Publication details

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport

Authors

FILIPOVIČ Jiří VÁVRA Ondřej PLHÁK Jan BEDNÁŘ David MARQUES Sérgio Manuel BREZOVSKÝ Jan MATYSKA Luděk DAMBORSKÝ Jiří

Type Article in Periodical
Magazine / Source IEEE/ACM Transactions on Computational Biology and Bioinformatics
MU Faculty or unit

Institute of Computer Science

Citation
WWW https://ieeexplore.ieee.org/document/8674575
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
Description 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/.
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