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DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions

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    DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening — A Versatile Tool for Benchmarking Docking Programs and Scoring Functions
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    † Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
    Phone: +49-7071-2974567. Fax: +49-7071-295637. E-mail: [email protected]
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    Journal of Chemical Information and Modeling

    Cite this: J. Chem. Inf. Model. 2011, 51, 10, 2650–2665
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    https://doi.org/10.1021/ci2001549
    Published July 21, 2011
    Copyright © 2011 American Chemical Society
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    Abstract

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    For widely applied in silico screening techniques success depends on the rational selection of an appropriate method. We herein present a fast, versatile, and robust method to construct demanding evaluation kits for objective in silico screening (DEKOIS). This automated process enables creating tailor-made decoy sets for any given sets of bioactives. It facilitates a target-dependent validation of docking algorithms and scoring functions helping to save time and resources. We have developed metrics for assessing and improving decoy set quality and employ them to investigate how decoy embedding affects docking. We demonstrate that screening performance is target-dependent and can be impaired by latent actives in the decoy set (LADS) or enhanced by poor decoy embedding. The presented method allows extending and complementing the collection of publicly available high quality decoy sets toward new target space. All present and future DEKOIS data sets will be made accessible at www.dekois.com.

    Copyright © 2011 American Chemical Society

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    Supporting Information

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    A schematic depiction of the binning procedure, tables with docking details and information regarding decoy sets, a protocol for the correction of DUD ligand sets, preparation of the DUD active sets for the construction of DEKOIS, a stochastic approach toward quantification of the number of latent actives in decoy sets, an alternative method to the doppelganger score for describing the most significant structural similarities between actives and decoys, 2D depictions of DUD decoys that are structurally closely related to DUD actives, effects of decoy scrambling experiments on the physicochemical property distributions, DOE plots and decoy embedding heat maps of the dissimilar decoy sets, an alternative method for conducting decoy scrambling experiments, DOE plots and decoy embedding heat maps of decoy sets for this alternative method to the decoy scrambling experiments, figures and tables with detailed information regarding the robustness experiments, and statistical analysis of the docking enrichment and DOE scores over all 40 targets. This material is available free of charge via the Internet at http://pubs.acs.org.

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    Cite this: J. Chem. Inf. Model. 2011, 51, 10, 2650–2665
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ci2001549
    Published July 21, 2011
    Copyright © 2011 American Chemical Society
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