Alexandre Bonvin bio photo

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

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BioExcel Summer School on Biomolecular Simulations 2020

On this page, you can find the links to the HADDOCK and metadynamics (using Gromacs) tutorials given during the 2020 BioExcel Online Summerschool on Biomolecular Simulations.

The first tutorial demonstrates how to model antibody-antigen complexes using various information in HADDOCK. It is based on the approach described in the following publications:

The second tutorial illustrates how metadynamics can be used to sample conformations of a binding pocket; those are subsequently used for docking a ligand using HADDOCK. The conformational sampling approach is following the EDES approach described in the following publication:

Tutorials

  • Metadynamics: This tutorial highlights the benefits of enhanced sampling using metadynamics to improve the predictive power of molecular docking for protein-small molecule targets, in the case of binding sites undergoing conformational changes. For this, we will first generate an ensemble of conformers for the target protein using GROMACS and PLUMED, before proceeding with the docking using HADDOCK.

  • HADDOCK2.4 antibody-antigen: This tutorial demonstrates how to use HADDOCK for the prediction of the three dimensional structure of antibody-antigen complexes.