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Property-Unmatched Decoys in Docking Benchmarks.

Reed M Stein1, Ying Yang1, Trent E Balius2

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|January 26, 2021
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Summary
This summary is machine-generated.

Optimizing molecular docking screens requires more than just property-matched decoys. New decoy sets (DUDE-Z, Goldilocks) and tools improve prospective performance assessment by including diverse molecular characteristics.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Enrichment of ligands versus property-matched decoys is standard for optimizing docking library screens.
  • Over-optimizing enrichment alone can lead to false confidence in prospective performance.

Purpose of the Study:

  • To develop improved decoy sets and tools for more reliable virtual screening assessment.
  • To mitigate over-optimization for specific interactions and account for diverse library molecules.

Main Methods:

  • Development of DUDE-Z (optimized DUD-E) and Goldilocks decoy sets.
  • Inclusion of charge extrema decoys and library characteristic decoys.
  • Analysis of enrichment calculation variability.

Main Results:

  • DUDE-Z and Goldilocks decoy sets were created to represent broader molecular characteristics.
  • New tools and decoy sets are available for improved virtual screening evaluation.
  • Variability in enrichment calculations can impact confidence in small differences.

Conclusions:

  • Relying solely on property-matched decoys can be misleading for virtual screening.
  • Incorporating diverse decoys enhances the reliability of docking library screen optimization.
  • New resources are provided to improve the assessment of prospective docking performance.