GOLD

GOLD has proven success in virtual screening, lead optimisation, and identifying the correct binding mode of active molecules.

   
Selective inhibitor SC-558 docking with the 1CX2 structure of COX-2 in GOLD

 

About GOLD docking software

Reliable:  Comprehensively validated and widely used, GOLD enables you to;

  • Make confident binding mode predictions.
  • Achieve high database enrichments.
  • Identify the correct binding mode reliably.

A range of independent studies have shown GOLD performs favourably against other docking tools, so you can be confident in your results.

 

Flexible: Proteins aren't rigid, and your docking should account for that. GOLD balances flexibility with computational demand, so you can;

  • Use ensemble docking to reflect different receptor binding site conformations.
  • Account for receptor flexibility through side-chain flexibility.
  • Avoid computationally expensive sequential docking into multiple protein structures.
  • Solve the challenge of model selection with the novel GOLD methodology for ensemble docking.

 

Configurable: Take full advantage of your knowledge of a protein-ligand system, to maximise performance. With GOLD you can;

  • Adjust speed versus accuracy, for efficient virtual screening of large compound libraries, to highly accurate, exhaustive sampling for lead optimisation.
  • Select from a wide range of scoring functions and customisable docking protocols, to give high performance on diverse receptor types.
  • Employ a wide range of constraints, for example to ensure key H-bond interactions are fulfilled, or bias towards a known binding motif.
  • Eliminate unfavourable ligand conformations using customisable torsion angle distributions and an extensive library of ring conformations from the CSD.

 

GOLD docking in the literature

Binding to GPCR target with good fit to experimental results

Salmas et al, ACS Chem. Neurosci. 2017

Binding affinity calculations of antipsychotics binding to dopamine receptor D2 (D2R), a GPCR target, were performed using GOLD. Ensemble docking and single-target docking were performed. Results fit well with experimental results.

Combining GOLD scoring functions for binding insights

Greenidge et al, Chem. Bio. & Drug Design. 2016

Here a group at Novartis rank the performance of the ChemPLP scoring function in GOLD. They find that combining different algorithms and scoring functions including GOLD provides the best insight - a function now possible through the Python API.

Whitepaper: Ultra-large docking with GOLD using cloud resources

CCDC - Download here

This whitepaper uses GOLD with AWS cloud to run docking against an ultra-large library of compounds. The paper covers the setup, security, costs and results of the test and finds good return of known active molecules among the ~126 million structures docked from ZINC.

Binding natural products and designing novel mimetics

Merk et al, J. Med. Chem. 2018

Three novel natural products targeting the retinoid X receptor were investigated using GOLD by a group at ETH Zurich. One was found to bind selectively to the beta form, and served as a template for ligand-based design of novel mimetics.

 

Find further GOLD case studies here.

Request an evaluation

To test GOLD for yourself, or ask us anything about GOLD for your docking and drug discovery, contact us using this form.