ArticleJournal of chemical information and modeling2021
Property-Unmatched Decoys in Docking Benchmarks.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
77 citing papers in PubMed.
- A Computational Framework for the Design and Development of Isoform Selective PI3Kα Inhibitors as Novel Anticancer Agents.Molecules (Basel, Switzerland) · 2026Article
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- Library Docking for Cannabinoid-2 Receptor Ligands.Journal of medicinal chemistry · 2026Article
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- ComTarget: Small-Molecule Target Prediction with Combinatorial Modeling.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Discovery of Covalent Ligands with AlphaFold3.Journal of the American Chemical Society · 2026Article
- A Comparative Review of Artificial Intelligence Applications in Small Molecule Versus Peptide Drug Discovery.International journal of molecular sciences · 2026Review
- Fine-Tuning DiffDock-L for Allosteric Kinase Docking.Journal of chemical information and modeling · 2026Article
- Library docking for Cannabinoid-2 Receptor ligands.bioRxiv : the preprint server for biology · 2026Article
- Prodrug-ML: prodrug-likeness prediction via machine learning on sampled negative decoys.Journal of computer-aided molecular design · 2026Article
- Integrating traditional and modern approaches for comprehensive pharmacophore map validation in drug discovery.Journal of computer-aided molecular design · 2026Review
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- LiraSearch-ultrafast ligand shape and electrostatic matching server.Bioinformatics advances · 2026Article
- Network pharmacology refined with non-ubiquity and decoy-controlled molecular docking reveals insights intoFrontiers in bioinformatics · 2026Article
- AnCurrent drug targets · 2026Article
- Discovery of Putative GyrB Inhibitors againstCurrent medicinal chemistry · 2026Article
- An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation.Frontiers in bioinformatics · 2026Article
- Ultra-large virtual screening unveils potent agonists of the neuromodulatory orphan receptor GPR139.Nature communications · 2025Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.