| VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford (UK): Oxford University Press, 2019, vol. 35, No 23, p. 4986-4993. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz386. |
Other formats:
BibTeX
LaTeX
RIS
@article{50027,
author = {Vávra, Ondřej and Filipovič, Jiří and Plhák, Jan and Bednář, David and Marques, Sérgio Manuel and Brezovský, Jan and Štourač, Jan and Matyska, Luděk and Damborský, Jiří},
article_location = {Oxford (UK)},
article_number = {23},
doi = {http://dx.doi.org/10.1093/bioinformatics/btz386},
keywords = {HALOALKANE DEHALOGENASE LINB; ENERGY LANDSCAPE; ACTIVE-SITE; DYNAMICS; MECHANISM; BINDING; RECOGNITION; KINETICS},
language = {eng},
issn = {1367-4803},
journal = {Bioinformatics},
title = {CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels},
url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz386/5488163},
volume = {35},
year = {2019}
}
TY - JOUR
ID - 50027
AU - Vávra, Ondřej - Filipovič, Jiří - Plhák, Jan - Bednář, David - Marques, Sérgio Manuel - Brezovský, Jan - Štourač, Jan - Matyska, Luděk - Damborský, Jiří
PY - 2019
TI - CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels
JF - Bioinformatics
VL - 35
IS - 23
SP - 4986-4993
EP - 4986-4993
PB - Oxford University Press
SN - 1367-4803
KW - HALOALKANE DEHALOGENASE LINB
KW - ENERGY LANDSCAPE
KW - ACTIVE-SITE
KW - DYNAMICS
KW - MECHANISM
KW - BINDING
KW - RECOGNITION
KW - KINETICS
UR - https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz386/5488163
N2 - Motivation Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins’ external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. Results CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock’s usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering.
ER -
VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. \textit{Bioinformatics}. Oxford (UK): Oxford University Press, 2019, vol.~35, No~23, p.~4986-4993. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz386.
|
