Visual Analysis of Biomolecular Cavities: State of the Art

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dc.contributor.authorKrone, Michaelen_US
dc.contributor.authorKozlíková, Barboraen_US
dc.contributor.authorLindow, Norberten_US
dc.contributor.authorBaaden, Marcen_US
dc.contributor.authorBaum, Danielen_US
dc.contributor.authorParulek, Juliusen_US
dc.contributor.authorHege, Hans-Christianen_US
dc.contributor.authorViola, Ivanen_US
dc.contributor.editorRoss Maciejewski and Timo Ropinski and Anna Vilanovaen_US
dc.date.accessioned2016-06-09T09:42:54Z
dc.date.available2016-06-09T09:42:54Z
dc.date.issued2016en_US
dc.description.abstractIn this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.en_US
dc.description.documenttypestar
dc.description.number3en_US
dc.description.sectionheadersBiomedical Visualizationen_US
dc.description.seriesinformationComputer Graphics Forumen_US
dc.description.volume35en_US
dc.identifier.doi10.1111/cgf.12928en_US
dc.identifier.issn1467-8659en_US
dc.identifier.pages527-551en_US
dc.identifier.urihttps://diglib.eg.org:443/handle/10
dc.identifier.urihttps://doi.org/10.1111/cgf.12928en_US
dc.publisherThe Eurographics Association and John Wiley & Sons Ltd.en_US
dc.subjectI.3.5 [Computer Graphics]en_US
dc.subjectComputational Geometry and Object Modelingen_US
dc.subjectBoundary representationsen_US
dc.subjectJ.3 [Computer Applications]en_US
dc.subjectLife and Medical Sciencesen_US
dc.subjectBiology and geneticsen_US
dc.titleVisual Analysis of Biomolecular Cavities: State of the Arten_US
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