Karel Berka

According to our database, Karel Berka authored at least 23 papers between 1986 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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., July, 2023

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., July, 2023

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, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar

Nucleic Acids Res., 2022

OverProt: secondary structure consensus for protein families.

Adam Midlik, Ivana Hutarová Vareková, Jan Hutar, Aliaksei Chareshneu, Karel Berka, Radka Svobodová Vareková

Bioinform., 2022

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, Su Datt Lam, Karel Berka, Ivana Hutarová Vareková, Radka Svobodová Vareková, Jonathan G. Lees, Christine A. Orengo

Nucleic Acids Res., 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

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

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

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

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, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar

Nucleic Acids Res., 2020

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

2019

MolMeDB: Molecules on Membranes Database.

Jakub Juracka, Martin Srejber, Michaela Melikova, Václav Bazgier, Karel Berka

Database J. Biol. Databases Curation, 2019

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

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

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, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak

Nucleic Acids Res., 2016

Ion Pathways in the Na⁺/K⁺-ATPase.

Petra Cechová, Karel Berka, Martin Kubala

J. Chem. Inf. Model., 2016

Exponential repulsion improves structural predictability of molecular docking.

Václav Bazgier, Karel Berka, Michal Otyepka, Pavel Banás

J. Comput. Chem., 2016

2015

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

2014

PDBsum additions.

Tjaart A. P. de Beer, Karel Berka, Janet M. Thornton, Roman A. Laskowski

Nucleic Acids Res., 2014

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

2013

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

2012

MOLE<i>online</i> 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

1986

Logik-Texte - kommentierte Auswahl zur Geschichte der modernen Logik (4. Aufl.).

Karel Berka, Lothar Kreiser

Akademie Verlag, 1986