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.
- Puhti: 2020
- DiscoveryStudio2019 server
- Download and install locally
License cover academic usage at universities and non-profit research institutes. See our CSD page for details.
GOLD is part of the Cambridge Crystallographic Database System. See our CSD page for installation and activation.
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 [NoMachine]. To set up the GOLD interactive environment:
module load ccdc
module load ccdc srun --ntasks=1 --time=00:10:00 --mem=1G --pty \ --account=<project> --partition=small --mail-type=BEGIN \ --mail-user=<your email address> bash # and wait for resources to be granted gold
We are currently developing a command and partition to provide interative resources more easily.
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
If you want to run GOLD in parallel, please contact us
Usage via Discovery Studio
GOLD is available in the DiscoveryStudio 2019 server at CSC.