Mol* Viewer: modern web app for 3D visualization and analysis
of large biomolecular structures

J 2021

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

SEHNAL, David, S. BITTRICH, M. DESHPANDE, Radka SVOBODOVÁ, K. BERKA et. al.

Basic information

Original name

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Authors

SEHNAL, David (203 Czech Republic, belonging to the institution), S. BITTRICH, M. DESHPANDE, Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution), K. BERKA, V. BAZGIER, S. VELANKAR, S.K. BURLEY, Jaroslav KOČA (203 Czech Republic, belonging to the institution) and A.S. ROSE

Edition

Nucleic acids research, Oxford, Oxford University Press, 2021, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 19.160

RIV identification code

RIV/00216224:14740/21:00122430

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkab314

UT WoS

000672775800055

Keywords in English

MOLECULAR-DYNAMICSDATABASE

Abstract

V originále

Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Links

EF16_013/0001777, research and development project

Name: ELIXIR-CZ: Budování kapacit

LM2018131, 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

Citovat

SEHNAL, David, S. BITTRICH, M. DESHPANDE, Radka SVOBODOVÁ, K. BERKA, V. BAZGIER, S. VELANKAR, S.K. BURLEY, Jaroslav KOČA and A.S. ROSE. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic acids research. Oxford: Oxford University Press, 2021, vol. 49, W1, p. "W431"-"W437", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkab314.

@article{1793640,
   author = {Sehnal, David and Bittrich, S. and Deshpande, M. and Svobodová, Radka and Berka, K. and Bazgier, V. and Velankar, S. and Burley, S.K. and Koča, Jaroslav and Rose, A.S.},
   article_location = {Oxford},
   article_number = {W1},
   doi = {http://dx.doi.org/10.1093/nar/gkab314},
   keywords = {MOLECULAR-DYNAMICSDATABASE},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures},
   url = {https://academic.oup.com/nar/article/49/W1/W431/6270780#267023333},
   volume = {49},
   year = {2021}
}

TY  - JOUR
ID  - 1793640
AU  - Sehnal, David - Bittrich, S. - Deshpande, M. - Svobodová, Radka - Berka, K. - Bazgier, V. - Velankar, S. - Burley, S.K. - Koča, Jaroslav - Rose, A.S.
PY  - 2021
TI  - Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
JF  - Nucleic acids research
VL  - 49
IS  - W1
SP  - "W431"-"W437"
EP  - "W431"-"W437"
PB  - Oxford University Press
SN  - 03051048
KW  - MOLECULAR-DYNAMICSDATABASE
UR  - https://academic.oup.com/nar/article/49/W1/W431/6270780#267023333
N2  - Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.
ER  -

SEHNAL, David, S. BITTRICH, M. DESHPANDE, Radka SVOBODOVÁ, K. BERKA, V. BAZGIER, S. VELANKAR, S.K. BURLEY, Jaroslav KOČA and A.S. ROSE. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2021, vol.~49, W1, p.~''W431''-''W437'', 7 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkab314.

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