Cited by 86Computational Drug Discovery MethodsProtein Degradation and Inhibitorsvaccines and immunoinformatics approaches

Benchmarking data sets for the evaluation of virtual ligand screening methods: review and perspectives.

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Lagarde, Nathalie, Zagury, Jean-François, Montes, Matthieu·2015·Journal of Chemical Information and Modeling

Abstract

Virtual screening methods are commonly used nowadays in drug discovery processes. However, to ensure their reliability, they have to be carefully evaluated. The evaluation of these methods is often realized in a retrospective way, notably by studying the enrichment of benchmarking data sets. To this purpose, numerous benchmarking data sets were developed over the years, and the resulting improvements led to the availability of high quality benchmarking data sets. However, some points still have to be considered in the selection of the active compounds, decoys, and protein structures to obtain optimal benchmarking data sets.

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Crossref · 10.1021/acs.jcim.5b00090

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  • The use of decoys instead of validated inactive compounds remains a major drawback for most datasets since no experimental activity is reported for them and confirmed inactive molecules are scarce.

    “The use of decoys instead of validated inactive compounds remains a major drawback for most datasets since no experimental activity are reported for them, and the number of confirmed inactive molecules is too scarce (Lagarde et al., 2015; Chaput et al., 2016b; Réau et al., 2018).”

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Authors
Lagarde, N., Zagury, J.-F., & Montes, M.
Affiliations
  • Conservatoire National des Arts et Métiers (FR)
  • Laboratoire Génomique, Bioinformatique et Applications, EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
Venue
Journal of Chemical Information and Modeling
Published
2015-06-18
Volume
55
Issue
7
Pages
1297-1307
ISSN
  • 1549-9596 (ISSN-L)
  • 1549-960X
OpenAlex
W2400913246
Cited by
85
References
93
Citations by year
2025: 5 · 2024: 10 · 2023: 3 · 2022: 6 · 2021: 9 · 2020: 8 · 2019: 10 · 2018: 10 · 2017: 13 · 2016: 6 · 2015: 5
FWCI
1.22
Type
journal article
Language
en
Open access
Locations
  • Journal of Chemical Information and Modeling (publishedVersion, other-oa)
  • PubMed (publishedVersion)
Funders
Conservatoire National des Arts et Métiers
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
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords
virtual screening, method evaluation, enrichment, active compounds, decoys, protein structure, drug discovery, retrospective evaluation
MeSH terms
Drug Evaluation, Preclinical, Humans, Ligands, Proteins, User-Computer Interface, Benchmarking

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