title: Virtual decoy sets for molecular docking benchmarks.
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.
authors.forename: Izhar
authors.initials: I
authors.lastname: Wallach
authors.forename: Ryan
authors.initials: R
authors.lastname: Lilien
mesh_terms: D000465:Algorithms; D019985:Benchmarking / Q000379:methods*; D019295:Computational Biology; D055808:Drug Discovery; D008024:Ligands; D008958:Models, Molecular; D014584:User-Computer Interface
chemical_list: D008024:Ligands