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@inproceedings{1389119,
author = {Vad, Viktor and Byška, Jan and Jurčík, Adam and Viola, Ivan and Gröller, Eduard M. and Hauser, Helwig and Marques, Sérgio Manuel and Damborský, Jiří and Kozlíková, Barbora},
address = {Bremen, Germany},
booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine},
editor = {S. Bruckner, A. Hennemuth, and B. Kainz},
keywords = {Protein;water molecule;trajectory;visualization},
howpublished = {elektronická verze "online"},
language = {eng},
location = {Bremen, Germany},
isbn = {978-3-03868-036-9},
pages = {33-42},
publisher = {Eurographics Workshop on Visual Computing for Biology and Medicine},
title = {Watergate: Visual Exploration of Water Trajectories in Protein Dynamics},
year = {2017}
}
TY - JOUR
ID - 1389119
AU - Vad, Viktor - Byška, Jan - Jurčík, Adam - Viola, Ivan - Gröller, Eduard M. - Hauser, Helwig - Marques, Sérgio Manuel - Damborský, Jiří - Kozlíková, Barbora
PY - 2017
TI - Watergate: Visual Exploration of Water Trajectories in Protein Dynamics
PB - Eurographics Workshop on Visual Computing for Biology and Medicine
CY - Bremen, Germany
SN - 9783038680369
KW - Protein;water molecule;trajectory;visualization
N2 - 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.
ER -
VAD, Viktor, Jan BYŠKA, Adam JURČÍK, Ivan VIOLA, Eduard M. GRÖLLER, Helwig HAUSER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ and Barbora KOZLÍKOVÁ. Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. Online. In S. Bruckner, A. Hennemuth, and B. Kainz. \textit{Eurographics Workshop on Visual Computing for Biology and Medicine}. Bremen, Germany: Eurographics Workshop on Visual Computing for Biology and Medicine, 2017, p.~33-42. ISBN~978-3-03868-036-9.
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