HADDOCK-related publications

This page lists haddock development articles.

The original JACS paper, together with an introduction to the study of biomolecular complexes and an application to the UbcH5-CNOT4 complex can be found online in Cyril Dominguez’s Ph.D. thesis:

“NMR-based docking of protein-protein complexes: the human UbcH5b-CNOT4 ubiquitination complex”,
Cyril Dominguez, Ph.D. Thesis, June 2004, ISBN 90-393-3721-7.

When using HADDOCK cite:

Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003). HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.
J. Am. Chem. Soc. 125, 1731-1737.
S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin
“HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets.”
Proteins: Struc. Funct. & Bioinformatic 69, 726-733 (2007).

When using the HADDOCK2.4 web service cite:

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).

And, if used, cite depending on the type of data and setting used the following publications:

The use of residual dipolar couplings in HADDOCK is described in:

A.D.J. van Dijk, D. Fushman and A.M.J.J. Bonvin (2005)
“Various strategies of using residual dipolar couplings in NMR-driven protein docking: Application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.”
Proteins: Struc. Funct. & Bioinformatics, 60, 367-381.

The use of diffusion anisotropy data in HADDOCK is described in:

A.D.J. van Dijk, R. Kaptein, R. Boelens and A.M.J.J. Bonvin “Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking”
J. Biomol. NMR, 34, 237-244 (2006).

The use of pseudo contact shift restraints in HADDOCK is described in:

C. Schmitz and A.M.J.J. Bonvin
“Protein-Protein HADDocking using exclusively Pseudocontact Shifts.”
J. Biomol. NMR, 50, 263-266 (2011).

The use of SAXS data to score HADDOCK models is described in:

E. Karaca and A.M.J.J. Bonvin.
“On the usefulness of Ion Mobility Mass Spectrometry and SAXS data in scoring docking decoys.”
Acta Cryst. D., D69, 683-694 (2013).

The quantitative use of chemical shifts to score HADDOCK models is described in:

D. Stratman, R. Boelens and A.M.J.J. Bonvin.
“Quantitative use of chemical shifts for the modelling of protein complexes.”
Proteins: Struc. Funct. & Bioinformatic, 79, 2662-2670 (2011).

Protein-peptide docking with HADDOCK is described in:

M. Trellet, A.S.J. Melquiond and A.M.J.J. Bonvin. .
“A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking.
PLoS ONE, 8(3) e58769 (2013).

Solvated protein-protein docking using HADDOCK is described in:

A.D.J. van Dijk and A.M.J.J. Bonvin “Solvated docking: introducing water i nto the modelling of biomolecular complexes.”
Bioinformatics, 22 2340-2347 (2006).

Solvated protein-protein docking with Kyte-Doolittle propensities using HADDOCK is described in:

P.L. Kastritis, K.M. Visscher, A.D.J. van Dijk and A.M.J.J. Bonvin.
“Solvated docking using Kyte-Doolittle-based water propensities.”
Proteins: Struc. Funct. & Bioinformatic., 81, 510-518 (2013).

Solvated protein-DNA docking using HADDOCK is described in:

M. van Dijk, K. Visscher, P.L. Kastritis and A.M.J.J. Bonvin. .
“Solvated protein-DNA docking using HADDOCK.”
J. Biomol. NMR, 56, 51-63 (2013).

Flexible protein-DNA docking using HADDOCK is described in:

M. van Dijk, A.D.J. van Dijk, V. Hsu, R. Boelens and A.M.J.J. Bonvin “Information-driven Protein-DNA Docking using HADDOCK: it is a matter of flexibility.”
Nucl. Acids Res., 34 3317-3325 (2006).
M. van Dijk and A.M.J.J. Bonvin.
“Pushing the limits of what is achievable in protein-DNA docking. Benchmarking HADDOCK’s performance.”
Nucl. Acid Res., 38, 5634-5647 (2010).

(Flexible) multibody docking using HADDOCK is described in:

E. Karaca and A.M.J.J. Bonvin.
“A multi-domain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes.”
Structure, 19 555-565(2011).
E. Karaca, A.S.J. Melquiond, S.J. de Vries, P.L. Kastritis and A.M.J.J. Bonvin.
“Building macromolecular assemblies by information-driven docking: Introducing the HADDOCK multi-body docking server.”
Mol. Cell. Proteomics, 9, 1784-1794 (2010).

Our results in CAPRI, the blind docking experiment, are described in (Note that entire issues of Protein are dedicated to CAPRI):

J.P.G.L.M. Rodrigues, A.S.J. Melquiond, E. Karaca, M. Trellet, M. Van Dijk, G.C.P. Van Zundert, C. Schmitz, S.J. de Vries, A. Bordogna, L. Bonati, P.L. Kastritis and A.M.J.J. Bonvin.
“Defining the limits of homology modelling in information-driven protein docking”
Proteins: Struc. Funct. & Bioinformatics, 81, 2119-2128 (2013).
S.J. de Vries, A.S.J. Melquiond, P.L. Kastritis, E. Karaca, A. Bordogna, M. van Dijk, J.P.G.L.M. Rodrigues and A.M.J.J. Bonvin.
“Strengths and weaknesses of data-driven docking in CAPRI”
Proteins: Struc. Funct. & Bioinformatic, 78, 3242-3249 (2010).
S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin “HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets.”
Proteins: Struc. Funct. & Bioinformatic, advanced online publication (2007).
A.D.J. van Dijk, S.J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou and A.M.J.J. Bonvin “Data-driven docking: HADDOCKs adventures in CAPRI.”
Proteins: Struc. Funct. & Bioinformatics, 60, 232-238 (2005).

Reviews on data-driven docking:

J.P.G.L.M Rodrigues and A.M.J.J. Bonvin.
“Integrative computational modeling of protein interactions.”
FEBS J., 281, 1988-2003 (2014).
H. van Ingen and A.M.J.J. Bonvin.
“Information-driven modeling of large macromolecular assemblies using NMR data.”
J. Magn. Reson. 241, 103-114 (2014).
E. Karaca and A.M.J.J. Bonvin.
“Advances in integrated modelling of biomolecular complexes.”
Methods, 59, 372-381 (2013).
P.L. Kastritis and A.M.J.J. Bonvin.
“Predicting and Dissecting High-order Molecular Complexity by Information-driven Biomolecular Docking”
In: Antimicrobial Drug Discovery. Emerging Strategies Adv. Mol. Cell. Microbiol., Eds G. Tegos and E. Mylokanis, CABI, 22, 232-246 (2012).
A.S.J. Melquiond, E. Karaca, P.L. Kastritis and A.M.J.J. Bonvin.
“Next challenges in protein-protein docking: From proteome to interactome and beyond.”
WIREs Computational Molecular Science, 2, 642-651 (2012).
Aalt D.J. van Dijk, Rolf Boelens and A.M.J.J. Bonvin (2005). “Data-driven docking for the study of biomolecular complexes.”
FEBS Journal, 272, 293-312.