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

• Main Authors: Simon A. Bray, Tharindu Senapathi, Christopher B. Barnett, Björn A. Grüning
• Format: Article
• Language: English
• Published: BMC 2020-09-01
• Series: Journal of Cheminformatics
• Subjects: Galaxy; Molecular Dynamics; Reproducible
• Online Access: http://link.springer.com/article/10.1186/s13321-020-00451-6

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, 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.