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Molecular Scaffold Hopping via Holistic Molecular Representation

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Protein-Ligand Interactions and Drug Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2266))

Abstract

Molecular descriptors encode a variety of molecular representations for computer-assisted drug discovery. Here, we focus on the Weighted Holistic Atom Localization and Entity Shape (WHALES) descriptors, which were originally designed for scaffold hopping from natural products to synthetic molecules. WHALES descriptors capture molecular shape and partial charges simultaneously. We introduce the key aspects of the WHALES concept and provide a step-by-step guide on how to use these descriptors for virtual compound screening and scaffold hopping. The results presented can be reproduced by using the code freely available from URL: github.com/ETHmodlab/scaffold_hopping_whales.

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Authors and Affiliations

  1. Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Zurich, Switzerland

    Francesca Grisoni & Gisbert Schneider

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  1. Francesca Grisoni
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  2. Gisbert Schneider
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Correspondence to Francesca Grisoni .

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Editors and Affiliations

  1. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Flavio Ballante

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Grisoni, F., Schneider, G. (2021). Molecular Scaffold Hopping via Holistic Molecular Representation. In: Ballante, F. (eds) Protein-Ligand Interactions and Drug Design. Methods in Molecular Biology, vol 2266. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1209-5_2

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  • DOI: https://doi.org/10.1007/978-1-0716-1209-5_2

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  • Publisher Name: Humana, New York, NY

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  • Online ISBN: 978-1-0716-1209-5

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