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GOLD

GOLD is a docking program for predicting how flexible molecules will bind to proteins. GOLD uses a genetic algorithm methodology for protein-ligand docking and allows full ligand and partial protein flexibility.

Available

  • Puhti: 2021
  • Discovery Studio 2019 server
  • Download and install locally

License

License covers academic usage at universities and non-profit research institutes. See our CSD page for details.

Usage

GOLD is a part of the Cambridge Crystallographic Database System. See our CSD page for installation and activation instructions.

GOLD can be used either from the command-line or via a graphical user interface (GUI) called Hermes. The best way to run a GUI remotely on Puhti is to use the Puhti web interface desktop. To set up the GOLD interactive environment, open a Host Terminal and run:

module load ccdc

This will load the latest version of CSD and GOLD. To run GOLD you can either enter hermes and navigate to the GOLD tab, or alternatively run gold which opens the GOLD wizard of Hermes directly. Note that the GUI performance can be somewhat slow as the Puhti web interface does not yet provide accelerated graphics.

Longer (non-interactive) jobs are best run as batch jobs:

#!/bin/bash -l
#SBATCH --partition=small
#SBATCH --ntasks=1
#SBATCH --account=<project>
#SBATCH --time=0:30:00    # time as hh:mm:ss

module load ccdc

gold_auto gold.conf

Note

If you want to run GOLD in parallel, please contact CSC Service Desk.

Usage via Discovery Studio

GOLD is also available via the Discovery Studio 2019 server at CSC. See our DS2019 documentation for installation instructions.

More information

Last edited Tue Mar 29 2022