| FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, 2020, vol. 17, No 5, p. 1625-1638. ISSN 1545-5963. Available from: https://dx.doi.org/10.1109/TCBB.2019.2907492. |
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@article{1514116,
author = {Filipovič, Jiří and Vávra, Ondřej and Plhák, Jan and Bednář, David and Marques, Sérgio Manuel and Brezovský, Jan and Matyska, Luděk and Damborský, Jiří},
article_location = {Los Alamitos},
article_number = {5},
doi = {http://dx.doi.org/10.1109/TCBB.2019.2907492},
keywords = {molecular docking; tunnel analysis; ligand transport; drug design; numerical optimization; restrained force field; volume discretization},
language = {eng},
issn = {1545-5963},
journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
title = {CaverDock: A Novel Method for the Fast Analysis of Ligand Transport},
url = {https://ieeexplore.ieee.org/document/8674575},
volume = {17},
year = {2020}
}
TY - JOUR
ID - 1514116
AU - Filipovič, Jiří - Vávra, Ondřej - Plhák, Jan - Bednář, David - Marques, Sérgio Manuel - Brezovský, Jan - Matyska, Luděk - Damborský, Jiří
PY - 2020
TI - CaverDock: A Novel Method for the Fast Analysis of Ligand Transport
JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics
VL - 17
IS - 5
SP - 1625-1638
EP - 1625-1638
PB - IEEE Computer Society
SN - 15455963
KW - molecular docking
KW - tunnel analysis
KW - ligand transport
KW - drug design
KW - numerical optimization
KW - restrained force field
KW - volume discretization
UR - https://ieeexplore.ieee.org/document/8674575
L2 - https://ieeexplore.ieee.org/document/8674575
N2 - Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. The result of CaverDock calculation is a ligand trajectory and an energy profile of transport process. CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories. Our method lies in between the geometrical approaches and molecular dynamics simulations. Contrary to the geometrical methods, it provides an evaluation of chemical forces. However, it is far less computationally demanding and easier to set up compared to molecular dynamics simulations. CaverDock will find a broad use in the fields of computational enzymology, drug design and protein engineering. The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.
ER -
FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. \textit{IEEE/ACM Transactions on Computational Biology and Bioinformatics}. Los Alamitos: IEEE Computer Society, 2020, vol.~17, No~5, p.~1625-1638. ISSN~1545-5963. Available from: https://dx.doi.org/10.1109/TCBB.2019.2907492.
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