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.

Základní údaje

Originální název

InVADo: Interactive Visual Analysis of Molecular Docking Data

Autoři

SCHÄFER, Marco (276 Německo), Nicolas BRICH (276 Německo), Jan BYŠKA (203 Česká republika, domácí), Sérgio Manuel MARQUES (620 Portugalsko, domácí), David BEDNÁŘ (203 Česká republika, domácí), Philipp THIEL (276 Německo), Barbora KOZLÍKOVÁ (203 Česká republika, domácí) a Michael KRONE (276 Německo, garant)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.200 v roce 2022

Organizační jednotka

Fakulta informatiky

DOI

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

UT WoS

001173975500011

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 25. 3. 2024 11:40, Mgr. Marie Šípková, DiS.

Anotace

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

Návaznosti

LM2018121, projekt VaV

Název: Výzkumná infrastruktura RECETOX (Akronym: RECETOX RI)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, RECETOX RI

LM2018131, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LM2018140, projekt VaV

Název: e-Infrastruktura CZ (Akronym: e-INFRA CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

LX22NPO5102, projekt VaV

Název: Národní ústav pro výzkum rakoviny (Akronym: NÚVR)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní ústav pro výzkum rakoviny, 5.1 EXCELES

Citovat

SCHÄFER, Marco, Nicolas BRICH, Jan BYŠKA, Sérgio Manuel MARQUES, David BEDNÁŘ, Philipp THIEL, Barbora KOZLÍKOVÁ a Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. IEEE Transactions on Visualization and Computer Graphics. IEEE Computer Society, 2024, roč. 30, č. 4, s. 1984-1997. ISSN 1077-2626. Dostupné z: 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 a Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. \textit{IEEE Transactions on Visualization and Computer Graphics}. IEEE Computer Society, 2024, roč.~30, č.~4, s.~1984-1997. ISSN~1077-2626. Dostupné z: https://dx.doi.org/10.1109/TVCG.2023.3337642.

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