Alexandre Bonvin bio photo

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

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Education & Tutorials of the Bonvin Lab

In this page you can find links to our educational material, namely tutorials on the usage of our software and material for courses we teach at Utrecht University.

Courses

  • Structural Bioinformatics & Modelling: A MSc course aimed at those interested in learning homology modelling, molecular simulation, and docking of biological molecules. All the material is freely available on our Github repository and makes use of Vagrant/Virtualbox.

Research projects

We offer various research projects to both bachelor and master students, all centered around our main research area: the development of reliable bioinformatics and computational approaches to predict, model and dissect biomolecular interactions at atomic level. Read more here.

Conferences and workshops

Tutorials

  • HADDOCK 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.

  • HADDOCK 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.

  • HADDOCK 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).

  • HADDOCK ligand binding site tutorial: A tutorial demonstrating the use of HADDOCK in ab-initio mode to screen for potential ligand binding sites. The information from the ab-initio run is then used to setup a binding pocket-targetet protein-ligand docking run. We use as example the multidrug exporter AcrB.

  • PowerFit tutorial: A small introduction into PowerFit to automatically place a high-resolution atomic structure in a lower-resolution cryo-electron microscopy density map.

  • PowerFit web server tutorial: A small introduction into PowerFit to automatically place a high-resolution atomic structure in a lower-resolution cryo-electron microscopy density map making use of our web portal (does not require Linux).

  • DisVis web server tutorial: A small introduction into DisVis to analyse the interaction space between two molecules from a set of restraints. It can help to filter out putative false positive restraints and predict key residues involved in the interaction from this set of restraints. It makes use of our web portal (does not require Linux).