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The HADDOCK web server for data-driven biomolecular docking

Nature Protocols volume 5, pages 883–897 (2010)Cite this article

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Abstract

Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOCK is a popular docking program that takes a data-driven approach to docking, with support for a wide range of experimental data. Here we present the HADDOCK web server protocol, facilitating the modeling of biomolecular complexes for a wide community. The main web interface is user-friendly, requiring only the structures of the individual components and a list of interacting residues as input. Additional web interfaces allow the more advanced user to exploit the full range of experimental data supported by HADDOCK and to customize the docking process. The HADDOCK server has access to the resources of a dedicated cluster and of the e-NMR GRID infrastructure. Therefore, a typical docking run takes only a few minutes to prepare and a few hours to complete.

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Figure 1: Flowchart of the HADDOCK server.
Figure 2: The HADDOCK server Easy interface.
Figure 3: Example of docking results from the HADDOCK server.

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Acknowledgements

This work was supported by The Netherlands Organization for Scientific Research (VICI grant no. 700.56.442 to A.B.) and the European Community (FP6 integrated Project SPINE2-COMPLEX, contract no. 032220; FP6 STREP project 'ExtendNMR', contract no. LSHG-CT-2005-018988; and FP7 e-Infrastructure 'e-NMR' I3 project, grant number 213010). The Dutch BiG Grid project with financial support from The Netherlands Organization for Scientific Research (NWO) is acknowledged for the use of the computing and storage facilities. We would like to thank J. Verhaal for critical reading of the manuscript.

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Authors and Affiliations

  1. Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Utrecht, The Netherlands

    Sjoerd J de Vries, Marc van Dijk & Alexandre M J J Bonvin

Authors
  1. Sjoerd J de Vries
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  2. Marc van Dijk
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  3. Alexandre M J J Bonvin
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Contributions

A.M.J.J.B. is the primary author of the HADDOCK program. S.J.d.V. developed the HADDOCK web server and the Spyder framework. M.v.D. developed the nucleic acid functionality of the server and the graphical design of the server web site. A.M.J.J.B. supervised the project. S.J.d.V. wrote the paper.

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Correspondence to Alexandre M J J Bonvin.

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The authors declare no competing financial interests.

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de Vries, S., van Dijk, M. & Bonvin, A. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5, 883–897 (2010). https://doi.org/10.1038/nprot.2010.32

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