Protein-ligand docking 101 - running a simulation in GOLD

Introduction

Molecular docking applications in drug discovery are varied, including structure-activity studies, lead optimisation, finding potential leads by virtual screening, providing binding hypotheses to facilitate predictions for mutagenesis studies and, also in assisting X-ray and cryogenic electron microscopy (cryo-EM) crystallography in the fitting of substrates and inhibitors to electron density.

GOLD (Genetic Optimisation for Ligand Docking) is a genetic algorithm for docking flexible ligands into protein binding sites. GOLD has been extensively tested and has shown excellent performance for pose prediction and good results for virtual screening.

Learning Outcomes

  • Familiarity of proteins, ligands and functional waters.
  • Familiarity of what protein ligand docking is and why you might want to perform it.
  • Familiarity with the GOLD interface and a step-by-step guide of the basic functionality.
  • Where to get started with your docking simulation.
  • The basics of how to run a standard protein-ligand dock with GOLD.

Requirements

  • The CSD installed and a current valid CSD licence active. For installation and licences visit the FAQs.
  • This module is designed for beginners of the docking software GOLD.


This module takes less than 90 minutes to complete.


Image of a protein with a ligand docked, with a zoom in the binding site and the GOLD logo at the front.


Well done on completing the module!

Next Steps

Feedback

How was it? Leave your feedback here– it takes less than 5 minutes.

Ready for more?

You can try more advanced settings and uses of GOLD with our self-guided workshops.

If you are going to use GOLD in your work, do not forget to reference it when you publish. Please refer to this FAQ for more information and for interesting reading.

Explore Bound!, a fun card game by the CCDC and the PDB, where you need to match proteins and ligands to win!

 


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