e-learning
High Throughput Molecular Dynamics and Analysis
Abstract
This tutorial provides an introduction to using high-throughput molecular dynamics to study protein-ligand interaction, as applied to the N-terminal domain of Hsp90 (heat shock protein 90).
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- 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?
Learning Objectives
- Learn about force-fields and MD parameterization
- Learn how to conduct MD simulation and analysis for a protein-ligand system
- Understand how different molecular interactions contribute to the binding affinity of various ligands for the Hsp90 protein.
Licence: Creative Commons Attribution 4.0 International
Keywords: Computational chemistry
Target audience: Students
Resource type: e-learning
Version: 18
Status: Active
Prerequisites:
Introduction to Galaxy Analyses
Learning objectives:
- Learn about force-fields and MD parameterization
- Learn how to conduct MD simulation and analysis for a protein-ligand system
- Understand how different molecular interactions contribute to the binding affinity of various ligands for the Hsp90 protein.
Date modified: 2024-06-14
Date published: 2020-05-20
Contributors: Björn Grüning, Christopher Barnett, Simon Bray, Tharindu Senapathi
Scientific topics: Computational chemistry
External resources:
Activity log
