CCDC GOLD Suite 4.12



The GOLD Suite consists of the following packages: Hermes for 3D visualisation pre- and post-docking, interactive docking setup.Hermes is a 3D visualiser with particular emphasis on functionality for the analysis of protein-ligand interactions.GOLD for protein-ligand docking:GOLD is a program for calculating the docking modes of small molecules in protein binding sites and is provided as part of the GOLD Suite, a package of programs for structure visualisation and manipulation (Hermes), for protein-ligand docking (GOLD) and for post-processing (GoldMine) and visualisation of docking results. Hermes acts as a hub for many of CCDCs products, for more information please refer to the Hermes product page.GoldMine for post-processing of docking results:GoldMine is a tool for post-processing of GOLD docking results. GoldMine can be used to combine and analyse several docking runs, e.g. docking runs carried out against different protein models may be combined within a GoldMine database and analysed for selectivity and specificity.Docking runs carried out using one protein model but scored using different scoring functions may also be combined and evaluated within a GoldMine database. GoldMine is provided as part of the GOLD Suite, a package of programs for structure visualisation and manipulation (Hermes), for protein-ligand docking (GOLD) and for post- processing (GoldMine) and visualisation of docking results.

GOLD features include:
A genetic algorithm (GA) for protein-ligand docking
An easy to use interface with interactive docking set-up via Hermes
A comprehensive docking set-up wizard
Full ligand flexibility
Partial protein flexibility, including protein side chain and backbone flexibility for up to ten user-defined residues
Energy functions partly based on conformational and non-bonded contact information from the CSD
A variety of constraint options
Improved flexible ring handling
Automatic consideration of cavity bound water molecules
Improved handling and control of metal coordination geometries
Improved parameterisation for kinases and heme-containing proteins
Automatic derivation of GA settings for particular ligands
A choice of GoldScore, ChemScore, Astex Statistical Potential (ASP) or Piecewise Linear Potential (PLP) scoring functions
Extensive options for customising or implementing new scoring functions through a Scoring Function Application Programming Interface, allowing users to modify the GOLD scoring-function mechanism in order to either: implement their own scoring function or enhance existing scoring functions; customise docking output
A ChemScore Receptor Depth Scaling (RDS) rescore option so that the score attributed to hydrogen bonds is scaled depending on the depth in the binding pocket
Automatic rescoring with an alternate scoring function at the end of a docking run.

General Hermes features include:
The ability to view protein and ligand structures from external files
Easy navigation of the protein structure and control of what is displayed
A selection of visualisation options including a choice of display styles, colours, labelling schemes, and the ability to hide and then re-display atoms, residues, ligands, water molecules, etc
Functionality to generate auxiliary objects such as centroids and ribbons
The ability to restrict the contents of the rendered image based on the Z coordinate of individual objects (i.e. apply Z-clipping)
The ability to measure and display distances, angles and torsion angles
The option to find and display hydrogen bonds and non-bonded clashes, and to customise how they are defined geometrically
Various display output options (e.g. png, jpg, bmp)
The ability to edit ligands either manually or automatically to Cambridge Structural Database (CSD) conventions
Stereoviewing functionality
The ability to define and calculate descriptors
Links to a pre-computed library of ligand geometries (Mogul)*
Links to a precomputed library of non-bonded interactions (IsoStar)*
* CSD System subscribers only

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