CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. - Barbora Kozlíková; Eva Sebestova; Vilém Sustr; Jan Brezovsky; Ondrej Strnad; Lukas Daniel; David Bednar; Antonín Pavelka; Martin Manak; Martin Bezdeka; Petr Benes; Matus Kotry; et al. (Bioinform., 2014)

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. - David Bednar; Koen Beerens; Eva Sebestova; Jaroslav Bendl; Sagar D. Khare; Radka Chaloupkova; Zbynek Prokop; Jan Brezovsky; David Baker 001; Jirí Damborský (PLoS Comput. Biol., 2015)

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)

CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. - Antonín Pavelka; Eva Sebestova; Barbora Kozlíková; Jan Brezovsky; Jirí Sochor; Jirí Damborský (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)