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Prof. RNDr. Karel Berka, Ph.D.

Professor of Biomolecular Chemistry and Structural Biology

Leading research in computational chemistry, structural bioinformatics, and biomolecular simulation at Palacký University Olomouc. Creating advanced software and database platforms to decipher protein structures, channels, and small-molecule membrane transport.

Explore Scientific Tools Get in Touch

ChemData Lab ChemData Lab

Research group in computational chemistry, structural bioinformatics, and database development

Our Focus Náš výzkum

The ChemData Lab at Palacký University Olomouc bridges chemical data science with biology and physics. We develop state-of-the-art tools and databases to study biomolecular systems, focusing on:

Biomacromolecular Channels: Analyzing tunnels, pores, and gates in proteins (developers of MOLEonline and ChannelsDB).
Membrane Simulations: Studying small-molecule interactions with phospholipid bilayers (developers of MolMeDB).
Drug Design & Machine Learning: Applying deep learning to predict transport kinetics and molecular properties.

Announcements

🎓 Thesis Opportunities (2026/2027)

We offer Bachelor, Master, and Ph.D. thesis topics for motivated students interested in computational chemistry, deep learning (PyTorch), and web service engineering:

Predicting small-molecule membrane transport kinetics using deep learning.
Geometric modeling of biomacromolecular channel gates in the AlphaFold Database.
Development of interactive web visualizations for protein channel profiling.

Students gain hands-on experience with modern computational toolkits. Contact Karel Berka (karel.berka@upol.cz) or visit Office 3.009 for details.

TeachingVýuka

I am actively involved in teaching at the Department of Physical Chemistry. My primary courses focus on computational chemistry, biomolecular simulations, and drug design.

For detailed information and teaching materials, visit the KFC Teaching Portal.

View Duties on STAG

Fyzikální chemie 1 & KFC/UOFCH
Foundations of physical chemistry KFC/ADD & KFC/DD
Advanced and foundational Drug Design KFC/COM & KFC/SAM
Computational chemistry and molecular modeling KFC/STBI & KFC/BIN
Structural bioinformatics

OutreachPopularizace vědy

I am passionate about making science accessible. I frequently participate in science popularization events like KSICHT and Pokusnice, and contribute to educational videos.

Department YouTube

ELIXIR-CZ YouTube

Key Collaborators Klíčoví spolupracovníci

Working together with leading Czech and international research institutions

Prof. Jiří Vondrášek, CSc.

IOCB Prague

Researching protein structural properties, biomolecular simulations, and leading scientific nodes and data services within the ELIXIR-CZ national infrastructure.

Collaborations on

ELIXIR-CZ Infrastructure & Research - Biological Data Management
J. Chem. Theory Comput. (2010) - Energy Matrix of Side-Chain Interactions

Prof. RNDr. Radka Svobodová, Ph.D.

CEITEC / Masaryk University, Brno

Co-development of software tools and databases for protein channel detection and visualization, including the MOLEonline and ChannelsDB platforms.

Collaborations on

FŠ

Prof. Ing. František Štěpánek, Ph.D.

UCT Prague (University of Chemistry and Technology)

Collaborating on chemical robotics and mathematical modeling of structured particles, focusing on the simulation and design of microscopic drug delivery systems ("chemical robots").

Collaborations on

Mol. Pharmaceutics (2023) - Prodrug Design for Liposomes
Mol. Syst. Des. Eng. (2021) - Screening for Thermoresponsive Liposomes

RNDr. Marian Novotný, Ph.D.

Charles University, Prague

Joint development of the "Alphafoldology" concept and scientific collaboration on structural bioinformatics workflows and resource integration within ELIXIR CZ.

Collaborations on

Alphafoldology Catalog - Catalog of Structural Biology ML Tools
ELIXIR-CZ Infrastructure - Scientific Collaboration & Workshops

Dr. David Sehnal, Ph.D.

CEITEC / Masaryk University, Brno

Collaborator on high-performance 3D visualization systems, bringing MolStar (Mol*) integration to MOLEonline and structural bioinformatics portals.

Collaborations on

ELIXIR Europe & PDB Nodes

International Infrastructure

Integrating databases and calculation workflows with European platforms, ensuring structural biology data remains open and FAIR.

