Multiscale Molecular Visualization

J 2019

Multiscale Molecular Visualization

MIAO, Haichao, Tobias KLEIN, David KOUŘIL, Peter MINDEK, Karsten SCHATZ et. al.

Basic information

Original name

Multiscale Molecular Visualization

Authors

MIAO, Haichao (40 Austria), Tobias KLEIN (276 Germany), David KOUŘIL (203 Czech Republic), Peter MINDEK (703 Slovakia), Karsten SCHATZ (276 Germany), Eduard M. GRÖLLER (40 Austria), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution), Tobias ISENBERG (276 Germany) and Ivan VIOLA (703 Slovakia, guarantor)

Edition

Journal of Molecular Biology, 2019, 0022-2836

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.760

RIV identification code

RIV/00216224:14330/19:00107174

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1016/j.jmb.2018.09.004

UT WoS

000463120800001

Keywords in English

molecular visualization;molecular dynamics;modelitics;DNA nanotechnology;visual abstraction

Abstract

V originále

We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.

Links

GC18-18647J, research and development project

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

Investor: Czech Science Foundation

Citovat

MIAO, Haichao, Tobias KLEIN, David KOUŘIL, Peter MINDEK, Karsten SCHATZ, Eduard M. GRÖLLER, Barbora KOZLÍKOVÁ, Tobias ISENBERG and Ivan VIOLA. Multiscale Molecular Visualization. Journal of Molecular Biology. 2019, vol. 431, No 6, p. 1049-1070. ISSN 0022-2836. Available from: https://dx.doi.org/10.1016/j.jmb.2018.09.004.

@article{1432796,
   author = {Miao, Haichao and Klein, Tobias and Kouřil, David and Mindek, Peter and Schatz, Karsten and Gröller, Eduard M. and Kozlíková, Barbora and Isenberg, Tobias and Viola, Ivan},
   article_number = {6},
   doi = {http://dx.doi.org/10.1016/j.jmb.2018.09.004},
   keywords = {molecular visualization;molecular dynamics;modelitics;DNA nanotechnology;visual abstraction},
   language = {eng},
   issn = {0022-2836},
   journal = {Journal of Molecular Biology},
   title = {Multiscale Molecular Visualization},
   url = {http://dx.doi.org/10.1016/j.jmb.2018.09.004},
   volume = {431},
   year = {2019}
}

TY  - JOUR
ID  - 1432796
AU  - Miao, Haichao - Klein, Tobias - Kouřil, David - Mindek, Peter - Schatz, Karsten - Gröller, Eduard M. - Kozlíková, Barbora - Isenberg, Tobias - Viola, Ivan
PY  - 2019
TI  - Multiscale Molecular Visualization
JF  - Journal of Molecular Biology
VL  - 431
IS  - 6
SP  - 1049-1070
EP  - 1049-1070
SN  - 00222836
KW  - molecular visualization;molecular dynamics;modelitics;DNA nanotechnology;visual abstraction
UR  - http://dx.doi.org/10.1016/j.jmb.2018.09.004
L2  - http://dx.doi.org/10.1016/j.jmb.2018.09.004
N2  - We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support interactive exploration within large structural biology assemblies up to the size of bacterial cells. We describe fundamental rendering techniques as well as approaches for element instantiation, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.
ER  -

MIAO, Haichao, Tobias KLEIN, David KOUŘIL, Peter MINDEK, Karsten SCHATZ, Eduard M. GRÖLLER, Barbora KOZLÍKOVÁ, Tobias ISENBERG and Ivan VIOLA. Multiscale Molecular Visualization. \textit{Journal of Molecular Biology}. 2019, vol.~431, No~6, p.~1049-1070. ISSN~0022-2836. Available from: https://dx.doi.org/10.1016/j.jmb.2018.09.004.

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