Intuitive, Reproducible High-Throughput Molecular Dynamics in Galaxy: a Tutorial
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.08.084780; this version posted May 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial Simon A. Bray1, Tharindu Senapathi2, Christopher B. Barnett2, , and Björn A. Grüning1, 1Department of Computer Science, University of Freiburg, Georges-Kohler-Allee 106, Freiburg, Germany 2Scientific Computing Research Unit, University of Cape Town, 7700 Cape Town, South Africa This paper is a tutorial developed for the data analysis platform references for further reading. It presumes that the user has Galaxy. The purpose of Galaxy is to make high-throughput a basic understanding of the Galaxy platform. The aim is computational data analysis, such as molecular dynamics, a to guide the user through the various steps of a molecular dy- structured, reproducible and transparent process. In this tu- namics study, from accessing publicly available crystal struc- torial we focus on 3 questions: How are protein-ligand systems tures, to performing MD simulation (leveraging the popular parameterized for molecular dynamics simulation? What kind GROMACS (6, 7) engine), to analysis of the results. of analysis can be carried out on molecular trajectories? How can high-throughput MD be used to study multiple ligands? Af- The entire analysis described in this article can be con- ter finishing you will have learned about force-fields and MD pa- ducted efficiently on any Galaxy server which has the rameterization, how to conduct MD simulation and analysis for needed tools.
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