HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. - Jaroslav Bendl; Jan Stourac; Eva Sebestova; Ondrej Vavra; Milos Musil; Jan Brezovsky; Jirí Damborský (Nucleic Acids Res., 2016)

Visual Analysis of Ligand Trajectories in Molecular Dynamics. - Adam Jurcík; Katarína Furmanová; Jan Byska; Vojtech Vonásek; Ondrej Vávra; Pavol Ulbrich; Helwig Hauser; Barbora Kozlíková (PacificVis, 2019)

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. - Ondrej Vavra; Jiri Filipovic; Jan Plhak; David Bednar; Sérgio M. Marques; Jan Brezovsky; Jan Stourac; Ludek Matyska; Jirí Damborský (Bioinform., 2019)

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. - Jan Stourac; Ondrej Vavra; Piia Kokkonen; Jiri Filipovic; Gaspar R. P. Pinto; Jan Brezovsky; Jirí Damborský; David Bednar (Nucleic Acids Res., 2019)

DockVis: Visual Analysis of Molecular Docking Trajectories. - Katarína Furmanová; Ondrej Vávra; Barbora Kozlíková; Jirí Damborský; Vojtech Vonásek; David Bednar; Jan Byska (Comput. Graph. Forum, 2020)

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. - Jiri Filipovic; Ondrej Vávra; Jan Plhak; David Bednar; Sérgio M. Marques; Jan Brezovsky; Ludek Matyska; Jirí Damborský (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. - Ondrej Vavra; Jakub Beránek; Jan Stourac; Martin Surkovský; Jiri Filipovic; Jirí Damborský; Jan Martinovic; David Bednar (Bioinform., 2023)

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. - Ondrej Vavra; Jonathan D. Tyzack; Farzan Haddadi; Jan Stourac; Jirí Damborský; Stanislav Mazurenko; Janet M. Thornton; David Bednar (J. Cheminformatics, 2024)