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: 2022.2, 2023.2
- Download and install locally
Run module spider ccdc to see module versions and how to load them.
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 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 compared to a local installation.
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
For docking several ligands in parallel, please have a look at the Python
script gold_multi in the
CSD Python API scripts repository.