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.
CITATION STYLE
Bray, S. A., Senapathi, T., Barnett, C. B., & Grüning, B. A. (2020). Intuitive, reproducible high-throughput molecular dynamics in Galaxy: A tutorial. Journal of Cheminformatics, 12(1). https://doi.org/10.1186/s13321-020-00451-6
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