Protein-protein docking

Best practice guide

As the name HADDOCK (High Ambiguity Driven protein-protein DOCKing) suggests, HADDOCK was originally developed for docking of proteins. Nowadays HADDOCK belongs to the state-of-the-art software in the protein-protein docking field, thus protein-protein documentation is the most comprehensive one. You can read more about protein-protein docking in following sections:

Tutorials
Publications
Settings
FAQ

Tutorials

HADDOCK2.4 local installation tutorial: A tutorial demonstrating the installation and use of a local installation of HADDOCK2.4. It demonstrates various docking scenarios. You will need for this a valid license of HADDOCK2.4.
HADDOCK2.4 basic protein-protein docking tutorial: A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.
HADDOCK2.4 MS cross-links tutorial: A tutorial demonstrating the use of cross-linking data from mass spectrometry to guide the docking in HADDOCK. This tutorial builds on our DisVis tutorial and illustrates various scenarios of using cross-linking data in HADDOCK. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis.
DISVIS/HADDOCK2.4 oligomer puzzle: In this tutorial you will have to solve an oligomer puzzle, namely predicting the correct oligomeric state of a symmetrical homomer complex based on a few (artificial) cross-links. The tutorial does not require any Linux expertise and only makes use of the DISVIS and HADDOCK web servers and PyMol for visualisation/analysis.
HADDOCK2.4 CA-CA restraints guided docking tutorial: A tutorial demonstrating a template-based approach to model protein-protein complexes. It combines the PS-HomPPI web server to find suitable templates and generate CA-CA distance restraints and HADDOCK for the CA-CA guided modelling. This tutorial does not require any Linux expertise and only makes use of the PS-HomPPI and HADDOCK web servers and PyMol for visualisation/analysis.
HADDOCK2.4 ab-initio, multi-body symmetrical docking tutorial: A tutorial demonstrating multi-body docking with HADDOCK using its ab-initio mode with symmetry restraints. It is based on a former CASP-CAPRI target (T70).
HADDOCK2.4 antibody-antigen docking tutorial: This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope. This tutorial does not require any Linux expertise and only makes use of our web servers and PyMol for visualisation/analysis.

Publications

A.M.J.J. Bonvin, E. Karaca, P.L. Kastritis & J.P.G.L.M. Rodrigues. Correspondence: Defining distance restraints in HADDOCK. Nature Protocols 13, 1503 (2018). Free online only access
A.M.J.J. Bonvin, C. Geng, M. van Dijk, E. Karaca, P. L. Kastritis, P.I. Koukos, Z. Kurkcuoglu, A.S.J. Melquiond, J.P.G.L.M. Rodrigues, J. Schaarschmidt, C. Schmitz, J. Roel-Touris, M.E. Trellet, S. de Vries, A. Vangone, L. Xue, G.C.P. van Zundert HADDOCK. In Encyclopedia of Biophysics, In press (2018).
G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J. Bonvin. The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes. J. Mol. Biol., 428, 720-725 (2016).
G.C.P. van Zundert, A.S.J. Melquiond and A.M.J.J. Bonvin. Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-EM data. Structure. 23, 949-960 (2015).
J.P.G.L.M Rodrigues, E. Karaca and A.M.J.J. Bonvin. Information-driven structural modelling of protein-protein interactions. Methods in Molecular Biology: Molecular Modelling of Proteins. Ed. Andreas Kokul. Humana Press Inc. 399-424 (2015).
G.C.P. van Zundert and A.M.J.J. Bonvin. Modeling protein-protein complexes using the HADDOCK webserver. Methods in Molecular Biology: Protein Structure Prediction. Ed. Daisuke Kihara. Humana Press Inc., 163-179 (2014).
A.M.J.J. Bonvin, M. van Dijk, E. Karaca, P.L. Kastritis, A.S.J. Melquiond, C. Schmitz and S.J. de Vries HADDOCK In Encyclopedia of Biophysics, Ed. G.C.K. Roberts, Springer-Verlag Berlin Heidelberg (2013).
C. Schmitz, A.S.J. Melquiond, S.J. de Vries, E. Karaca, M. van Dijk, P.L. Kastritis and A.M.J.J. Bonvin Protein-protein docking with HADDOCK In: NMR in Mechanistic Systems Biology. Ed. I. Bertini, K.S. McGreevy and G. Parigi, Wiley-Blackwell, 512-535.
P.L. Kastritis, A.D.J. van Dijk and A.M.J.J. Bonvin Explicit Treatment of Water Molecules in Data-Driven Protein-Protein Docking: The Solvated HADDOCKing Approach Methods in Molecular Biology 819, Part 5, 355-374 (2012)
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).
P.L. Kastritis, I.H. Moal, H. Hwang, Z. Weng, P.A. Bates, A.M.J.J. Bonvin and J. Janin A structure-based benchmark for protein-protein binding affinity. Prot. Sci., 20, 482-41 (2011).
A.S.J. Melquiond and A.M.J.J. Bonvin Data-driven docking: using external information to spark the biomolecular rendez-vous. In: Protein-protein complexes: analysis, modelling and drug design. Edited by M. Zacharrias, Imperial College Press, 2010. p 183-209.
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). Download the final author version here.
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897 (2010).
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin The Prediction of Macromolecular Complexes by Docking. In: Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK (2009).
S. de Vries and A.M.J.J. Bonvin How proteins get in touch: Interface prediction in the study of biomolecular complexes. Curr. Pept. and Prot. Research, 9, 394-406 (2008).
A.D.J. van Dijk and A.M.J.J. Bonvin Solvated docking: introducing water into the modelling of biomolecular complexes.
S.J. de Vries and A.M.J.J. Bonvin Intramolecular surface contacts contain information about protein-protein interface regions. Bioinformatics, 22 2094-2098 (2006).
A.M.J.J. Bonvin Flexible protein-protein docking. Curr. Opin. Struct. Biol., 16, 194-200 (2006).
S.J. de Vries, A.D.J. van Dijk and A.M.J.J. Bonvin WHISCY: WHat Information does Surface Conservation Yield? Application to data-driven docking. Proteins: Struc. Funct. & Bioinformatics, 63, 479-489 (2006).
A.D.J. van Dijk, R. Boelens and A.M.J.J. Bonvin Data-driven docking for the study of biomolecular complexes. FEBS Journal, 272, 293-312 (2005).
C. Dominguez, R. Boelens and A.M.J.J. Bonvin HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737 (2003).

Settings

Default settings are optimal for protein-protein docking, however one can still modify parameters, such as number of generated models.

More about optimal settings for different docking scenarios can be found here.

FAQ

A special section about docking of mutations with HADDOCK is dedicated in the frequently asked questions page.

Any more questions about protein-protein docking with HADDOCK? Have a look at our HADDOCK bioexcel forum hosted by . There is a very high chance that your problem has already been addressed.