Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Ondrej Vavra Ondrej Vávra

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. 114 2024 December 16 J. Cheminformatics 1 https://doi.org/10.1186/s13321-024-00907-z db/journals/jcheminf/jcheminf16.html#VavraTHSDMTB24 streams/journals/jcheminf

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. 2023 August 39 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btad443 db/journals/bioinformatics/bioinformatics39.html#VavraBSSFDMB23

Katarína Furmanová Ondrej Vávra Barbora Kozlíková Jirí Damborský Vojtech Vonásek David Bednar Jan Byska DockVis: Visual Analysis of Molecular Docking Trajectories. 452-464 2020 39 Comput. Graph. Forum 6 https://doi.org/10.1111/cgf.14048 db/journals/cgf/cgf39.html#FurmanovaVKDVBB20

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. 1625-1638 2020 17 IEEE ACM Trans. Comput. Biol. Bioinform. 5 https://doi.org/10.1109/TCBB.2019.2907492 https://www.wikidata.org/entity/Q92743995 db/journals/tcbb/tcbb17.html#FilipovicVPBMBM20

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. 4986-4993 2019 35 Bioinform. 23 https://doi.org/10.1093/bioinformatics/btz386 https://www.wikidata.org/entity/Q91937609 db/journals/bioinformatics/bioinformatics35.html#VavraFPBMBSMD19

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. W414-W422 2019 47 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkz378 https://www.wikidata.org/entity/Q92203022 db/journals/nar/nar47.html#StouracVKFPBDB19

Adam Jurcík Katarína Furmanová Jan Byska Vojtech Vonásek Ondrej Vávra Pavol Ulbrich Helwig Hauser Barbora Kozlíková Visual Analysis of Ligand Trajectories in Molecular Dynamics. 212-221 2019 PacificVis https://doi.org/10.1109/PacificVis.2019.00032 conf/apvis/2019 db/conf/apvis/pacificvis2019.html#JurcikFBVVUHK19

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. W479-W487 2016 44 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkw416 https://www.wikidata.org/entity/Q30388053 db/journals/nar/nar44.html#BendlSSVMBD16

Piia BartosPiia Kokkonen David Bednar Jaroslav Bendl Jakub Beránek Jan Brezovsky Jan Byska Jirí Damborský Jiri Filipovic Katarína Furmanová Farzan Haddadi Helwig Hauser Adam Jurcík Barbora Kozlíková Sérgio M. Marques Jan Martinovic Ludek Matyska Stanislav Mazurenko Milos Musil Gaspar R. P. Pinto Jan Plhak Eva Sebestova Jan Stourac Martin Surkovský Janet M. Thornton Jonathan D. Tyzack Pavol Ulbrich Vojtech Vonásek