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.

Basic information

Original name

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

Authors

BYŠKA, Jan (203 Czech Republic, guarantor, belonging to the institution), Thomas TRAUTNER (40 Austria), Sérgio Manuel MARQUES (620 Portugal, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, belonging to the institution), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution) and Manuela WALDNER (40 Austria)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.116

RIV identification code

RIV/00216224:14330/19:00107361

Organization unit

Faculty of Informatics

DOI

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

UT WoS

000481468200035

Keywords in English

Molecular Visualization;Design Studies;Focus + Context Techniques

Abstract

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.

Links

GC18-18647J, research and development project

Name: Vizuální analýza interakcí proteinů a ligandů (Acronym: PROLINT)

Investor: Czech Science Foundation

Citovat

BYŠKA, Jan, Thomas TRAUTNER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ and Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum. Wiley-Blackwell, 2019, vol. 38, No 3, p. 441-453. ISSN 0167-7055. Available from: 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 and Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. \textit{Computer Graphics Forum}. Wiley-Blackwell, 2019, vol.~38, No~3, p.~441-453. ISSN~0167-7055. Available from: https://dx.doi.org/10.1111/cgf.13701.

Detailed Information on Publication Record