MoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voids

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dc.contributor.authorByska, Janen_US
dc.contributor.authorJurcik, Adamen_US
dc.contributor.authorGröller, M. Eduarden_US
dc.contributor.authorViola, Ivanen_US
dc.contributor.authorKozlikova, Barboraen_US
dc.contributor.editorH. Carr, K.-L. Ma, and G. Santuccien_US
dc.date.accessioned2015-05-22T12:50:42Z
dc.date.available2015-05-22T12:50:42Z
dc.date.issued2015en_US
dc.description.abstractStudying the characteristics of proteins and their inner void space, including their geometry, physico-chemical properties and dynamics are instrumental for evaluating the reactivity of the protein with other small molecules. The analysis of long simulations of molecular dynamics produces a large number of voids which have to be further explored and evaluated. In this paper we propose three new methods: two of them convey important properties along the long axis of a selected void during molecular dynamics and one provides a comprehensive picture across the void. The first two proposed methods use a specific heat map to present two types of information: an overview of all detected tunnels in the dynamics and their bottleneck width and stability over time, and an overview of a specific tunnel in the dynamics showing the bottleneck position and changes of the tunnel length over time. These methods help to select a small subset of tunnels, which are explored individually and in detail. For this stage we propose the third method, which shows in one static image the temporal evolvement of the shape of the most critical tunnel part, i.e., its bottleneck. This view is enriched with abstract depictions of different physicochemical properties of the amino acids surrounding the bottleneck. The usefulness of our newly proposed methods is demonstrated on a case study and the feedback from the domain experts is included. The biochemists confirmed that our novel methods help to convey the information about the appearance and properties of tunnels in a very intuitive and comprehensible manner.en_US
dc.description.number3en_US
dc.description.sectionheadersBiomedical Visualizationen_US
dc.description.seriesinformationComputer Graphics Forumen_US
dc.description.volume34en_US
dc.identifier.doi10.1111/cgf.12612en_US
dc.identifier.pages001-010en_US
dc.identifier.urihttps://doi.org/10.1111/cgf.12612en_US
dc.publisherThe Eurographics Association and John Wiley & Sons Ltd.en_US
dc.subjectI.3.6 [Computer Graphics]en_US
dc.subjectPicture/Image Generationen_US
dc.subjectLine and curve generationen_US
dc.titleMoleCollar and Tunnel Heat Map Visualizations for Conveying Spatio-Temporo-Chemical Properties Across and Along Protein Voidsen_US
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34-Issue 3
EuroVis15: Eurographics Conference on Visualization