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Endocrine Disruptome—An Open Source Prediction Tool for Assessing Endocrine Disruption Potential through Nuclear Receptor Binding

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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Inf. Model. 2014, 54, 4, 1254-1267
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    Endocrine Disruptome—An Open Source Prediction Tool for Assessing Endocrine Disruption Potential through Nuclear Receptor Binding
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    † Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
    ‡ Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
    § EN-FIST Centre of Excellence, Dunajska 156, 1000 Ljubljana, Slovenia
    *E-mail: [email protected]
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    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2014, 54, 4, 1254–1267
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    https://doi.org/10.1021/ci400649p
    Published March 14, 2014
    Copyright © 2014 American Chemical Society
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    Abstract

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    Predicting the endocrine disruption potential of compounds is a daunting but essential task. Here we report a new tool for this purpose that we have termed Endocrine Disruptome. It is a free and simple-to-use Web service that runs on an open source platform called Docking interface for Target Systems (DoTS). The molecular docking is handled via AutoDock Vina. Compounds are docked to 18 integrated and well-validated crystal structures of 14 different human nuclear receptors: androgen receptor; estrogen receptors α and β; glucocorticoid receptor; liver X receptors α and β; mineralocorticoid receptor; peroxisome proliferator activated receptors α, β/δ, and γ; progesterone receptor; retinoid X receptor α; and thyroid receptors α and β. Endocrine Disruptome is free of charge and available at http://endocrinedisruptome.ki.si.

    Copyright © 2014 American Chemical Society

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    Supporting Information

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    Structure input page (Figure S1); receptor overview page (Figure S2); clustering with RDKit (code snippet S1); functions for calculating ROC, EF1%, and AUC (code snippet S2); script for calculating score, PPV, and NPV at a given Se or Sp (code snippet S3); statistical parameters for each threshold (Table S1); and resolution and ligand data for all of the crystal structures (Table S2). This material is available free of charge via the Internet at http://pubs.acs.org.

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    This article is cited by 106 publications.

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    Cite this: J. Chem. Inf. Model. 2014, 54, 4, 1254–1267
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    Published March 14, 2014
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