Cited by 2,412Computational Drug Discovery MethodsProtein Degradation and InhibitorsAdvanced Chemical Physics Studies

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Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.

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Mysinger, Michael M., Carchia, Michael, Irwin, John. J., Shoichet, Brian K.·2012·Journal of Medicinal Chemistry

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Abstract

A key metric to assess molecular docking remains ligand enrichment against challenging decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for optimization have emerged. Here we describe an improved benchmarking set that includes more diverse targets such as GPCRs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from ChEMBL, each with 50 property-matched decoys drawn from ZINC. To ensure chemotype diversity, we cluster each target's ligands by their Bemis-Murcko atomic frameworks. We add net charge to the matched physicochemical properties and include only the most dissimilar decoys, by topology, from the ligands. An online automated tool (http://decoys.docking.org) generates these improved matched decoys for user-supplied ligands. We test this data set by docking all 102 targets, using the results to improve the balance between ligand desolvation and electrostatics in DOCK 3.6. The complete DUD-E benchmarking set is freely available at http://dude.docking.org.

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Authors: Mysinger, M. M., Carchia, M., Irwin, J. J., & Shoichet, B. K.
Affiliations: University of California, San Francisco (US)
Corresponding author: Irwin, John. J.
Shoichet, Brian K.
ORCID: Irwin, John. J.
Shoichet, Brian K.
Venue: Journal of Medicinal Chemistry
Publisher: American Chemical Society (ACS)
Published: 2012-07-05
Volume: 55
Issue: 14
Pages: 6582-6594
ISSN: 0022-2623 (ISSN-L)
1520-4804
DOI: 10.1021/jm300687e
PMC: PMC3405771
OpenAlex: W1968319881
Semantic Scholar: 3b2ffd1b7ce968924e9046b0a0ff3a1f2b033de9
Cited by: 2,412
References: 54
Citations by year: 2026: 231 · 2025: 285 · 2024: 283 · 2023: 243 · 2022: 279 · 2021: 247 · 2020: 207 · 2019: 162 · 2018: 123 · 2017: 96 · 2016: 101 · 2015: 77 · 2014: 44 · 2013: 28 · 2012: 3
FWCI: 52.20
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: other-oa
pubs.acs.org/page/policy/authorchoice_termsofuse.html (vor)
Locations: Journal of Medicinal Chemistry (publishedVersion, other-oa)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: National Institutes of Health
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords: DUD-E, decoy generation, G protein-coupled receptors, ion channels, ligand clustering, net charge, electrostatics, ChEMBL, zinc, decoy database
MeSH terms: Humans, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Proteins, Reference Standards, Cluster Analysis, Benchmarking, Drug Discovery

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