Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

Update: The paper is now published in the Journal of Cheminformatics.

On July 18th, as part of BCC 2020, we will be running an introductory tutorial on molecular dynamics in Galaxy, based on our recent preprint 'Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial'. The online training will be led jointly by representatives from the European Galaxy Team (Simon Bray) and the University of Cape Town (Chris Barnett, Tharindu Senapathi).

You are very welcome to join us and find out more about tools and workflows for molecular dynamics! Registration can be done via the BCC website (early registration ends on July 10th) and prices start at $3 per training.

Abstract

This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy is to make high-throughput computational data analysis, such as molecular dynamics (MD), a structured, reproducible and transparent process. In this tutorial we focus on 3 questions: How are protein-ligand systems parameterized for molecular dynamics simulation? What kind of analysis can be carried out on molecular trajectories? How can high-throughput MD be used to study multiple ligands? After finishing you will have learned about force-fields and MD parameterization, how to conduct MD simulation and analysis for a protein-ligand system, and understand how different molecular interactions contribute to the binding affinity of ligands to the Hsp90 protein.