Publication details

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

Authors

VAD Viktor BYŠKA Jan JURČÍK Adam VIOLA Ivan GRÖLLER Eduard M. HAUSER Helwig MARQUES Sérgio Manuel DAMBORSKÝ Jiří KOZLÍKOVÁ Barbora

Year of publication 2017
Type Article in Proceedings
Conference Eurographics Workshop on Visual Computing for Biology and Medicine
MU Faculty or unit

Faculty of Informatics

Citation
Field Informatics
Keywords Protein;water molecule;trajectory;visualization
Description The function of proteins is tightly related to their interactions with other molecules. The study of such interactions often requires to track the molecules that enter or exit specific regions of the proteins. This is investigated with molecular dynamics simulations, producing the trajectories of thousands of water molecules during hundreds of thousands of time steps. To ease the exploration of such rich spatio-temporal data, we propose a novel workflow for the analysis and visualization of large sets of water-molecule trajectories. Our solution consists of a set of visualization techniques, which help biochemists to classify, cluster, and filter the trajectories and to explore the properties and behavior of selected subsets in detail. Initially, we use an interactive histogram and a time-line visualization to give an overview of all water trajectories and select the interesting ones for further investigation. Further, we depict clusters of trajectories in a novel 2D representation illustrating the flows of water molecules. These views are interactively linked with a 3D representation where we show individual paths, including their simplification, as well as extracted statistical information displayed by isosurfaces. The proposed solution has been designed in tight collaboration with experts to support specific tasks in their scientific workflows. They also conducted several case studies to evaluate the usability and effectiveness of our new solution with respect to their research scenarios. These confirmed that our proposed solution helps in analyzing water trajectories and in extracting the essential information out of the large amount of input data.
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