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Related Experiment Videos

Improving database enrichment through ensemble docking.

Shashidhar Rao1, Paul C Sanschagrin, Jeremy R Greenwood

  • 1Schrödinger, Inc, 120 West 45th Street, New York, NY, 10036, USA.

Journal of Computer-Aided Molecular Design
|February 7, 2008
PubMed
Summary
This summary is machine-generated.

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Using multiple receptor conformations in virtual screening doesn't always improve results. A new method identifies specific ensembles that enhance the enrichment of active compounds, outperforming single receptors.

Area of Science:

  • Computational Chemistry
  • Drug Discovery
  • Structural Biology

Background:

  • Structure-based virtual screening (SBVS) aims to identify active compounds using receptor structures.
  • Ensembling multiple receptor conformations is hypothesized to improve SBVS enrichment.
  • The effectiveness of receptor ensembles in SBVS requires careful selection and validation.

Purpose of the Study:

  • To develop and validate a method for selecting optimal receptor ensembles for structure-based virtual screening.
  • To assess the performance of selected ensembles compared to single receptor models.
  • To identify specific ensemble combinations that improve the enrichment of active compounds.

Main Methods:

  • Studied the p38 MAP kinase system as a model.

Related Experiment Videos

  • Developed a method to select ensembles based on mean GlideScore of top-ranked ligands.
  • Screened a database of active and decoy ligands against selected ensembles.
  • Evaluated enrichment factors for single, two-, and three-receptor ensembles.

    • Main Results:

    • A majority of randomly selected receptor ensembles did not improve active compound enrichment.
    • A small fraction of ensembles, particularly those with up to three receptors, significantly improved enrichment.
    • The mean GlideScore metric effectively identified ensembles yielding superior enrichment.
    • Ensembles of two receptors generally outperformed single receptors; ensembles of three consistently yielded optimal enrichment.

    Conclusions:

    • Ensemble selection is critical for successful structure-based virtual screening.
    • The proposed mean GlideScore method offers a computationally efficient way to identify effective receptor ensembles.
    • Optimized receptor ensembles, especially those of three structures, can substantially enhance the identification of active compounds in virtual screening.