GOLD Suite Patch
This patch will update Linux and Windows GOLD Suite 5.0 installations
(Hermes 1.4, GOLD 5.0 and GoldMine 1.3) to version 5.0.1 (Hermes 1.4.1, GOLD 5.0.1 and GoldMine 1.3.1).
If you do not have GOLD Suite 5.0 installed, please download the full
GOLD Suite installer.
The following issues have been addressed:
- GOLD Suite Version 5.1
- GOLD Version 5.1
- The queuing mechanism has been implemented for both
foreground and background run options. If no licences are available when
submitting a job users will now be given the option to queue the job
which will then be run once a licence becomes available [13113 and
13185].
- The default scoring function has been changed from GoldScore
to CHEMPLP [13186 and 13187].
- The torsion angle distributions file gold.tordist which can
be used by GOLD to restrict the ligand conformational space sampled by
the genetic algorithm.has been extended to include additional torsion
fragments [12662].
- The maximum number of proteins that can be specified in an
ensemble docking has been increased from 20 to 50 [12909].
- GoldMine licensing has been simplified and now uses the GOLD
licence key. As a result GoldMine can now be run on any machine for which you
have a valid platform licence [13189].
- Various improvements have been made to the PBS cluster
scripts in order to make it easier to run parallel GOLD jobs under PBS Pro [13193].
- Recent virtual screening studies have lead to new best
practice protocols for various target classes. Configuration file template
protocols have been updated accordingly [13214].
- A memory error when using automatic rescoring in conjunction
with active site waters has been fixed. This problem occurred when the
simplex failed to generate a higher scoring pose than the input solution
[13001].
- A problem whereby the ChemScore hydrogen bonding scaling
mechanism fails in ensemble mode and thus the wrong protein structure might be returned
as the best scoring one has been fixed [12803].
- Handling of protein mol2 files has been made more robust
and water extraction on longer fails with poorly designated protein mol2 files
[12734].
- A bug which sometimes resulted in the information about the
flexible residues not being retained in the gold.conf file has been fixed
[12754].
- A bug which prevented GOLD from propagating the filename to
the Save GOLD Configuration window if it contained an additional full stop e.g.
"gold.flex.conf" has been fixed [12768].
- By switch off generation of the ChemScore clash and lipo
grids which are currently not required by PLP potential memory issues with ChemPLP (in
ensemble mode) have been resolved [13195].
- Handling of chain identifier has been improved so that the
GOLD wizard no longer creates protein mol2 files with incorrect chain definitions
[12739].
- A bug which resulted in rising memory usage when running the
ASP scoring function in conjunction with active waters has been addressed [13222].
- A problem which might prevented rescoring with Chemscore
RDS has been fixed [13269].
- Hermes Version 1.5
- A problem which prevented default fonts not being displayed
correctly when using non-standard screen resolutions has been resolved
[10730].
- Various improvements have been made to Hermes for setting up
and accessing the IsoStar server [13092 and 13224].
- GoldMine Version 1.4
- A GoldMine can now be created directly from the command line [13246].
- GoldMine hotspots provide a means of visually observing
average trends in the docking solutions and can be used to calculate new
descriptors. Hotspots can now be created and exported directly from the
command line [13251].
- GoldMine can now write out hotspots in .grd format grids
[13229].
- It is now possible to create a GoldMine for ensemble dockings
from a set or subset of ligand and protein files [13273].
- A problem with the export of complexes from GoldMine has been
fixed [13209].
- A bug which resulted in GoldMine hotspot files taking too
long to write out has been fixed [12971].
- A problem whereby the GoldMine export dialogue presented
unnecessary and empty descriptors has been fixed [10849].
- GOLD Suite Version 5.0.1
- GOLD Version 5.0.1
- A bug in the binding site detection algorithm when docking into an ensemble has been fixed.
- It is again possible to specify an input fitting points file.
- Atom labels are no longer renamed when the input protein file format is PDB.
- Hermes Version 1.4.1
- An occasional crash caused by loading some protein files via the GOLD setup dialog has been fixed.
- When outputting a docking complex file from an ensemble, the correct protein is now used.
- GoldMine Version 1.3.1
- An occasional GoldMine database creation failure with individual GOLD solution files has been fixed.
Patch installation
The preferred method for both Linux and Windows is to use the
autoupdate method - start Hermes and select
Help -> Check for Updates and follow the prompts to install. Then restart Hermes.
If, for some reason, the autoupdate process does not work correctly, the patch installers
may be downloaded using the links below.
When running the patch installer by hand, you will need to ensure that the Installation directory
specified is the top level of your GOLD Suite installation.
Successful patch installation may be verified by:
- running a GOLD job and checking for the words GOLD DOCKING RUN (GOLD v5.0.1) in
the gold_protein.log file.
- running Hermes, clicking
Help -> About Hermes and checking for Hermes v1.4.1.
- running Hermes, clicking
GoldMine -> About GoldMine and checking for GoldMine Plugin version 1.3.1.
If you have any feedback or problems, please contact
our user support team at:
support@ccdc.cam.ac.uk
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