Welcome to CaverDock documentation!
CaverDock is a tool designed for rapid analysis of ligand transport processes in receptors [1, 2]. It models the transportation of a ligand – a substrate, a product, an inhibitor, a co-factor or a co-solvent – from the outside environment into the receptor active or binding site (or vice versa).
The input for the calculation is a receptor structure in the PDB format and a ligand structure in the PDBQT format. The outputs are the ligand’s trajectory and the energetic profile of the process. CaverDock implements a novel algorithm based on molecular docking that produces a contiguous ligand trajectory and estimates the binding energy along the pathway.
The current version of CaverDock uses CAVER [3] for the pathway identification and a heavily modified AutoDock Vina 1.1.2 [4] as the docking engine. The tool is much faster than molecular dynamic simulations (usually 2-20 min per job), making it suitable even for virtual screening. The software is extremely easy to use since in its minimalistic configuration it requires only the setup for AutoDock Vina and the geometry of the tunnel.
The following groups and colleagues have significantly contributed to the development of CaverDock:
Loschmidt Laboratories, Masaryk University, Brno, Czech Republic https://loschmidt.chemi.muni.cz/peg/
Jiří Filipovič and Petra Němcová, Institute of Computer Science, Masaryk University, Brno, Czech Republic https://www.ics.muni.cz/
Martin Šurkovský and Jakub Beránek, IT4Innovations, Ostrava, Czech Republic https://www.it4i.cz/
Vojtěch Vonásek and Michal Minařík, Multi-Robot Systems group, Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic https://mrs.fel.cvut.cz
Contact us
E-mail: caver@caver.cz
How to cite
Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, and David Bednar. pyCaverDock: Python Implementation of the Popular Tool for Analysis of Ligand Transport with Advanced Caching and Batch Calculation Support. Bioinformatics (submitted), XX(XX):XX–XX, 2023.
Jiri Filipovic, Ondrej Vavra, Jan Plhak, David Bednar, Sergio M Marques, Jan Brezovsky, Ludek Matyska, and Jiri Damborsky. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM transactions on computational biology and bioinformatics, 17(5):1625–1638, 2019. doi:10.1109/TCBB.2019.2907492.
Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sergio M Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, and Jiri Damborsky. CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels. Bioinformatics, 35(23):4986–4993, 2019. doi:10.1093/bioinformatics/btz386.
Acknowledgement
This work was supported by:
Czech Grant Agency (20-15915Y)
Czech Ministry of Education (Elixir CZ - LM2018131 and LM2015047)
European Regional Development Fund (INBIO - CZ.02.1.01/0.0/0.0/16_026/0008451)
Licence for commercial use
Contact us: enantis@enantis.com
