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    • 37-Issue 3
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    Analyzing Residue Surface Proximity to Interpret Molecular Dynamics

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    Date
    2018
    Author
    Lichtenberg, Nils
    Menges, Raphael
    Ageev, Vladimir
    George, Ajay Abisheck Paul
    Heimer, Pascal
    Imhof, Diana
    Lawonn, Kai
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    Abstract
    The surface of a molecule holds important information about the interaction behavior with other molecules. In dynamic folding or docking processes, residues of amino acids with different properties change their position within the molecule over time. The atoms of the residues that are accessible to the solvent can directly contribute to binding interactions, while residues buried within the molecular structure contribute to the stability of the molecule. Understanding patterns and causality of structural changes is important for experts in the pharmaceutical domain, e.g., in the process of drug design. We apply an iterative computation of the Solvent Accessible Surface in order to extract virtual layers of a molecule. The extraction allows to track the movement of residues in the body of the molecule, with respect to the distance of the residue to the surface or the core during dynamics simulations. We visualize the obtained layer information for the complete time span of the molecular dynamics simulation as a 2D-map and for individual time-steps as a 3D-representation of the molecule. The data acquisition has been implemented alongside with further analysis functionality in a prototypical application, which is available to the public domain. We underline the feasibility of our approach with a study from the pharmaceutical domain, where our approach has been used for novel insights into the folding behavior of μ-conotoxins.
    BibTeX
    @article {10.1111:cgf.13427,
    journal = {Computer Graphics Forum},
    title = {{Analyzing Residue Surface Proximity to Interpret Molecular Dynamics}},
    author = {Lichtenberg, Nils and Menges, Raphael and Ageev, Vladimir and George, Ajay Abisheck Paul and Heimer, Pascal and Imhof, Diana and Lawonn, Kai},
    year = {2018},
    publisher = {The Eurographics Association and John Wiley & Sons Ltd.},
    ISSN = {1467-8659},
    DOI = {10.1111/cgf.13427}
    }
    URI
    http://dx.doi.org/10.1111/cgf.13427
    https://diglib.eg.org:443/handle/10.1111/cgf13427
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    Eurographics Association copyright © 2013 - 2020 
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    Theme by @mire NV
    System hosted at  Graz University of Technology.
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