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Cited by 3,735Computational Drug Discovery MethodsMachine Learning in Materials ScienceAdvanced Chemical Physics Studies

The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.

Beware of q2!

Golbraikh, Alexander, Tropsha, Alexander·2002·Journal of Molecular Graphics and Modelling
DOI 10.1016/s1093-3263(01)00123-1
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Abstract

Validation is a crucial aspect of any quantitative structure-activity relationship (QSAR) modeling. This paper examines one of the most popular validation criteria, leave-one-out cross-validated R2 (LOO q2). Often, a high value of this statistical characteristic (q2 > 0.5) is considered as a proof of the high predictive ability of the model. In this paper, we show that this assumption is generally incorrect. In the case of 3D QSAR, the lack of the correlation between the high LOO q2 and the high predictive ability of a QSAR model has been established earlier [Pharm. Acta Helv. 70 (1995) 149; J. Chemomet. 10(1996)95; J. Med. Chem. 41 (1998) 2553]. In this paper, we use two-dimensional (2D) molecular descriptors and k nearest neighbors (kNN) QSAR method for the analysis of several datasets. No correlation between the values of q2 for the training set and predictive ability for the test set was found for any of the datasets. Thus, the high value of LOO q2 appears to be the necessary but not the sufficient condition for the model to have a high predictive power. We argue that this is the general property of QSAR models developed using LOO cross-validation. We emphasize that the external validation is the only way to establish a reliable QSAR model. We formulate a set of criteria for evaluation of predictive ability of QSAR models.

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Research works printed but not linked: 6

  1. S. Clementi, S. Wold, How to choose the proper statistical method, in: H. van de Waterbeemd (Ed.), Chemometrics Methods in Molecular Design, VCH, Weinheim, 1995, pp. 319–338.
  2. S. Wold, PLS for multivariate linear modeling, in: H. van de Waterbeemd (Ed.), Chemometrics Methods in Molecular Design, VCH, Weinheim, 1995, pp. 195–218.
  3. L.B. Kier, L.H. Hall, Molecular Connectivity in Structure–Activity Analysis, Wiley, New York, 1986.
  4. D. Bonchev, Overall connectivity and molecular complexity, in: J. Devillers, A.T. Balaban (Eds.), Topological Indices and Related Descriptors, Gordon and Breach, Reading, UK, 1999, pp. 361–401.
  5. R.D. Clark, D.G. Sprous, J.M. Leonard, Validating models based on large dataset, in: H.-D. Höltje, W. Sippl (Eds.), Rational Approaches to Drug Design. Proceedings of the 13th European Symposium on Quantitative Structure–Activity Relationships, Prous Sci., 2001, 475–485.
  6. A. Golbraikh, D. Bonchev, Y.-D. Xiao, A. Tropsha, Novel chiral topological descriptors and their applications to QSAR, in: H.-D. Höltje, W. Sippl (Eds.), Rational Approaches to Drug Design. Proceedings of the 13th European Symposium on Quantitative Structure–Activity relationships, Aug. 27–Sept. 1, 2000, Duesseldorf, Germany, Prous Science, 2001, 219–223.

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Metadata

Authors
Golbraikh, A., & Tropsha, A.
Affiliations
University of North Carolina at Chapel Hill (US)
Corresponding author
Tropsha, Alexander
ORCID
Venue
Journal of Molecular Graphics and Modelling
Publisher
Elsevier BV
Published
2002-01
Volume
20
Issue
4
Pages
269-276
ISSN
1093-3263 (ISSN-L)
DOI
10.1016/s1093-3263(01)00123-1
OpenAlex
W2087661061
Cited by
3,735
References
39
Citations by year
2026: 133 · 2025: 164 · 2024: 179 · 2023: 174 · 2022: 194 · 2021: 197 · 2020: 215 · 2019: 189 · 2018: 200 · 2017: 174 · 2016: 181 · 2015: 175 · 2014: 197 · 2013: 203 · 2012: 202
FWCI
52.71
Type
journal article
Language
en
Open access
closed
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations
  • Journal of Molecular Graphics and Modelling (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
Keywords
leave-one-out cross-validation, QSAR model validation, predictive power, external validation, 2D molecular descriptors, overfitting, model evaluation metrics
MeSH terms
Data Interpretation, Statistical, Ligands, Mathematical Computing, Models, Molecular, Receptors, Histamine H1, Steroids, Transcortin, Databases, Factual, Quantitative Structure-Activity Relationship, Ecdysteroids

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