{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Bray SA"],"funding":["Bundesministerium für Bildung und Forschung","European Research Council","Deutsche Forschungsgemeinschaft","University of Cape Town’s Research Committee","University of Cape Town's Research Committee"],"pagination":["54"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7488338"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["12(1)"],"pubmed_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."],"journal":["Journal of cheminformatics"],"pubmed_title":["Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial."],"pmcid":["PMC7488338"],"funding_grant_id":["116362","992/1 2012","115215","031L0101B/031L0101C","031 A538A/A538C","824087"],"pubmed_authors":["Bray SA","Barnett CB","Gruning BA","Senapathi T"],"additional_accession":[]},"is_claimable":false,"name":"Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial.","description":"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.","dates":{"release":"2020-01-01T00:00:00Z","publication":"2020 Sep","modification":"2024-11-09T22:08:42.462Z","creation":"2020-09-26T07:13:50Z"},"accession":"S-EPMC7488338","cross_references":{"pubmed":["33431030"],"doi":["10.1186/s13321-020-00451-6"]}}