InVADo: Interactive Visual Analysis of Molecular Docking Data

J 2024

InVADo: Interactive Visual Analysis of Molecular Docking Data

SCHÄFER, Marco, Nicolas BRICH, Jan BYŠKA, Sérgio Manuel MARQUES, David BEDNÁŘ et. al.

Basic information

Original name

InVADo: Interactive Visual Analysis of Molecular Docking Data

Authors

SCHÄFER, Marco (276 Germany), Nicolas BRICH (276 Germany), Jan BYŠKA (203 Czech Republic, belonging to the institution), Sérgio Manuel MARQUES (620 Portugal, belonging to the institution), David BEDNÁŘ (203 Czech Republic, belonging to the institution), Philipp THIEL (276 Germany), Barbora KOZLÍKOVÁ (203 Czech Republic, belonging to the institution) and Michael KRONE (276 Germany, guarantor)

Edition

IEEE Transactions on Visualization and Computer Graphics, IEEE Computer Society, 2024, 1077-2626

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.200 in 2022

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1109/TVCG.2023.3337642

UT WoS

001173975500011

Keywords in English

proteins; drugs; visualization; data visualization; three-dimensional displays; receptor (biochemistry); carbon

Abstract

V originále

Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the protein and ligand selection, their preparation, and the docking process itself, followed by the evaluation of the results. However, the most commonly used docking software provides no or very basic evaluation possibilities. Scripting and external molecular viewers are often used, which are not designed for an efficient analysis of docking results. Therefore, we developed InVADo, a comprehensive interactive visual analysis tool for large docking data. It consists of multiple linked 2D and 3D views. It filters and spatially clusters the data, and enriches it with post-docking analysis results of interactions and functional groups, to enable well-founded decision-making. In an exemplary case study, domain experts confirmed that InVADo facilitates and accelerates the analysis workflow. They rated it as a convenient, comprehensive, and feature-rich tool, especially useful for virtual screening. Like what

Links

LM2018121, research and development project

Name: Výzkumná infrastruktura RECETOX (Acronym: RECETOX RI)

Investor: Ministry of Education, Youth and Sports of the CR, RECETOX RI

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

LM2018140, research and development project

Name: e-Infrastruktura CZ (Acronym: e-INFRA CZ)

Investor: Ministry of Education, Youth and Sports of the CR

LX22NPO5102, research and development project

Name: Národní ústav pro výzkum rakoviny (Acronym: NÚVR)

Investor: Ministry of Education, Youth and Sports of the CR, National institute for cancer research, 5.1 EXCELES

Citovat

SCHÄFER, Marco, Nicolas BRICH, Jan BYŠKA, Sérgio Manuel MARQUES, David BEDNÁŘ, Philipp THIEL, Barbora KOZLÍKOVÁ and Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. IEEE Transactions on Visualization and Computer Graphics. IEEE Computer Society, 2024, vol. 30, No 4, p. 1984-1997. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2023.3337642.

@article{2345857,
   author = {Schäfer, Marco and Brich, Nicolas and Byška, Jan and Marques, Sérgio Manuel and Bednář, David and Thiel, Philipp and Kozlíková, Barbora and Krone, Michael},
   article_number = {4},
   doi = {http://dx.doi.org/10.1109/TVCG.2023.3337642},
   keywords = {proteins; drugs; visualization; data visualization; three-dimensional displays; receptor (biochemistry); carbon},
   language = {eng},
   issn = {1077-2626},
   journal = {IEEE Transactions on Visualization and Computer Graphics},
   title = {InVADo: Interactive Visual Analysis of Molecular Docking Data},
   url = {https://ieeexplore.ieee.org/document/10334517},
   volume = {30},
   year = {2024}
}

TY  - JOUR
ID  - 2345857
AU  - Schäfer, Marco - Brich, Nicolas - Byška, Jan - Marques, Sérgio Manuel - Bednář, David - Thiel, Philipp - Kozlíková, Barbora - Krone, Michael
PY  - 2024
TI  - InVADo: Interactive Visual Analysis of Molecular Docking Data
JF  - IEEE Transactions on Visualization and Computer Graphics
VL  - 30
IS  - 4
SP  - 1984-1997
EP  - 1984-1997
PB  - IEEE Computer Society
SN  - 10772626
KW  - proteins
KW  - drugs
KW  - visualization
KW  - data visualization
KW  - three-dimensional displays
KW  - receptor (biochemistry)
KW  - carbon
UR  - https://ieeexplore.ieee.org/document/10334517
N2  - Molecular docking is a key technique in various fields like structural biology, medicinal chemistry, and biotechnology. It is widely used for virtual screening during drug discovery, computer-assisted drug design, and protein engineering. A general molecular docking process consists of the protein and ligand selection, their preparation, and the docking process itself, followed by the evaluation of the results. However, the most commonly used docking software provides no or very basic evaluation possibilities. Scripting and external molecular viewers are often used, which are not designed for an efficient analysis of docking results. Therefore, we developed InVADo, a comprehensive interactive visual analysis tool for large docking data. It consists of multiple linked 2D and 3D views. It filters and spatially clusters the data, and enriches it with post-docking analysis results of interactions and functional groups, to enable well-founded decision-making. In an exemplary case study, domain experts confirmed that InVADo facilitates and accelerates the analysis workflow. They rated it as a convenient, comprehensive, and feature-rich tool, especially useful for virtual screening. Like what
ER  -

SCHÄFER, Marco, Nicolas BRICH, Jan BYŠKA, Sérgio Manuel MARQUES, David BEDNÁŘ, Philipp THIEL, Barbora KOZLÍKOVÁ and Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. \textit{IEEE Transactions on Visualization and Computer Graphics}. IEEE Computer Society, 2024, vol.~30, No~4, p.~1984-1997. ISSN~1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2023.3337642.

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