Protein-ligand docking 101 - running a simulation in GOLD
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.
- 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.
- 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.