HotSpot Wizard: a web server for identification of hot spots in protein engineering. - Antonín Pavelka; Eva Chovancová; Jirí Damborský (Nucleic Acids Res., 2009)

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. - Eva Chovancová; Antonín Pavelka; Petr Benes; Ondrej Strnad; Jan Brezovsky; Barbora Kozlíková; Artur Góra; Vilém Sustr; Martin Klvana; Petr Medek; Lada Biedermannová; Jiri Sochor; et al. (PLoS Comput. Biol., 2012)

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)

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. - Jaroslav Bendl; Jan Stourac; Ondrej Salanda; Antonín Pavelka; Eric D. Wieben; Jaroslav Zendulka; Jan Brezovsky; Jirí Damborský (PLoS Comput. Biol., 2014)

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)

MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures. - Anthony R. Bradley; Alexander S. Rose; Antonín Pavelka; Yana Valasatava; Jose M. Duarte; Andreas Prlic; Peter W. Rose (PLoS Comput. Biol., 2017)

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. - Adam Jurcík; David Bednar; Jan Byska; Sérgio M. Marques; Katarína Furmanová; Lukas Daniel; Piia Kokkonen; Jan Brezovsky; Ondrej Strnad; Jan Stourac; Antonín Pavelka; Martin Manak; et al. (Bioinform., 2018)