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 Community Forum tutorials

In this page you can find links to the tutorials given during the BioExcel Community Forum 2017. Those tutorials are first attempts to setup a workflow between HADDOCK, CPMD and GROMACS for the covalent docking of a ligand into the active site of a protein. It does not aim (yet) at providing a well-established protocol but rather open discussions and shows the actual limits of the different methods to solve this issue.

This tutorial is an initiative of the Integrative Modelling and Hybrid Mathodes Interest Groups nested at BioExcel. Feedbacks/questions are more than welcome!

You can actively contribute to the dedicated topic on our forum

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Tutorials

  • HADDOCK covalent binding: A tutorial demonstrating the use of HADDOCK to covalently bind a ligand into a receptor.

  • CPMD: A tutorial demonstrating the use of the CPMD to get the topology and parameters of a covalent ligand bound to a protein.