Modeling Protein–Protein Complexes Using the HADDOCK Webserver “Modeling Protein Complexes with HADDOCK”

Part of the Methods in Molecular Biology book series (MIMB, volume 1137)


Protein–protein interactions lie at the heart of most cellular processes. Determining their high-resolution structures by experimental methods is a nontrivial task, which is why complementary computational approaches have been developed over the years. To gain structural and dynamical insight on an atomic scale in these interactions, computational modeling must often be complemented by low-resolution experimental information. For this purpose, we developed the user-friendly HADDOCK webserver, the interface to our biomolecular docking program, which can make use of a variety of low-resolution data to drive the docking process. In this chapter, we explain the use of the HADDOCK webserver based on the real-life Lys48-linked di-ubiquitin case, which led to the 2BGF PDB model. We demonstrate the use of chemical shift perturbation data in combination with residual dipolar couplings and further highlight a few other cases where our software was successfully used. The HADDOCK webserver is available to the science community for free at


Docking Protein–protein interactions Biomolecular complexes NMR Ubiquitinitation 



Financial support from the Dutch Foundation for Scientific Research (NWO) (ECHO grant no. 711.011.009 and VICI grant no. 700.56.442) and the European Union (FP7 e-Infrastructure grant WeNMR no. 261572) is acknowledged.


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Faculty of Science - Chemistry, Bijvoet Center for Biomolecular ResearchUtrecht UniversityCH UtrechtThe Netherlands

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