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

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.

SUBMITTER: Bray SA

PROVIDER: S-EPMC7488338 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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

Bray Simon A SA Senapathi Tharindu T Barnett Christopher B CB Grüning Björn A BA

Journal of cheminformatics 20200910 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 ...[more]

PMID: 33431030

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