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GOLD

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General Description

GOLD - 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 visualization and manipulation (Hermes), for protein-ligand docking (GOLD) and for post-processing (GoldMine) and visualization of docking results. Hermes acts as a hub for many of CCDC's products, for more information please refer to the Hermes product page.

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
    * The choice of either:
          o Partial protein flexibility, including protein side chain and backbone flexibility for up to ten user-defined residues
          o The ability to dock into multiple models of the same or different proteins, i.e. ensemble docking 
    * 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. 

Basic Usage

module load gold
 
 gold

 hermes

 goldmine

Useful Options


Further Information

See the official website: GOLD Suite