Virtual Decoy Sets for Molecular Docking Benchmarks

Citations Over TimeTop 10% of 2011 papers

Abstract

Virtual docking algorithms are often evaluated on their ability to separate active ligands from decoy molecules. The current state-of-the-art benchmark, the Directory of Useful Decoys (DUD), minimizes bias by including decoys from a library of synthetically feasible molecules that are physically similar yet chemically dissimilar to the active ligands. We show that by ignoring synthetic feasibility, we can compile a benchmark that is comparable to the DUD and less biased with respect to physical similarity.

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