Analysis of Long Molecular Dynamics Simulations Using
Interactive Focus+Context Visualization

J 2019

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization

BYŠKA, Jan, Thomas TRAUTNER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ et. al.

Základní údaje

Originální název

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization

Autoři

BYŠKA, Jan (203 Česká republika, garant, domácí), Thomas TRAUTNER (40 Rakousko), Sérgio Manuel MARQUES (620 Portugalsko, domácí), Jiří DAMBORSKÝ (203 Česká republika, domácí), Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Manuela WALDNER (40 Rakousko)

Vydání

Computer Graphics Forum, Wiley-Blackwell, 2019, 0167-7055

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10200 1.2 Computer and information sciences

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.116

Kód RIV

RIV/00216224:14330/19:00107361

Organizační jednotka

Fakulta informatiky

DOI

http://dx.doi.org/10.1111/cgf.13701

UT WoS

000481468200035

Klíčová slova anglicky

Molecular Visualization;Design Studies;Focus + Context Techniques

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 17. 2. 2023 20:49, Mgr. Michaela Hylsová, Ph.D.

Anotace

V originále

Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. Guided by requirements derived from multiple focus groups with protein engineering experts, we designed and developed a novel interactive visual analysis approach for long and crowded MD simulations. In this approach, we link a dynamic 3D focus+context visualization with a 2D chart of time series data to guide the detection and navigation towards important spatio-temporal events. The 3D visualization renders elements of interest in more detail and increases the temporal resolution dependent on the time series data or the spatial region of interest. In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. Finally, we derived design guidelines for interactive visual analysis of complex MD simulation data.

Návaznosti

GC18-18647J, projekt VaV

Název: Vizuální analýza interakcí proteinů a ligandů (Akronym: PROLINT)

Investor: Grantová agentura ČR, Visual Analysis of Protein-Ligand Interactions

Citovat

BYŠKA, Jan, Thomas TRAUTNER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ a Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum. Wiley-Blackwell, 2019, roč. 38, č. 3, s. 441-453. ISSN 0167-7055. Dostupné z: https://dx.doi.org/10.1111/cgf.13701.

@article{1521596,
   author = {Byška, Jan and Trautner, Thomas and Marques, Sérgio Manuel and Damborský, Jiří and Kozlíková, Barbora and Waldner, Manuela},
   article_number = {3},
   doi = {http://dx.doi.org/10.1111/cgf.13701},
   keywords = {Molecular Visualization;Design Studies;Focus + Context Techniques},
   language = {eng},
   issn = {0167-7055},
   journal = {Computer Graphics Forum},
   title = {Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization},
   url = {http://dx.doi.org/10.1111/cgf.13701},
   volume = {38},
   year = {2019}
}

TY  - JOUR
ID  - 1521596
AU  - Byška, Jan - Trautner, Thomas - Marques, Sérgio Manuel - Damborský, Jiří - Kozlíková, Barbora - Waldner, Manuela
PY  - 2019
TI  - Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization
JF  - Computer Graphics Forum
VL  - 38
IS  - 3
SP  - 441-453
EP  - 441-453
PB  - Wiley-Blackwell
SN  - 01677055
KW  - Molecular Visualization;Design Studies;Focus + Context Techniques
UR  - http://dx.doi.org/10.1111/cgf.13701
L2  - http://dx.doi.org/10.1111/cgf.13701
N2  - Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. Guided by requirements derived from multiple focus groups with protein engineering experts, we designed and developed a novel interactive visual analysis approach for long and crowded MD simulations. In this approach, we link a dynamic 3D focus+context visualization with a 2D chart of time series data to guide the detection and navigation towards important spatio-temporal events. The 3D visualization renders elements of interest in more detail and increases the temporal resolution dependent on the time series data or the spatial region of interest. In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. Finally, we derived design guidelines for interactive visual analysis of complex MD simulation data.
ER  -

BYŠKA, Jan, Thomas TRAUTNER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ a Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. \textit{Computer Graphics Forum}. Wiley-Blackwell, 2019, roč.~38, č.~3, s.~441-453. ISSN~0167-7055. Dostupné z: https://dx.doi.org/10.1111/cgf.13701.

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