Property-Unmatched Decoys in Docking Benchmarks

Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of enrichment alone can mislead, leading to false confidence in prospective performance. This can arise by over-optimizing for enrichment against property-matched decoys, without considering the full spectrum of molecules to be found in a true large library screen. Adding decoys representing charge extrema helps mitigate over-optimizing for electrostatic interactions. Adding decoys that represent the overall characteristics of the library to be docked allows one to sample molecules not represented by ligands and property-matched decoys but that one will encounter in a prospective screen. An optimized version of the DUD-E set (DUDE-Z), as well as Extrema and sets representing broad features of the library (Goldilocks), is developed here. We also explore the variability that one can encounter in enrichment calculations and how that can temper one's confidence in small enrichment differences. The new tools and new decoy sets are freely available at http://tldr.docking.org and http://dudez.docking.org.

Automated summary

The enrichment of ligands compared to property-matched decoys is commonly used in docking library screens, but over-optimizing for enrichment alone can lead to false confidence in prospective performance. By adding decoys representing charge extrema and overall characteristics of the library being docked, one can sample molecules not represented by the ligands and property-matched decoys, improving the accuracy of future screening results.