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.

Základní údaje

Originální název

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics

Autoři

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

Vydání

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

Nakladatel

Eurographics Workshop on Visual Computing for Biology and Medicine

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/17:00094923

Organizační jednotka

Fakulta informatiky

ISBN

978-3-03868-036-9

Klíčová slova anglicky

Protein;water molecule;trajectory;visualization

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 26. 4. 2018 12:43, doc. RNDr. Barbora Kozlíková, Ph.D.

Anotace

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.

Návaznosti

GA16-07965S, projekt VaV

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

Investor: Grantová agentura ČR, Řízená evoluce dynamických elementů v enzymech s využitím mikrofluidních čipů

LM2015047, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2015051, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX RI)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Výzkumná infrastruktura RECETOX

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

LO1214, projekt VaV

Název: Centrum pro výzkum toxických látek v prostředí (Akronym: RECETOX)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum pro výzkum toxických látek v prostředí

Citovat

VAD, Viktor; Jan BYŠKA; Adam JURČÍK; Ivan VIOLA; Eduard M. GRÖLLER; Helwig HAUSER; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ a 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, s. 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  - CONF
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 a 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, s.~33-42. ISBN~978-3-03868-036-9.

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