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@inbook{1757928,
author = {Hozzová, Jana and Vávra, Ondřej and Bednář, David and Filipovič, Jiří},
address = {New York},
booktitle = {Protein-Ligand Interactions and Drug Design},
doi = {http://dx.doi.org/10.1007/978-1-0716-1209-5_6},
editor = {Flavio Ballante},
keywords = {Tunnel analysis; Ligand transport; Molecular docking; Drug design; Enzyme engineering; Ligand screening},
howpublished = {tištěná verze "print"},
language = {eng},
location = {New York},
isbn = {978-1-0716-1208-8},
pages = {105-124},
publisher = {Humana, New York, NY},
title = {Simulation of Ligand Transport in Receptors Using CaverDock},
url = {https://doi.org/10.1007/978-1-0716-1209-5_6},
year = {2021}
}
TY - CHAP
ID - 1757928
AU - Hozzová, Jana - Vávra, Ondřej - Bednář, David - Filipovič, Jiří
PY - 2021
TI - Simulation of Ligand Transport in Receptors Using CaverDock
VL - Methods in Molecular Biology, vol 2266
PB - Humana, New York, NY
CY - New York
SN - 9781071612088
KW - Tunnel analysis
KW - Ligand transport
KW - Molecular docking
KW - Drug design
KW - Enzyme engineering
KW - Ligand screening
UR - https://doi.org/10.1007/978-1-0716-1209-5_6
N2 - Interactions between enzymes and small molecules lie in the center of many fundamental biochemical processes. Their analysis using molecular dynamics simulations have high computational demands, geometric approaches fail to consider chemical forces, and molecular docking offers only static information. Recently, we proposed to combine molecular docking and geometric approaches in an application called CaverDock. CaverDock is discretizing enzyme tunnel into discs, iteratively docking with restraints into one disc after another and searching for a trajectory of the ligand passing through the tunnel. Here, we focus on the practical side of its usage describing the whole method: from getting the application, and processing the data through a workflow, to interpreting the results. Moreover, we shared the best practices, recommended how to solve the most common issues, and demonstrated its application on three use cases.
ER -
HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. \textit{Protein-Ligand Interactions and Drug Design}. New York: Humana, New York, NY, 2021, p.~105-124. Methods in Molecular Biology, vol 2266. ISBN~978-1-0716-1208-8. Available from: https://dx.doi.org/10.1007/978-1-0716-1209-5\_{}6.
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