Benchmarking sets for molecular docking.

Huang, Niu; Shoichet, Brian K.; Irwin, John J.

doi:10.1021/jm0608356

Cited by 1,318Computational Drug Discovery MethodsProtein Degradation and InhibitorsCholinesterase and Neurodegenerative Diseases

Benchmarking sets for molecular docking.

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Huang, Niu, Shoichet, Brian K., Irwin, John J.·2006·Journal of Medicinal Chemistry

DOI 10.1021/jm0608356PMC PMC3383317

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Abstract

Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98,266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40x40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.

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DUD-E is an enhanced version of the original DUD set and has been widely used to train and validate scoring functions.
“The DUD-E dataset is an enhanced version of the original DUD set and has been widely used to train and validate scoring functions (Huang et al., 2006; Mysinger et al., 2012).”
From Empirical scoring functions for structure-based virtual screening: applications, critical aspects, and challenges (2018) · cites this paper as Huang et al., 2006

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Authors: Huang, N., Shoichet, B. K., & Irwin, J. J.
Affiliations: University of California, San Francisco (US)
Corresponding author: Shoichet, Brian K.
ORCID: Huang, Niu
Shoichet, Brian K.
Irwin, John J.
Venue: Journal of Medicinal Chemistry
Publisher: American Chemical Society (ACS)
Published: 2006-10-26
Volume: 49
Issue: 23
Pages: 6789-6801
ISSN: 0022-2623 (ISSN-L)
1520-4804
DOI: 10.1021/jm0608356
PMC: PMC3383317
OpenAlex: W2127760066
Cited by: 1,318
References: 84
Citations by year: 2026: 37 · 2025: 41 · 2024: 37 · 2023: 47 · 2022: 60 · 2021: 70 · 2020: 64 · 2019: 75 · 2018: 67 · 2017: 75 · 2016: 71 · 2015: 98 · 2014: 89 · 2013: 97 · 2012: 100
FWCI: 38.12
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Journal of Medicinal Chemistry (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: Inha University
National Institutes of Health
National Institute of General Medical Sciences (GM71896, GM59957, R01GM059957, R01GM071896)
Topics: Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
Health Sciences › Medicine › Pharmacology › Cholinesterase and Neurodegenerative Diseases
Keywords: molecular docking, decoy database, cross-docking, virtual screening
MeSH terms: Adenosine Deaminase, Aldehyde Reductase, Binding Sites, Pharmaceutical Preparations, Inhibins, Ligands, Models, Molecular, Protein Binding, Protein Conformation, Proteins, Receptors, Estrogen, Thymidine Kinase, Drug Design, Databases, Factual, Quantitative Structure-Activity Relationship, p38 Mitogen-Activated Protein Kinases

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