References

Referred publications

[1]

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.

[2]

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.

[3]

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, and others. CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Computational Biology, pages e1002708, 2012. doi:10.1371/journal.pcbi.1002708.

[4]

Oleg Trott and Arthur J Olson. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2):455–461, 2010. doi:10.1002/jcc.21334.

[5]

Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar Pinto, Jan Brezovsky, Jiri Damborsky, and David Bednar. Caver Web 1.0: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport. Nucleic Acids Research, 47(W1):W414–W422, 05 2019. doi:10.1093/nar/gkz378.

Related publications

• Ondrej Vavra, Jiri Damborsky, and David Bednar. Fast Approximative Methods for Study of Ligand Transport and Rational Design of Improved Enzymes for Biotechnologies. Biotechnology Advances, 60:108009, 2022. doi:https://doi.org/10.1016/j.biotechadv.2022.108009.

• Milos Musil, Andrej Jezik, Marie Jankujova, Jan Stourac, Jakub Galgonek, Saltuk Mustafa Eyrilmez, Jiri Vondrasek, Jiri Damborsky, and David Bednar. Fully Automated Virtual Screening Pipeline of FDA-Approved Drugs Using Caver Web. Computational and Structural Biotechnology Journal, 20:6512–6518, 2022. doi:https://doi.org/10.1016/j.csbj.2022.11.031.

• Gaspar P. Pinto, Ondrej Vavra, Sergio M. Marques, Jiri Filipovic, David Bednar, and Jiri Damborsky. Screening of World Approved Drugs against Highly Dynamical Spike Glycoprotein of SARS-CoV-2 using CaverDock and Machine Learning. Computational and Structural Biotechnology Journal, 19:3187–3197, 2021. doi:https://doi.org/10.1016/j.csbj.2021.05.043.

• Piia Kokkonen, David Bednar, Gaspar Pinto, Zbynek Prokop, and Jiri Damborsky. Engineering Enzyme Access Tunnels. Biotechnology Advances, 37(6):107386, 2019. Microbial Engineering Biotechnologies. doi:https://doi.org/10.1016/j.biotechadv.2019.04.008.

• Gaspar P Pinto, Ondrej Vavra, Jiri Filipovic, Jan Stourac, David Bednar, and Jiri Damborsky. Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. Frontiers in Chemistry, 7:709, 2019. doi:https://doi: 10.3389/fchem.2019.00709.