Collaborations on

Nucleic Acids Res. (2026) - Atomic Charge Calculator III
bioRxiv (2026) - Similarity Search in AlphaFold DB (AlphaFind v2)

Publications Publikace

Key scientific articles detailing our methodologies and tools

Article

PROPTIMUS LIVE: local constrained α-carbon optimization of proteins

Tomáš Svoboda, Michal Mikuš, Lukáš Bohuš, Tomáš Raček, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová, Ondřej Schindler

Nucleic Acids Research, 2026

AlphafoldologyVisualization

DOI Link
Article

Atomic Charge Calculator III: a modern platform for calculating partial atomic charges

Tomáš Raček, Martin Pilát, Ondřej Schindler, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová

Nucleic Acids Research, 2026

ToolsVisualizationChannels

DOI Link
Article

The impact of FDM infill parameters on tensile mechanical properties

Jan Urbánek, Karel Berka

Preprint / Manuscript, 2026

Other / General

DOI Link
Article

Dense yet flexible: how ladderanes found in anammox bacteria impact phospholipid membrane structure and properties

Terezie Císařová, Martin Balouch, Jaroslav Hanuš, Karel Berka, Vojtěch Kouba, František Štěpánek

Physical Chemistry Chemical Physics, 2026

ToolsLipid MembranesChannels

DOI Link
Article

MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update)

Tomáš Raček, Dušan Vel’ký, Gabriela Bučeková, Ondřej Schindler, Ivana Hutařová Vařeková, Anna Špačková, Václav Bazgier, Karel Berka, Radka Svobodová

Bioinformatics, 2025, 41(9)

ChannelsDatabasesSelectedToolsVisualization

DOI Link GitHub
Article

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Ondřej Schindler, Tomáš Svoboda, Adrián Rošinec, Tomáš Raček, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová

Nucleic Acids Research, 2025, 53(W1), W457-W462

DatabasesToolsVisualization

DOI Link
Article

Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021-2022)

Timotej Šúri, Lucie Pfeiferová, Matěj Bezdíček, Jan Svatoň, Vladimír Hampl, Karel Berka, Helena Jiřincová, Martina Lengerová, Martin Kolísko, Alexander Nagy, Ruth Tachezy, Jan Bartoš, Petr Brož, Vojtěch Bystrý, Martin Čech, Monika Čechová, Jiří Černý, Kateřina Chudějová, Iva Dolinová, Pavel Dřevínek, Edvard Ehler, Alena Fialová, Filip Franko, Viktor Furman, Zoltán Füssy, Markéta Gančarčíková, Alejandro Jiménez González, Marián Hajdúch, Blanka Hamplová, Václav Hejret, Petr Holub, Patrik Horna, Miluše Hradilová, Štěpánka Hrdá, Magdalena Jančářová, Michaela Jaroměřská, Eduard Ježo, Daniel Klimeš, Šárka Kocourková, Jana Kozáková, Martin Kracík, Jan Kubovčiak, Jana Fialová Kučerová, Jan Kynčl, Matej Lexa, Monika Liptáková, Jan Macháň, Barbora Macková, Marek Malý, Kateřina Matějová, Luděk Matyska, Hana Medová, Ondřej Moravčík, Jakub Mrázek, Serafim Nenarokov, Eva Niklova, Marian Novotný, Jaroslav Nunvář, Adam Obr, Hana Orlíková, Josef Pasulka, Helena Paszeková, Ingrid Poláková, Martin Pospíšek, Miroslav Ruda, Jana Šáchová, Eric Salomaki, Jeffrey Silberman, Radek Šíma, Branislav Šiška, Rastislav Slavkovský, Klára Sobotíková, Kateřina Štillerová, Viktor Stránecký, Alexander Tice, Boris Tichý, Markéta Tomková, Karolína Trachtová, Sebastian Cristian Treitli, Jaromíra Večeřová, David Vostřák, Jan Vrbský, Monika Wisniewska, Artsemi Yushkevich, Tomáš Zajíc, Martin Zmuda, Michal Kolář, Jan Pačes

Scientific Reports, 2025, 15(1)

Channels

DOI Link
Article

Gromacs MetaDump: a tool for extracting GROMACS simulation metadata

Adrián Rošinec, Terézia Slanináková, Tomáš Pavlík, Róbert Randiak, Tomáš Svoboda, Tomáš Raček, Gabriela Bučeková, Ondřej Schindler, Matej Antol, Aleš Křenek, Karel Berka, Radka Svobodová

Journal of Cheminformatics, 2025, 17(1)

ToolsChannels

DOI Link
Article

Pathogenicity patterns in cytochrome P450 family

Anna Špačková, Nina Kadášová, Ivana Hutařová Vařeková, Karel Berka

Bioinformatics Advances, 2025, 5(1)

ToolsDrug DesignChannels

DOI Link
Article

2025 Ownership and Maintenance of FAIRsharing record: MolMeDB

Karel Berka et al.

