FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA a 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, roč. 17, č. 5, s. 1625-1638. ISSN 1545-5963. Dostupné z: 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 a 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, roč.~17, č.~5, s.~1625-1638. ISSN~1545-5963. Dostupné z: https://dx.doi.org/10.1109/TCBB.2019.2907492.
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