Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations

Julius Parulek, Cagatay Turkay, Nathalie Reuter, Ivan Viola

Molecular surfaces provide a suitable way to analyze and to study the evolution and interaction of molecules. \ The analysis is often concerned with visual identification of binding sites of ligands to a host macromolecule. \ We present a novel technique that is based on implicit representation, which extracts all potential binding sites and allows an advanced $3D$ visualization of these sites in the context of the molecule. \ We utilize implicit function sampling strategy to obtain potential cavity samples and graph algorithms to extract arbitrary cavity components defined by simple graphs. \ Moreover, we propose how to interactively visualize these graphs in the context of the molecular surface. \ We also introduce a system of linked views depicting various graph parameters that are used to perform a more elaborative study on created graphs.

BioVis 2012 Information

The New UCSC Cancer Genomics BrowserUser-guided Segmentation of Thoracic Computed Tomography Data for Electrical Impedance Tomography Image ReconstructionVisualization and Exploration of 3D Toponome DataTractography in Context: Multimodal Visualization of Probabilistic Tractograms in Anatomical ContextUsing a Mathematical Graph Framework for Visualization of Inheritance Patterns in Commercial Plant PedigreesExtending The Grammar of Graphics for Biological Data VisualizationcompreheNGSive: A Tool for Exploring Next-Gen Sequencing VariantsMedSavant: Visual Analytics for Genetic Variation DatasetsBulk Synchronous VisualizationGetting Into Visualization of Large Biological Data SetsAracari: exploration of eQTL data through visualizationAn Abstract View of Associations Between Diseases and Developmental Gene SetsCan Adjacency Matrices help in the exploration and understanding of Multi-Omics Data?StratomeX: Enabling Visualization-Driven Cancer Subtype AnalysisGenomeRing: alignment visualization based on SuperGenome coordinatesScalable Interactive Analysis of Retinal Astrocyte NetworksVisual Analysis of Genome-wide Tracts of Homozygosity