University of Oxford, UK – FAIRsharing, 2025

DatabasesLipid MembranesSelected

GitHub
Article

Meta-analysis of permeability literature data shows possibilities and limitations of popular methods

Kateřina Storchmannová, Martin Balouch, Jakub Juračka, František Štěpánek, Karel Berka

Preprint / Manuscript, 2024

Drug DesignChannelsDatabasesLipid MembranesSelected

DOI Link
Article

Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs

Klára Odehnalová, Martin Balouch, Kateřina Storchmannová, Eliška Petrová, Magdalena Konefał, Aleš Zadražil, Karel Berka, Jiří Brus, František Štěpánek

Molecular Pharmaceutics, 2024, 21(6), 2673-2683

Drug DesignLipid MembranesChannels

DOI Link
Article

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

Anna Špačková, Ondřej Vávra, Tomáš Raček, Václav Bazgier, David Sehnal, Jiří Damborský, Radka Svobodová, David Bednář, Karel Berka

Nucleic Acids Research, 2024, 52(D1), D413-D418

ChannelsDatabasesSelectedToolsAlphafoldology

DOI Link GitHub
Article

Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0

Anna Špačková, Václav Bazgier, Tomáš Raček, David Sehnal, Radka Svobodová, Karel Berka

Methods in Molecular Biology, 2024, 219-233

DatabasesChannelsVisualizationSelected

DOI Link GitHub
Article

2024 Ownership and Maintenance of FAIRsharing record: ValidatorDB

Karel Berka et al.

University of Oxford, UK – FAIRsharing, 2024

Databases
Article

ChannelsDB 2.0

Karel Berka et al.

Preprint / Manuscript, 2023

DatabasesChannelsSelected

GitHub
Article

Computational Prodrug Design Methodology for Liposome Formulability Enhancement of Small-Molecule APIs

Martin Balouch, Kateřina Storchmannová, František Štěpánek, Karel Berka

Molecular Pharmaceutics, 2023, 20(4), 2119-2127

Drug DesignLipid MembranesChannels

DOI Link
Article

Expanding the squaramide library as mycobacterial ATP synthase inhibitors: innovative synthetic pathway and biological evaluation

Jan Chasák, Lauren Oorts, Milan Dak, Veronika Šlachtová, Václav Bazgier, Karel Berka, Linda De Vooght, Natalia Smiejkowska, Kevin Van Calster, Laurence Van Moll, Davie Cappoen, Paul Cos, Lucie Brulíková

Bioorganic & Medicinal Chemistry, 2023, 95, 117504

Drug Design

DOI Link
Article

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 Rose, Vladimír Horský, Alessio Cantara, Radka Svobodová, Karel Berka, David Sehnal

Nucleic Acids Research, 2023, 51(W1), W326-W330

ToolsVisualizationChannels

DOI Link
Article

Small change – big consequence: The impact of C15-C16 double bond in a D‑ring of estrone on estrogen receptor activity

Petr Vonka, Lucie Rarova, Vaclav Bazgier, Vlastimil Tichy, Tamara Kolarova, Jitka Holcakova, Karel Berka, Miroslav Kvasnica, Jana Oklestkova, Eva Kudova, Miroslav Strnad, Roman Hrstka

The Journal of Steroid Biochemistry and Molecular Biology, 2023, 233, 106365

Channels

DOI Link
Article

αCharges: partial atomic charges for AlphaFold structures in high quality

Ondřej Schindler, Karel Berka, Alessio Cantara, Aleš Křenek, Dominik Tichý, Tomáš Raček, Radka Svobodová

Nucleic Acids Research, 2023, 51(W1), W11-W16

ToolsAlphafoldologyVisualizationChannels

DOI Link
Article

Antitumour drugs targeting tau R3 VQIVYK and Cys322 prevent seeding of endogenous tau aggregates by exogenous seeds

