@article{Bray-2020-htmd,
author = {Bray, Simon A. and Senapathi, Tharindu and Barnett, Christopher B. and Grüning, Björn A.},
title = {Intuitive,  reproducible high-throughput molecular dynamics in Galaxy: a tutorial},
journal = {Journal of Cheminformatics},
year = {2020},
doi = {10.1186/s13321-020-00451-6},
volume = {12},
user = {miladim},
publisher = {Springer Science and Business Media {LLC}},
number = {1},
month = {sep},
issn = {1367-4803},
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.}}
}