Alexandre Bonvin bio photo

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

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HADDOCK3 tutorials

In this page you can find links to tutorials on the usage of the new modular HADDOCK3 version. HADDOCK3 has been and is developed under the umbrella of the BioExcel Center of Excellence for Computational Biomolecular Research and in collaboration with the Netherlands e-Science Center.

Note that HADDOCK3 is still in heavy development and as such the software is evolving quickly.

  • HADDOCK3 documentation Documentation for HADDOCK3 including installation instructions.

  • HADDOCK3 antibody-antigen docking: This tutorial demonstrates the use of HADDOCK3 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. It illustrates the modularity of HADDOCK3 by introducing a new workflow not possible under the current HADDOCK2.X versions. As HADDOCK3 only exists as a command line version, this tutorial does require some basic Linux expertise.

  • HADDOCK3 protein-glycan modelling and docking: This tutorial shows how to use HADDOCK3 to dock a glycan to a protein, provided that some information exists about the protein binding site.

  • HADDOCK3 antibody-antigen docking for bioexcel 2024 workshop: This tutorial demonstrates the use of HADDOCK3 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and a loose definition of the epitope determined through NMR experiments. As HADDOCK3 only exists as a command line version, this tutorial does require some basic Linux expertise.

  • Haddock3 basic protein-DNA docking tutorial: This tutorial demonstrates the use of Haddock3 for predicting the structure of a protein-DNA complex in which two protein units bind to the double-stranded DNA in a symmetrical manner (reference structure 3CRO). In addition to provided ambiguous restraints used to drive the docking, symmetry restraints are also defined to enforce symmetrical binding to the protein. This tutorial is using a local version of Haddock3, and therefore requires the use of a terminal and some basic command line expertise.