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
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NMR & Molecular Modelling: A bachelor course dealing with both NMR and modelling. This link will bring you the computer practical for this course in which you will be modelling a protein-protein complex based on NMR chemical shift data.
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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.
Online lectures
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Recordings of the Computer Aided Drugs Design ELIXIR 3D-BioInfo webinar by Prof. Bonvin (April 18th, 2023) on
Shape-restrainted modelling of protein-small molecule complexes with HADDOCK:View recorded webinar (30 min.)
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Recordings of the BioExcel summerschool HADDOCK lectures by Prof. Bonvin (June 7th, 2021):
View recorded lecture Part I (46 min.)
View recorded lecture Part II (43 min.)
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Recording of a CCPBioSim lecture by Prof. Bonvin on the topic of binding affinity (Oct. 7th, 2020):
View recorded lecture (27 min.)
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Live demo of the HADDOCK2.4 thematic service. This demo given at the EOSC-Hub week 2020 conference shows in particular how to setup a refinement run in HADDOCK2.4 to assess the impact of a mutation, using the interaction between SARS-CoV2 RBD domain and a peptide extracted from the ACE2 receptor as an example.
View demo
Tutorials
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Consult our HADDOCK best practice guide - a must read before starting to use HADDOCK!
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Tutorials for HADDOCK version 2.4: Various tutorials from basic protein-protein docking, to the use of cross-linking data, symmetry and homology informations to guide the docking, and advanced modelling of protein-ligand complexes.
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New!: Tutorials for HADDOCK version 3.0: The first HADDOCK3 tutorial to install and run HADDOCK3 to model an antibody-antigen complex.
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Tutorials for DisVis and Powerfit: Tutorials about rigid-body fitting into cryo-EM maps and assessing the information content of cross-linking data.
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Integrative modelling of the RNA polymerase III apo complex: A combination of our DISVIS, POWERFIT and HADDOCK2.4 portals using cross-links and cryo-EM data to model a large macromolecular assembly.
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2018 BioExcel summerschool metadynamics / HADDOCK / CPMD tutorials