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    Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins

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    Date
    2019
    Author
    Schatz, Karsten ORCID
    Krone, Michael ORCID
    Bauer, Tabea L.
    Ferrario, Valerio
    Pleiss, Jürgen ORCID
    Ertl, Thomas
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    Abstract
    We present a novel abstract visualization for the binding sites of proteins. Binding sites play an essential role in enzymatic reactions and are, thus, often investigated in structural biology. They are typically located within cavities. The shape and properties of the cavity influence whether and how easily a substrate can reach the active site where the reaction is triggered. Molecular surface visualizations can help to analyze the accessibility of binding sites, but are typically prone to visual clutter. Our novel abstract visualization shows the cavity containing the binding site as well as the surface region directly surrounding the cavity entrance in a simplified manner. The resulting visualization resembles a hat, where the brim depicts the surrounding surface region and the crown the cavity. Hence, we dubbed our abstraction Molecular Sombrero, using the Spanish term for 'hat'. Our abstraction is less cluttered than traditional molecular surface visualizations. It highlights important parameters, like cavity diameter, by mapping them to the shape of the sombrero. The visual abstraction also facilitates an easy side-by-side comparison of different data sets. We show the applicability of our Molecular Sombreros to different real-world use cases.
    BibTeX
    @inproceedings {bm.20191248,
    booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine},
    editor = {Kozlíková, Barbora and Linsen, Lars and Vázquez, Pere-Pau and Lawonn, Kai and Raidou, Renata Georgia},
    title = {{Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins}},
    author = {Schatz, Karsten and Krone, Michael and Bauer, Tabea L. and Ferrario, Valerio and Pleiss, Jürgen and Ertl, Thomas},
    year = {2019},
    publisher = {The Eurographics Association},
    ISSN = {2070-5786},
    ISBN = {978-3-03868-081-9},
    DOI = {10.2312/vcbm.20191248}
    }
    URI
    https://doi.org/10.2312/vcbm.20191248
    https://diglib.eg.org:443/handle/10.2312/vcbm20191248
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    System hosted at  Graz University of Technology.
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