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Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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Protein-protein docking

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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

  • 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


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.