Remote BioExcel Winter School on Biomolecular Simulations

30 Nov 2020, 09:00 → 4 Dec 2020, 17:00 Europe/Amsterdam

Alexandre Bonvin (eNMR/WeNMR (via Dutch NGI))

The winter school will include lectures and hands-on sessions on the following topics:

• Molecular Dynamics simulations
• Biomolecular Docking
• Free energy calculations
• Advanced sampling methods (Metadynamics)
• BioExcel Building Blocks (BioBB)

During the hands-on computer practicals you will make use of the BioExcel flagship software and tools: e.g. GROMACS, HADDOCK, PMX, BioBB. The trainers, developers and/or experts in the use of the software, will provide guidance and support.

Learning goal: 
The winter school is intended for researchers (primarily PhD and post-docs) using or planning to use bio-molecular modeling and simulation in their everyday research. Familiarity with Linux and basic knowledge of molecular modelling software is a requirement.

Online tutorials:
For participants not yet familiar with HADDOCK we recommend to try to follow on their own before the workshop the following basis HADDOCK tutorial.

• 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 http://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-proteinprotein-basic

During the workshop we will follow the following tutorials:

• HADDOCK2.4 antibody-antigen docking tutorial: This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope. This tutorial does not require any Linux expertise and only makes use of our web servers and PyMol for visualisation/analysis. https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/
   
• LightDock+HADDOCK membrane proteins tutorial: This tutorial demonstrates the use of LightDock for predicting the structure of membrane receptor – soluble protein complex using the topological information provided by the membrane to guide the modelling process. The resulting LightDock models are then refined using HADDOCK. https://www.bonvinlab.org/education/HADDOCK24/LightDock-membrane-proteins

 

HADDOCK2.4 basic protein-protein docking tutorial