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.
module load gold gold hermes goldmine
See the official website: GOLD Suite