DockVis: Visual Analysis of Molecular Docking Trajectories

J 2020

DockVis: Visual Analysis of Molecular Docking Trajectories

FURMANOVÁ, Katarína; Ondřej VÁVRA; Barbora KOZLÍKOVÁ; Jiří DAMBORSKÝ; Vojtěch VONÁSEK et al.

Základní údaje

Originální název

DockVis: Visual Analysis of Molecular Docking Trajectories

Autoři

FURMANOVÁ, Katarína ; Ondřej VÁVRA; Barbora KOZLÍKOVÁ ; Jiří DAMBORSKÝ; Vojtěch VONÁSEK; David BEDNÁŘ a Jan BYŠKA

Vydání

Computer Graphics Forum, Wiley-Blackwell, 2020, 0167-7055

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10200 1.2 Computer and information sciences

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.078

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14330/20:00114201

Organizační jednotka

Fakulta informatiky

Klíčová slova anglicky

visual analysis; molecular docking; trajectory; ligand

Štítky

143180

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 17. 2. 2023 20:54, Mgr. Michaela Hylsová, Ph.D.

Anotace

V originále

Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein-ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way,we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package (www.caver.cz).

Návaznosti

GC18-18647J, projekt VaV

Název: Vizuální analýza interakcí proteinů a ligandů (Akronym: PROLINT)

Investor: Grantová agentura ČR, Visual Analysis of Protein-Ligand Interactions

LM2015047, 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

Citovat

FURMANOVÁ, Katarína; Ondřej VÁVRA; Barbora KOZLÍKOVÁ; Jiří DAMBORSKÝ; Vojtěch VONÁSEK; David BEDNÁŘ a Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum. Wiley-Blackwell, 2020, roč. 39, č. 6, s. 452-464. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.14048.

@article{1664236,
   author = {Furmanová, Katarína and Vávra, Ondřej and Kozlíková, Barbora and Damborský, Jiří and Vonásek, Vojtěch and Bednář, David and Byška, Jan},
   article_number = {6},
   doi = {https://doi.org/10.1111/cgf.14048},
   keywords = {visual analysis; molecular docking; trajectory; ligand},
   language = {eng},
   issn = {0167-7055},
   journal = {Computer Graphics Forum},
   title = {DockVis: Visual Analysis of Molecular Docking Trajectories},
   url = {http://onlinelibrary.wiley.com/doi/10.1111/cgf.14048},
   volume = {39},
   year = {2020}
}

TY  - JOUR
ID  - 1664236
AU  - Furmanová, Katarína - Vávra, Ondřej - Kozlíková, Barbora - Damborský, Jiří - Vonásek, Vojtěch - Bednář, David - Byška, Jan
PY  - 2020
TI  - DockVis: Visual Analysis of Molecular Docking Trajectories
JF  - Computer Graphics Forum
VL  - 39
IS  - 6
SP  - 452-464
EP  - 452-464
PB  - Wiley-Blackwell
SN  - 01677055
KW  - visual analysis
KW  - molecular docking
KW  - trajectory
KW  - ligand
UR  - http://onlinelibrary.wiley.com/doi/10.1111/cgf.14048
L2  - http://onlinelibrary.wiley.com/doi/10.1111/cgf.14048
N2  - Computation of trajectories for ligand binding and unbinding via protein tunnels and channels is important for predicting possible protein-ligand interactions. These highly complex processes can be simulated by several software tools, which provide biochemists with valuable information for drug design or protein engineering applications. This paper focuses on aiding this exploration process by introducing the DockVis visual analysis tool. DockVis operates with the multivariate output data from one of the latest available tools for the prediction of ligand transport, CaverDock. DockVis provides the users with several linked views, combining the 2D abstracted depictions of ligands and their surroundings and properties with the 3D view. In this way,we enable the users to perceive the spatial configurations of ligand passing through the protein tunnel. The users are initially visually directed to the most relevant parts of ligand trajectories, which can be then explored in higher detail by the follow-up analyses. DockVis was designed in tight collaboration with protein engineers developing the CaverDock tool. However, the concept of DockVis can be extended to any other tool predicting ligand pathways by the molecular docking. DockVis will be made available to the wide user community as part of the Caver Analyst 3.0 software package (www.caver.cz).
ER  -

FURMANOVÁ, Katarína; Ondřej VÁVRA; Barbora KOZLÍKOVÁ; Jiří DAMBORSKÝ; Vojtěch VONÁSEK; David BEDNÁŘ a Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. \textit{Computer Graphics Forum}. Wiley-Blackwell, 2020, roč.~39, č.~6, s.~452-464. ISSN~0167-7055. Dostupné z: https://doi.org/10.1111/cgf.14048.

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