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    Visual Abstractions of Solvent Pathlines near Protein Cavities

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    Date
    2008
    Author
    Bidmon, Katrin
    Grottel, Sebastian
    Bös, Fabian
    Pleiss, Jürgen
    Ertl, Thomas ORCID
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    Abstract
    Water is known to play a crucial role in protein structure, flexibility and activity. The use of molecular dynamics simulations allows detailed studies of complex protein-solvent interactions. Cluster analysis and density-based approaches have been successfully used for the identification and analysis of conserved water molecules and hydration patterns of proteins. However, appropriate tools for analysing long-time molecular dynamics simulations with respect to tracking and visualising the paths of solvent molecules are lacking. Our method focuses on visualising the solvent paths entering and leaving cavities of the protein and allows to study the route and dynamics of the exchange of tightly bound internal water molecules with the bulk solvent. The proposed visualisation also represents dynamic properties such as direction and velocity in the solvent. Especially, by clustering similar pathlines with respect to designated properties the visualisation can be abstracted to represent the principal paths of solvent molecules through the cavities. Its application in the analysis of long-time scale molecular dynamics simulations not only confirmed conjectures based on previous manual observations made by chance, but also led to novel insights into the dynamical and structural role of water molecules and its interplay with protein structure.
    BibTeX
    @article {10.1111:j.1467-8659.2008.01227.x,
    journal = {Computer Graphics Forum},
    title = {{Visual Abstractions of Solvent Pathlines near Protein Cavities}},
    author = {Bidmon, Katrin and Grottel, Sebastian and Bös, Fabian and Pleiss, Jürgen and Ertl, Thomas},
    year = {2008},
    publisher = {The Eurographics Association and Blackwell Publishing Ltd.},
    ISSN = {1467-8659},
    DOI = {10.1111/j.1467-8659.2008.01227.x}
    }
    URI
    http://dx.doi.org/10.1111/j.1467-8659.2008.01227.x
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    • 27-Issue 3
    • EuroVis08: Joint Eurographics - IEEE VGTC Symposium on Visualization

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    Eurographics Association copyright © 2013 - 2023 
    Send Feedback | Contact - Imprint | Data Privacy Policy | Disable Google Analytics
    Theme by @mire NV
    System hosted at  Graz University of Technology.
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