BioExcel Summer School on Biomolecular Simulations 2020

On this page, you can find the links to the HADDOCK and metadynamics (using Gromacs) tutorials given during the 2020 BioExcel Online Summerschool on Biomolecular Simulations.

The first tutorial demonstrates how to model antibody-antigen complexes using various information in HADDOCK. It is based on the approach described in the following publications:

• F. Ambrosetti, Zuzana Jandova and A.M.J.J. Bonvin. A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver. ArXiv, 2005.03283 (2020).

• F. Ambrosetti, B. Jiménez-García, J. Roel-Touris and A.M.J.J. Bonvin. Modeling Antibody-Antigen Complexes by Information-Driven Docking. Structure, 28, 119-129 (2020). Preprint freely available from here.

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.

  NOTE that there is an updated version of this tutorial here) which we are recommending to follow instead.

• HADDOCK2.4 antibody-antigen: This tutorial demonstrates how to use HADDOCK for the prediction of the three dimensional structure of antibody-antigen complexes.