Narendran Annadurai, Lukáš Malina, Mario Salmona, Luisa Diomede, Antonio Bastone, Alfredo Cagnotto, Margherita Romeo, Martin Šrejber, Karel Berka, Michal Otyepka, Marián Hajdúch, Viswanath Das

The FEBS Journal, 2022, 289(7), 1929-1949

Drug Design

DOI Link
Article

Novel heterocyclic hydroxamates as inhibitors of the mycobacterial zinc metalloprotease Zmp1 to probe its mechanism of function

Milan Dak, Veronika Šlachtová, Marek Šebela, Václav Bazgier, Karel Berka, Natalia Smiejkowska, Lauren Oorts, Davie Cappoen, Lucie Brulíková

European Journal of Medicinal Chemistry, 2022, 244, 114831

Drug Design

DOI Link
Article

OverProt: secondary structure consensus for protein families

Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Aliaksei Chareshneu, Karel Berka, Radka Svobodová

Bioinformatics, 2022, 38(14), 3648-3650

Visualization

DOI Link
Article

PDBe-KB: collaboratively defining the biological context of structural data

Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D Levy, Nir London, Jose Ramon Macias, Madhusudhan M Srivatsan, 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, Paweł Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S Sorzano, Jan Stourac, Joanna I Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C E Tosatto, Wim Vranken, Mark N Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar

Nucleic Acids Research, 2022, 50(D1), D534-D542

DatabasesToolsChannels

DOI Link
Article

ELIXIR and Toxicology: a community in development

Marvin Martens, Rob Stierum, Emma L. Schymanski, Chris T. Evelo, Reza Aalizadeh, Hristo Aladjov, Kasia Arturi, Karine Audouze, Pavel Babica, Karel Berka, Jos Bessems, Ludek Blaha, Evan E. Bolton, Montserrat Cases, Dimitrios Ε. Damalas, Kirtan Dave, Marco Dilger, Thomas Exner, Daan P. Geerke, Roland Grafström, Alasdair Gray, John M. Hancock, Henner Hollert, Nina Jeliazkova, Danyel Jennen, Fabien Jourdan, Pascal Kahlem, Jana Klanova, Jos Kleinjans, Todor Kondic, Boï Kone, Iseult Lynch, Uko Maran, Sergio Martinez Cuesta, Hervé Ménager, Steffen Neumann, Penny Nymark, Herbert Oberacher, Noelia Ramirez, Sylvie Remy, Philippe Rocca-Serra, Reza M. Salek, Brett Sallach, Susanna-Assunta Sansone, Ferran Sanz, Haralambos Sarimveis, Sirarat Sarntivijai, Tobias Schulze, Jaroslav Slobodnik, Ola Spjuth, Jonathan Tedds, Nikolaos Thomaidis, Ralf J.M. Weber, Gerard J.P. van Westen, Craig E. Wheelock, Antony J. Williams, Hilda Witters, Barbara Zdrazil, Anže Županič, Egon L. Willighagen

F1000Research, 2021, 10, 1129

Drug Design

DOI Link
Article

2DProts: database of family-wide protein secondary structure diagrams

Ivana Hutařová Vařeková, Jan Hutař, Adam Midlik, Vladimír Horský, Eva Hladká, Radka Svobodová, Karel Berka

Bioinformatics, 2021, 37(23), 4599-4601

DatabasesToolsVisualization

DOI Link
Article

CATH: increased structural coverage of functional space

Ian Sillitoe, Nicola Bordin, Natalie 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 Hutařová Varekova, Radka Svobodova, Jon Lees, Christine A Orengo

Nucleic Acids Research, 2021, 49(D1), D266-D273

ToolsDrug Design

DOI Link
Article

In silico screening of drug candidates for thermoresponsive liposome formulations

Martin Balouch, Martin Šrejber, Marek Šoltys, Petra Janská, František Štěpánek, Karel Berka

Molecular Systems Design & Engineering, 2021, 6(5), 368-380

Drug DesignLipid MembranesChannels

DOI Link
Article

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose

Nucleic Acids Research, 2021, 49(W1), W431-W437

DatabasesToolsVisualizationChannels

DOI Link
Article

Optimized SQE atomic charges for peptides accessible via a web application

Ondřej Schindler, Tomáš Raček, Aleksandra Maršavelski, Jaroslav Koča, Karel Berka, Radka Svobodová

