| FURMANOVÁ, Katarína, Ondřej VÁVRA, Barbora KOZLÍKOVÁ, Jiří DAMBORSKÝ, Vojtěch VONÁSEK, David BEDNÁŘ and Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum. Wiley-Blackwell, 2020, vol. 39, No 6, p. 452-464. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14048. |
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@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 = {http://dx.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 and Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. \textit{Computer Graphics Forum}. Wiley-Blackwell, 2020, vol.~39, No~6, p.~452-464. ISSN~0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14048.
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