Logik-Texte - kommentierte Auswahl zur Geschichte der modernen Logik (4. Aufl.). - Karel Berka; Lothar Kreiser (Akademie Verlag, 1986)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. - Karel Berka; Ondrej Hanák; David Sehnal; Pavel Banás; Veronika Navrátilová; Deepti Jaiswal Kundu; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2012)

MOLE 2.0: advanced approach for analysis of biomacromolecular channels. - David Sehnal; Radka Svobodová Vareková; Karel Berka; Lukás Pravda; Veronika Navrátilová; Pavel Banás; Crina-Maria Ionescu; Michal Otyepka; Jaroslav Koca (J. Cheminformatics, 2013)

Anatomy of enzyme channels. - Lukás Pravda; Karel Berka; Radka Svobodová Vareková; David Sehnal; Pavel Banás; Roman A. Laskowski; Jaroslav Koca; Michal Otyepka (BMC Bioinform., 2014)

PDBsum additions. - Tjaart A. P. de Beer; Karel Berka; Janet M. Thornton; Roman A. Laskowski (Nucleic Acids Res., 2014)

Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. - Veronika Navrátilová; Markéta Paloncýová; Michaela Kajsová; Karel Berka; Michal Otyepka (J. Chem. Inf. Model., 2015)

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

Ion Pathways in the Na+/K+-ATPase. - Petra Cechová; Karel Berka; Martin Kubala (J. Chem. Inf. Model., 2016)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 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)

ChannelsDB: database of biomacromolecular tunnels and pores. - Lukás Pravda; David Sehnal; Radka Svobodová Vareková; Veronika Navrátilová; Dominik Tousek; Karel Berka; Michal Otyepka; Jaroslav Koca (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)

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. - Tomás Racek; Ondrej Schindler; Dominik Tousek; Vladimír Horský; Karel Berka; Jaroslav Koca; Radka Svobodová Vareková (Nucleic Acids Res., 2020)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

2DProts: database of family-wide protein secondary structure diagrams. - Ivana Hutarová Vareková; Jan Hutar; Adam Midlik; Vladimír Horský; Eva Hladká; Radka Svobodová Vareková; Karel Berka (Bioinform., 2021)

Optimized SQE atomic charges for peptides accessible via a web application. - Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová Vareková (J. Cheminformatics, 2021)

Correction to: Optimized SQE atomic charges for peptides accessible via a web application. - Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová Vareková (J. Cheminformatics, 2021)

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)

CATH: increased structural coverage of functional space. - Ian Sillitoe; Nicola Bordin; Natalie L. Dawson; Vaishali P. Waman; Paul Ashford; Harry M. Scholes; Camilla S. M. Pang; Laurel Woodridge; Clemens Rauer; Neeladri Sen; Mahnaz Abbasian; Sean Le Cornu; et al. (Nucleic Acids Res., 2021)

OverProt: secondary structure consensus for protein families. - Adam Midlik; Ivana Hutarová Vareková; Jan Hutar; Aliaksei Chareshneu; Karel Berka; Radka Svobodová Vareková (Bioinform., 2022)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. - Aliaksei Chareshneu; Adam Midlik; Crina-Maria Ionescu; Alexander S. Rose; Vladimír Horský; Alessio Cantara; Radka Svobodová Vareková; Karel Berka; David Sehnal (Nucleic Acids Res., 2023)

αCharges: partial atomic charges for AlphaFold structures in high quality. - Ondrej Schindler; Karel Berka; Alessio Cantara; Ales Krenek; Dominik Tichý; Tomás Racek; Radka Svobodová Vareková (Nucleic Acids Res., 2023)