biostudies-literatureBray SABundesministerium für Bildung und ForschungEuropean Research CouncilDeutsche ForschungsgemeinschaftUniversity of Cape Town’s Research CommitteeUniversity of Cape Town's Research Committee54https://www.ebi.ac.uk/biostudies/studies/S-EPMC7488338biostudies-literatureUnknown12(1)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.Journal of cheminformaticsIntuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial.PMC7488338116362992/1 2012115215031L0101B/031L0101C031 A538A/A538C824087Bray SABarnett CBGruning BASenapathi TfalseIntuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial.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.2020-01-01T00:00:00Z2020 Sep2024-11-09T22:08:42.462Z2020-09-26T07:13:50ZS-EPMC74883383343103010.1186/s13321-020-00451-6