In this workshop, you will learn how to use free energy tools with an application to drug discovery. We will use open-source free energy tools and the Galaxy Platform (BRIDGE) to calculate absolute and relative free energies of protein-ligand binding with T4 Lysozyme as a usecase. Setting up free energy molecular simulations, using scripts, the Linux command line and using HPC resources can be complex. Further not all steps are repeatable. With the Galaxy Project platform, BRIDGE and Galaxy Comp Chem we aim to provide a web application to assist researchers in conducting repeatable computer simulations and analysis using curated workflows.
Target Audience: Are you keen to learn how to calculate absolute and relative free energies of protein-ligand binding for drug discovery?
Prerequisites: At least an undergraduate level chemistry, biology, physics or similar background. Some experience viewing and working with molecular structures. Have a read through the Galaxy training material on GitHub - https://galaxyproject.github.io/training-material/topics/computational-chemistry/
Special requirements: Bring a laptop. All remote computing resources will be provided. Install molecular viewer e.g. VMD. If possible have Virtualbox with Ubuntu/Centos installed.