BioExcel

On this page, you can find the links to the HADDOCK and metadynamics (using Gromacs) tutorials given during the BioExcel Summer School on Biomolecular Simulations 2019 in Pula, Italy.

The first tutorial demonstrates the use of cross-linking data from mass spectrometry to guide protein-protein docking in HADDOCK.

The second tutorial illustrates how metadynamics can be used to sample conformations of a binding pocket; those are subsequently used for docking a ligand using HADDOCK. The conformational sampling approach is following the EDES approach described in the following publication:

• A. Basciu, G. Malloci, F. Pietrucci, A.M.J.J. Bonvin and A.V. Vargiu. Holo-like and druggable protein conformations from enhanced-sampling of binding pocket shape. J. Chem. Inf. and Mod. 59, 1515-1528 (2019).