Visual Abstractions of Solvent Pathlines near Protein Cavities

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dc.contributor.authorBidmon, Katrinen_US
dc.contributor.authorGrottel, Sebastianen_US
dc.contributor.authorBös, Fabianen_US
dc.contributor.authorPleiss, Jürgenen_US
dc.contributor.authorErtl, Thomasen_US
dc.contributor.editorA. Vilanova, A. Telea, G. Scheuermann, and T. Moelleren_US
dc.date.accessioned2014-02-21T18:45:12Z
dc.date.available2014-02-21T18:45:12Z
dc.date.issued2008en_US
dc.description.abstractWater 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.en_US
dc.description.number3en_US
dc.description.seriesinformationComputer Graphics Forumen_US
dc.description.volume27en_US
dc.identifier.issn1467-8659en_US
dc.identifier.urihttps://doi.org/10.1111/j.1467-8659.2008.01227.xen_US
dc.publisherThe Eurographics Association and Blackwell Publishing Ltd.en_US
dc.titleVisual Abstractions of Solvent Pathlines near Protein Cavitiesen_US
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