Výpis publikací

ŠPAČKOVÁ, Anna, Ondřej VÁVRA, Tomáš RAČEK, Václav BAZGIER, David SEHNAL, Jiří DAMBORSKÝ, Radka SVOBODOVÁ, David BEDNÁŘ a Karel BERKA. ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Research. Oxford University Press, 2024, roč. 52, D1, s. "D413"-"D418", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad1012.

VÁVRA, Ondřej, J. TYZACK, Faraneh HADDADI, Jan DVORSKÝ, Jiří DAMBORSKÝ, Stanislav MAZURENKO, J.M. THORNTON a David BEDNÁŘ. Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2024, roč. 16, č. 1, s. 1-14. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-024-00907-z.

ŠPAČKOVÁ, Anna, Ondřej VÁVRA, Tomáš RAČEK, Václav BAZGIER, David SEHNAL, Jiří DAMBORSKÝ, Radka SVOBODOVÁ a Karel BERKA. ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

VÁVRA, Ondřej, Jakub BERANEK, Jan ŠTOURAČ, Martin SURKOVSKY, Jiří FILIPOVIČ, Jiří DAMBORSKÝ, Jan MARTINOVIC a David BEDNÁŘ. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinformatics. Oxford: Oxford University Press, 2023, roč. 39, č. 8, s. 1-3. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btad443.

VÁVRA, Ondřej, Jiří DAMBORSKÝ a David BEDNÁŘ. Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies. Biotechnology Advances. Elsevier, 2022, roč. 60, November, s. 1-12. ISSN 0734-9750. Dostupné z: https://dx.doi.org/10.1016/j.biotechadv.2022.108009.

DAMBORSKÝ, Jiří, David BEDNÁŘ, Zbyněk PROKOP, Martin MAREK, Stanislav MAZURENKO, Jan ŠTOURAČ, Sérgio Manuel MARQUES, Gabriela Filipa FONSECA PINTO, Joan PLANAS IGLESIAS, Miloš MUSIL, Jiří HON, Ondřej VÁVRA, Rayyan Tariq KHAN, Jiří FILIPOVIČ a Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Sérgio Manuel MARQUES, Jiří FILIPOVIČ, David BEDNÁŘ a Jiří DAMBORSKÝ. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2021, roč. 19, May, s. 3187-3197. ISSN 2001-0370. Dostupné z: https://dx.doi.org/10.1016/j.csbj.2021.05.043.

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ a Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. Protein-Ligand Interactions and Drug Design. New York: Humana, New York, NY, 2021, s. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. Dostupné z: https://dx.doi.org/10.1007/978-1-0716-1209-5_6.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA a Jiří DAMBORSKÝ. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, 2020, roč. 17, č. 5, s. 1625-1638. ISSN 1545-5963. Dostupné z: https://dx.doi.org/10.1109/TCBB.2019.2907492.

FURMANOVÁ, Katarína, Ondřej VÁVRA, Barbora KOZLÍKOVÁ, Jiří DAMBORSKÝ, Vojtěch VONÁSEK, David BEDNÁŘ a Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum. Wiley-Blackwell, 2020, roč. 39, č. 6, s. 452-464. ISSN 0167-7055. Dostupné z: https://dx.doi.org/10.1111/cgf.14048.

ŠTOURAČ, Jan, Ondřej VÁVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Jan BREZOVSKÝ, Jiří DAMBORSKÝ a David BEDNÁŘ. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic acids research. Oxford: Oxford University Press, 2019, roč. 47, W1, s. 414-422. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkz378.

VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA a Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford: Oxford University Press, 2019, roč. 35, č. 23, s. 4986-4993. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btz386.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Jiří FILIPOVIČ, Jan ŠTOURAČ, David BEDNÁŘ a Jiří DAMBORSKÝ. Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. FRONTIERS IN CHEMISTRY. LAUSANNE: FRONTIERS MEDIA SA, 2019, roč. 7, OCT 29 2019, s. 1-14. ISSN 2296-2646. Dostupné z: https://dx.doi.org/10.3389/fchem.2019.00709.

JURČÍK, Adam, Katarína FURMANOVÁ, Jan BYŠKA, Vojtěch VONÁSEK, Ondřej VÁVRA, Pavol ULBRICH, Helwig HAUSER a Barbora KOZLÍKOVÁ. Visual Analysis of Ligand Trajectories in Molecular Dynamics. Online. In IEEE Pacific Visualization Symposium 2019. Bangkok, Thailand: IEEE, 2019, s. 212-221. ISBN 978-1-5386-9226-4. Dostupné z: https://dx.doi.org/10.1109/PacificVis.2019.00032.

BURYŠKA, Tomáš, Petra BABKOVÁ, Ondřej VÁVRA, Jiří DAMBORSKÝ a Zbyněk PROKOP. A Haloalkane Dehalogenase From a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, 2018, roč. 84, č. 2, s. 1-13. ISSN 0099-2240.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA a Jiří DAMBORSKÝ. CaverDock 1.0. 2017.

BENDL, J., Jan ŠTOURAČ, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ a Jiří DAMBORSKÝ. HotSpot Wizard 2.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research. Oxford University Press, 2016, roč. 44, W1, s. "W479"-"W487", 9 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkw416.

ŠTOURAČ, Jan, Jaroslav BENDL, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ a Jiří DAMBORSKÝ. HotSpot Wizard 2.0. 2015.