Výpis publikací

MARQUES, Sérgio Manuel; Simeon BORKO; Ondřej VÁVRA; Jan DVORSKÝ; Petr KOHOUT; Petr KABOUREK; Lukáš HEJTMÁNEK; Jiří DAMBORSKÝ a David BEDNÁŘ. Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins. Nucleic Acids Research. Oxford: Oxford University Press, 2025, roč. 53, May 2025, s. "W132"-"W142", 11 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaf399.

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.

HADDADI, Faraneh; Ondřej VÁVRA; David BEDNÁŘ; Stanislav MAZURENKO a Jiří DAMBORSKÝ. Klasifikátor vazebných kapes v proteinech založený na strojovém učení. 2024.

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.