GOLD

Flexible protein-ligand docking

Description

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.

SILVER is a post-processing tool for the docking results.

Version

Available GOLD versions:

• GOLD Suite 5.0.1 is installed on Murska (murska.csc.fi)
• GOLD 4.1, 3.2 and SILVER 1.1.1 are installed on Murska (murska.csc.fi)
• GOLD 4.1 available through SOMA2 modeling environment (GUI through web browser)
• Release notes for GOLD Suite 5.0.1, including new features and modifications.

Usage

GOLD can be used either from the command line or via a graphical user interface (GUI). To set up the GOLD (and SILVER) interactive environment:

module load gold

This will load the latest version of GOLD. To start interactive session on a compute node, type:

bsub -I -W 4:00 xterm
gold

Longer jobs must be run as batch jobs, see below.

NOTE: Due to the limited number of licenses available, please take other users into account when running GOLD. On Murska, current maximum number of processors for a parallel run is 4.

The PVM daemon must be running before parallel GOLD dockings can be started. After docking, the PVM daemon should be stopped and all its generated files removed. In principle it is possible to run several docking jobs simultaneously, but if two PVM jobs run on the same node, problems might arise

Murska

This example job script is for a serial job. Submit it on Murska with:

bsub < job-gold41-murskaser.job

This example job script would start a job on 4 CPU's.

bsub < job-gold41-murskapar.job

Usage via SOMA2

GOLD 4.0 can be used via the SOMA2 modelling environment. An example can be found on page 56 in the CSC:s Chemistry Modeling Guide.

Usage via Disciovery Studio

GOLD can be used with locally installed Disocvery Studio molecular modeling program

• Instructions for using the GOLD interface in Disocvery Studio
  

Additional Information

• The GOLD homepage
• GOLD online documentation
• GOLD 3.1 käytössä Sepelissä (PDF), from @CSC 4/2006 (in Finnish)

Contacts

Please contact Nino Runeberg for further information.