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2020 – today
- 2024
[j7]Ondrej Vavra, Jonathan D. Tyzack, Farzan Haddadi, Jan Stourac, Jirí Damborský, Stanislav Mazurenko, Janet M. Thornton, David Bednar:
Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. J. Cheminformatics 16(1): 114 (2024)- 2023
- [j6]Ondrej Vavra, Jakub Beránek
, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar:
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinform. 39(8) (2023) - 2020
- [j5]Katarína Furmanová, Ondrej Vávra, Barbora Kozlíková, Jirí Damborský, Vojtech Vonásek, David Bednar, Jan Byska:
DockVis: Visual Analysis of Molecular Docking Trajectories. Comput. Graph. Forum 39(6): 452-464 (2020) - [j4]Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský:
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE ACM Trans. Comput. Biol. Bioinform. 17(5): 1625-1638 (2020)
2010 – 2019
- 2019
- [j3]Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský:
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinform. 35(23): 4986-4993 (2019) - [j2]Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar:
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res. 47(Webserver-Issue): W414-W422 (2019) - [c1]Adam Jurcík, Katarína Furmanová, Jan Byska, Vojtech Vonásek, Ondrej Vávra, Pavol Ulbrich, Helwig Hauser, Barbora Kozlíková:
Visual Analysis of Ligand Trajectories in Molecular Dynamics. PacificVis 2019: 212-221 - 2016
- [j1]Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský:
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Res. 44(Webserver-Issue): W479-W487 (2016)
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