HT4: Databases

T6 (tutorial): How to perform ensemble docking with GOLD?

In this hands-on session participants will learn how to perform ensemble docking using the CCDC’s docking software GOLD.

Learning outcomes:

  • The basics of ensemble docking.
  • How to use the Hermes interface, the CCDC’s 3D visualizer for proteins.
  • Step-by-step set-up of an ensemble docking simulation in GOLD, including:
    • Superimposing the protein structures;
    • Binding site definition;
    • Ligand selection and ligand flexibility;
    • Functional waters.
  • Visualization and analysis of ensemble docking results.