Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F17%3A00094923" target="_blank" >RIV/00216224:14330/17:00094923 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

Original language 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.

Czech name

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Czech description

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Type

D - Article in proceedings

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

Eurographics Workshop on Visual Computing for Biology and Medicine

ISBN

9783038680369

ISSN

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e-ISSN

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Number of pages

10

Pages from-to

33-42

Publisher name

Eurographics Workshop on Visual Computing for Biology and Medicine

Place of publication

Bremen, Germany

Event location

Bremen

Event date

Jan 1, 2017

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

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