCK2.4 webserver: https://wenmr.science.uu.nl/haddock2.4

Getting the software: license form

Questions about HADDOCK or looking for support? Ask BioExcel

HADDOCK best practice guide - A must read when starting to use our software!

An introduction to HADDOCK2.4/5: View the SBGrid [webinar]:

View recorded lecture

(https://www.youtube.com/watch?v=PDfFOUqdt5I) (June 29th, 2021).

Two lectures about integrative modelling and HADDOCK: Recording of a lecture by Prof. Bonvin at the 2021 BioExcel summerschool:

View recorded lecture Part I (46 min.)

View recorded lecture Part II (43 min.)

Publications:

When using HADDOCK cite:

Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J. Am. Chem. Soc. 125, 1731-1737 (2003).
R.V. Honorato, M.E. Trellet, B. Jiménez-García1, J.J. Schaarschmidt, M. Giulini, V. Reys, P.I. Koukos, J.P.G.L.M. Rodrigues, E. Karaca, G.C.P. van Zundert, J. Roel-Touris, C.W. van Noort, Z. Jandová, A.S.J. Melquiond and A.M.J.J. Bonvin. The HADDOCK2.4 web server: A leap forward in integrative modelling of biomolecular complexes. Nature Prot., Advanced Online Publication DOI: 10.1038/s41596-024-01011-0 (2024).

For additional citations when using specific modules see also our publication page.

Acknowledgments:

HADDOCK was originally derived from ARIA scripts by Michael Nilges and Jens Linge.

J.P. Linge, M. Habeck, W. Rieping and M. Nilges (2003). ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315-316.

The ongoing development of HADDOCK is the result of a team effort and in particular contributions from Cyril Dominguez, Aalt-Jan van Dijk, Sjoerd de Vries, Marc van Dijk, Ezgi Karaca, Panagiotis Kastritis, Adrien Melquiond, Mikael Trellet, Gydo van Zundert and Joao Rodrigues are acknowledged.

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