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This page lists haddock development articles.
HADDOCK development papers
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. | Read More >>

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. | Read More >>
  • 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 (2007) HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins: Struc. Funct. & Bioinformatic 69, 726-733. | Read More >>

And, if used, cite in addition any publication related to the use of RDCs, diffusion anisotropy data, protein-DNA docking and/or solvated docking (see below)

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. | Read More >>
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 (2006) Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. J. Biomol. NMR, 34, 237-244. | Read More >>
Solvated docking using HADDOCK is described in:
  • A.D.J. van Dijk and A.M.J.J. Bonvin (2006) Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics, 22 2340-2347. | Read More >>
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 (2006) "Information-driven Protein-DNA Docking using HADDOCK: it is a matter of flexibility." Nucl. Acids Res., 34 3317-3325. | Read More >>
Our results in CAPRI, the blind docking experiment, are described in (Note that entire issues of Protein are dedicated to CAPRI):
  • A.D.J. van Dijk, S.J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou and A.M.J.J. Bonvin (2005) "Data-driven docking: HADDOCKs adventures in CAPRI." Proteins: Struc. Funct. & Bioinformatics, 60, 232-238. | Read More >>
  • 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 (2007) "HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets." Proteins: Struc. Funct. & Bioinformatic, advanced online publication. | Read More >>
The following review on data-driven docking is freely available for download:
  • Aalt D.J. van Dijk, Rolf Boelens and Alexandre M.J.J. Bonvin (2005) "Data-driven docking for the study of biomolecular complexes." FEBS Journal,272, 293-312. | Read More >>