Exponential repulsion improves structural predictability of molecular docking. - Václav Bazgier; Karel Berka; Michal Otyepka; Pavel Banás (J. Comput. Chem., 2016)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). - Lukás Pravda; David Sehnal; Dominik Tousek; Veronika Navrátilová; Václav Bazgier; Karel Berka; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2018)

MolMeDB: Molecules on Membranes Database. - Jakub Juracka; Martin Srejber; Michaela Melikova; Václav Bazgier; Karel Berka (Database J. Biol. Databases Curation, 2019)

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. - David Sehnal; Sebastian Bittrich; Mandar S. Deshpande; Radka Svobodová Vareková; Karel Berka; Václav Bazgier; Sameer Velankar; Stephen K. Burley; Jaroslav Koca; Alexander S. Rose (Nucleic Acids Res., 2021)