GOLD Suite Release Notes

 

Introduction

Supported Platforms

GOLD Bug Fixes

Support

 

Introduction

This document details the bug fixes contained in the GOLD 5.0.1 update. A complete list of of new features, modifications and bug fixes for GOLD 5.0, Hermes 1.4 and GoldMine 1.3 can be found at: http://www.ccdc.cam.ac.uk/support/documentation/#gold.

 

GOLD Suite Programs

•	Hermes: for 3D visualisation pre- and post-docking and interactive docking setup.

•	GOLD: for protein-ligand docking.

•	GoldMine: for post-processing of docking results.

 

Supported Platforms

GOLD Suite programs (Hermes, GOLD and GoldMine) are supported on the following platforms and operating systems:

 

•	Windows - Intel compatible, 32 bit, Windows 2000/XP/Vista/7

•	Linux - Intel compatible, 32 bit (and 64 bit for GOLD):

•	RedHat Enterprise 4 & 5

•	SuSE Linux Enterprise [Desktop|Server] 10

•	Debian 4.0, 5.0 Note: As we add support for newer versions of Linux, support for older versions may have to be withdrawn.

 

This is the last release of GOLD Suite that will be supported on Windows 2000. Please refer to the CCDC website for the latest news on supported platforms.

 

If you choose to use a version other than those listed above we cannot guarantee the GOLD Suite will work correctly, although we will attempt to assist you with any problems you may encounter.

 

If you are interested in the GOLD Suite of programs for a different platform please contact support.

 

Important Notice

Changes have been made to GOLD's default settings, specifically:

•	Full Simplex relaxation of the final pose retrieved from the GA now occurs.

•	Internal energy offset is now switched on by default.

•	The solvent accessibility requirements for polar fitting points have been relaxed.

These changes have been demonstrated to show benefit when tested in house.In some cases these changes could lead to higher scores for poses generated by GOLD 5.0 and later compared to those generated by 4.1. Care must therefore be taken if you are using the scoring function values when comparatively analysing runs created by GOLD 4.1 and GOLD 5.0 and later versions together. It is possible to revert to GOLD 4.1 default settings in later versions of the software, the instructions of which are as follows:

•	Switch off RELAX_LIGAND (in gold.params), i.e. set RELAX_LIGAND = 0.

•	Deactivate the Use the internal ligand energy offset tick box in the Fitness & Search Options window of the GOLD interface, or set relative ligand energy = 0 in the gold.conf.

•	Deactivate the Force all H bond donors/acceptors to be treated as solvent accessible tickbox in the Define Binding Site window of the GOLD interface, or set solvate_all = 0 in the gold.conf.

 

GOLD Bug Fixes

•	A bug in the binding site detection algorithm when docking into an ensemble has been fixed.

•	Issues to do with loading files into Hermes via the GOLD wizard have been resolved.

•	Hermes now outputs complex files from a docked ensemble that contain both the protein and ligand.

•	A problem with loading solutions into GoldMine has been fixed.

•	It is now possible to use a previously saved fit_points.mol2 file in a GOLD docking.

 

Support

User guides for Hermes, GOLD and GoldMine are available from the CCDC website in HTML and PDF format:

http://www.ccdc.cam.ac.uk/support/documentation/

The GOLD configuration file gold.conf is also fully documented and can be found at the above page on our website.

 

Scientific and technical FAQs are also available from the CCDC website:

http://www.ccdc.cam.ac.uk/support/faqs_downloads/

 

If you require more information about these or any other matters concerning GOLD Suite, please contact CCDC User Support at:

 

Email: support@ccdc.cam.ac.uk

Tel: +44 1223 336022