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 2018

On this page, you can find the links to the tutorials given during the BioExcel Summer School on Biomolecular Simulations 2018 in Pula, Italy.

The first two tutorials (HADDOCK covalent binding and CPMD) are first attempts to setup a workflow between HADDOCK and CPMD for the covalent docking of a ligand into the active site of a protein. It shall not be seen, yet, as a well-established protocol for the modelling of covalently bound ligands but rather as a preliminary work to address this particular challenge in protein-small molecules docking, emphasizing the potential of HADDOCK, coupled with CPMD, to predict accurately the binding and get insights into the energetics of the covalent reaction. You can actively contribute to the dedicated topic on our forum

The last Metadynamics 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. Note that we updated our protocols. Accordingly the current link will point you to the 2019 version of this tutorial. In this tutorial, we will first generate an ensemble of conformers for the target protein using GROMACS and PLUMED, before proceeding with the docking using HADDOCK You can actively contribute to the dedicated topic on our forum

All tutorials are an initiative of the Integrative Modelling and Hybrid Methodes Interest Groups, nested at the Centre of Excellence for Computational Biomolecular Research - BioExcel. Feedbacks/questions are more than welcome!


  • HADDOCK covalent binding: This tutorial demonstrates how to use HADDOCK for the prediction of the three dimensional structure of a covalently bound ligand onto a receptor.

  • CPMD: This tutorial shows how to run CPMD calculations to get the topology and parameters of a covalently bound protein-ligand complex.

  • Metadynamics: This tutorial explains how to perform metadynamics simulations to enhance the comformational sampling of a binding site on a protein to improve molecular docking predictions.

    NOTE that there is an updated version of this tutorial here which we are recommending to follow.