Watergate: Visual Exploration of Water Trajectories in Protein
Dynamics

D 2017

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

VAD, Viktor, Jan BYŠKA, Adam JURČÍK, Ivan VIOLA, Eduard M. GRÖLLER et. al.

Basic information

Original name

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

Authors

VAD, Viktor (348 Hungary), Jan BYŠKA (203 Czech Republic), Adam JURČÍK (203 Czech Republic, belonging to the institution), Ivan VIOLA (703 Slovakia), Eduard M. GRÖLLER (40 Austria), Helwig HAUSER (40 Austria), Sérgio Manuel MARQUES (620 Portugal, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution) and Barbora KOZLÍKOVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Bremen, Germany, Eurographics Workshop on Visual Computing for Biology and Medicine, p. 33-42, 10 pp. 2017

Publisher

Eurographics Workshop on Visual Computing for Biology and Medicine

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

RIV identification code

RIV/00216224:14330/17:00094923

Organization unit

Faculty of Informatics

ISBN

978-3-03868-036-9

Keywords in English

Protein;water molecule;trajectory;visualization

Abstract

V originále

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.

Links

GA16-07965S, research and development project

Name: Řízená evoluce dynamických elementů v enzymech s využitím mikrofluidních čipů

Investor: Czech Science Foundation

LM2015047, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LM2015051, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

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. 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.

@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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