Module: Computational Chemistry

Galaxy is not just for Biology!

Tutorial Video

Description:

Molecular dynamics (MD) is a method to simulate molecular motion by iterative application of Newton’s laws of motion. 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).
Length: 1 hour 40 minutes
Captions: Simon Bray
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
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.
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