CCDC GOLD 3.0.1 IRIX

GOLD is a program for calculating the docking modes of small molecules
into protein binding sites. The product of a collaboration between the
University of Sheffield, GlaxoSmithKline plc and CCDC, GOLD is very
highly regarded within the molecular modelling community for its
accuracy and reliability.

GOLD features:

- A genetic algorithm (GA) for protein-ligand docking
- Full ligand flexibility and partial protein flexibility during docking
- Energy functions partly based on conformational and non-bonded contact
information from the CSD
- A choice of scoring functions: GoldScore, ChemScore and User defined
score. The GOLD Scoring Function Application Programming Interface (API)
allows users to modify the GOLD scoring-function mechanism in order to:
- implement their own scoring function or enhance existing scoring functions
- customise docking output
- A variety of constraint options
- SILVER, for post-processing docking results
- Automatic consideration of cavity bound water molecules
- Improved handling and control of metal coordination geometries
- Automatic derivation of GA settings for particular ligands

GOLD has been fully validated against 305 diverse and extensively
checked protein-ligand complexes from the PDB (CCDC/Astex Test Set). 72%
of GOLD's top-ranked solutions were found to be accurate using stringent
success criteria.

GOLD's genetic algorithm parameters are optimised for virtual screening
applications. GOLD is optimised for parallel execution on processor
networks; a distributed version of GOLD is available for use on
commercial PC GRID systems.

SILVER - Post-processing of Docking Results

SILVER is a new program included for use with GOLD and can be used to
post-process docking results for large numbers of ligands. SILVER allows
easy set-up and calculation of a variety of customisable descriptors
(parameters that describe dockings) that quantify, amongst other things:

- the hydrogen-bonding interactions that occur between protein and docked ligand
- the H-bond interactions that do not occur, e.g. a protein H-bond donor
that is prevented from forming a hydrogen bond by a ligand hydrophobic group
- other close contacts between protein and ligand the buried surface area
of the ligand, or of certain types of atoms in the ligand (e.g. hydrophobic atoms)
- whether particular regions of the binding site are occupied by the ligand
- simple properties such as the number of H-bonding ligand atoms,molecular
weight of ligand, number of rotatable bonds

Although not its primary purpose, SILVER also serves as a browser for
visualising protein-ligand dockings from GOLD.


http://www.ccdc.cam.ac.uk/products/life_sciences/gold/

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