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Best Practices for Constructing Reproducible QSAR Models

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Ecotoxicological QSARs

Part of the book series: Methods in Pharmacology and Toxicology ((MIPT))

Abstract

Quantitative structure-activity/property relationship (QSAR/QSPR) has been instrumental in unraveling the origins of the mechanism of action for biological activity of interest by means of mathematical formulation as a function of the physicochemical description of chemical structures. Of the growing number of QSAR models being published in the literature, it is estimated that the majority of these models are not reproducible given the heterogeneity of the components of the QSAR model setup (e.g., descriptor, learning algorithm, learning parameters, open-source and commercial software, different software versions, etc.) and the limited availability of the underlying raw data and analysis source codes used to construct these models. This inherently poses a challenge for newcomers and practitioners in the field to reproduce or make use of the published QSAR models. However, this is expected to change in light of the growing momentum for open data and data sharing that are being encouraged by funders, publishers, and journals as well as driven by the nextageneration of researchers who embrace open science for pushing science forward. This chapter examines these issues and provides general guidelines and best practices for constructing reproducible QSAR models.

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Acknowledgement

This work is supported by the Research Career Development Grant (No. RSA6280075) from the Thailand Research Fund.

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Authors and Affiliations

  1. Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand

    Chanin Nantasenamat

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  1. Chanin Nantasenamat
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Correspondence to Chanin Nantasenamat .

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Editors and Affiliations

  1. Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India

    Kunal Roy

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Nantasenamat, C. (2020). Best Practices for Constructing Reproducible QSAR Models. In: Roy, K. (eds) Ecotoxicological QSARs. Methods in Pharmacology and Toxicology. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0150-1_3

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  • DOI: https://doi.org/10.1007/978-1-0716-0150-1_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0149-5

  • Online ISBN: 978-1-0716-0150-1

  • eBook Packages: Springer Protocols

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