BioExcel Summer School on Biomolecular Simulations 2019

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).

Tutorials

• Metadynamics: This tutorial highlights the benefits of enhanced sampling using metadynamics to improve the predictive power of molecular docking for protein-small molecule targets, in the case of binding sites undergoing conformational changes. For this, we will first generate an ensemble of conformers for the target protein using GROMACS and PLUMED, before proceeding with the docking using HADDOCK.

• HADDOCK2.4 MS cross-links tutorial: This tutorial demonstrates the use of cross-linking data from mass spectrometry to guide protein-protein docking in HADDOCK. It illustrates the use of both interface information and specific distance restraints to guide protein-protein docking. This tutorial builds on our DisVis tutorial and illustrates various scenarios of using cross-linking data in HADDOCK.