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

Authors:
Ondrej Vavra
Ondrej Vavra
Christian-Albrechts-Universität zu Kiel
Sergio M Marques
Sergio M Marques
Cittadella Universitaria
Italy
Jan Brezovsky
Jan Brezovsky
Loschmidt Laboratories
Jiri Damborsky
Jiri Damborsky
Masaryk University
Czech Republic

IEEE/ACM Trans Comput Biol Bioinform 2019 Mar 26. Epub 2019 Mar 26.

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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Source
http://dx.doi.org/10.1109/TCBB.2019.2907492DOI Listing
March 2019
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