Simulation of Organic and Bio Molecules

The molecular docking and all-atom molecular dynamics simulations is an extremely powerful combination of techniques routinely applied in modern structure-based drug discovery workflows. This course will provide an introduction to how to work with protein-ligand complexes using atomistic simulations and molecular docking/virtual screening/lead optimisation tools. We will cover the principles of protein-ligand docking, virtual screening and structure-guided optimisation. This will provide a starting point for protein-ligand molecular dynamics simulations and how to analyse them. We will follow best practices from the literature (Living J Comput Mol Sci. 2019; 1(1)) and will discuss common issues around identifying good protein structures for simulations, but also how to effectively parametrise ligands and how to use MDAnalysis for the analysis of simulations of the protein-ligand complexes. We will use a blended learning environment mixing lectures and workshops.