Journal of Cheminformatics, 2021, 13(1)

ToolsChannels

DOI Link
Article

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Adam Midlik, Veronika Navrátilová, Taraka Ramji Moturu, Jaroslav Koča, Radka Svobodová, Karel Berka

Scientific Reports, 2021, 11(1)

ToolsDrug Design

DOI Link
Article

Cytokinin fluoroprobe and receptor CRE1/AHK4 localize to both plasma membrane and endoplasmic reticulum

Karolina Kubiasová, Juan Carlos Montesinos, Olga Šamajová, Jaroslav Nisler, Václav Mik, Lucie Plíhalová, Ondřej Novák, Peter Marhavý, David Zalabák, Karel Berka, Karel Doležal, Petr Galuszka, Jozef Šamaj, Miroslav Strnad, Eva Benková, Ondřej Plíhal, Lukáš Spíchal

Nature Communications, 2020

Drug DesignLipid Membranes

DOI Link
Article

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

Tomáš Raček, Ondřej Schindler, Dominik Toušek, Vladimír Horský, Karel Berka, Jaroslav Koča, Radka Svobodová

Nucleic Acids Research, 2020, 48(W1), W591-W596

ToolsVisualizationChannels

DOI Link
Article

Dextrans as Permeation Markers and Carriers for Oral Transmucosal Drug Delivery

Karel Berka et al.

CHEMICKE LISTY, 2020

Drug DesignLipid Membranes
Article

High-performance macromolecular data delivery and visualization for the web

David Sehnal, Radka Svobodová, Karel Berka, Alexander S. Rose, Stephen K. Burley, Sameer Velankar, Jaroslav Koča

Acta Crystallographica Section D Structural Biology, 2020, 76(12), 1167-1173

ToolsVisualizationChannels

DOI Link
Article

Molmedb - database about interactions of molecules with membranes

Karel Berka et al.

Preprint / Manuscript, 2020

Lipid MembranesDatabasesChannelsSelected

GitHub
Article

Novel thiazolidinedione-hydroxamates as inhibitors of Mycobacterium tuberculosis virulence factor Zmp1

Veronika Šlachtová, Marek Šebela, Eveline Torfs, Lauren Oorts, Davie Cappoen, Karel Berka, Václav Bazgier, Lucie Brulíková

European Journal of Medicinal Chemistry, 2020, 185, 111812

Drug Design

DOI Link
Article

PDBe-KB: a community-driven resource for structural and functional annotations

Mihaly Varadi, John Berrisford, Mandar Deshpande, Sreenath S Nair, Aleksandras Gutmanas, David Armstrong, Lukas Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J Barton, Karel Berka, Tom Blundell, Neera Borkakoti, Jose Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivak, Manjeet Kumar, Emmanuel D Levy, F Madeira, M S Madhusudhan, Henry J Martell, Stuart MacGowan, Jake E McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro Radusky, Antonio Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodova, Jonathan Tyzack, Alfonso Valencia, Eloy Villasclaras Fernandez, Wim Vranken, Mark Wass, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar

Nucleic Acids Research, 2020, 48(D1), D344-D353

DatabasesToolsChannels

DOI Link
Article

Visualization and Analysis of Protein Structures with LiteMol Suite

David Sehnal, Radka Svobodová, Karel Berka, Lukáš Pravda, Adam Midlik, Jaroslav Koča

Methods in Molecular Biology, 2020, 1-13

VisualizationChannels

DOI Link
Article

In vitro testing of flash-frozen sublingual membranes for storage and reproducible permeability studies of macromolecular drugs from solution or nanofiber mats

Pavel Berka, Denisa Stránská, Vladimír Semecký, Karel Berka, Pavel Doležal

International Journal of Pharmaceutics, 2019, 572, 118711

Drug DesignLipid MembranesChannels

DOI Link
Article

MolMeDB: Molecules on Membranes Database

Jakub Juračka, Martin Šrejber, Michaela Melíková, Václav Bazgier, Karel Berka

Database, 2019, 2019

Drug DesignChannelsDatabasesLipid MembranesSelectedTools

DOI Link GitHub
Article

Automated Family-Wide Annotation of Secondary Structure Elements.

Adam Midlik, Ivana Hutařová Vařeková, Jan Hutař, Taraka Ramji Moturu, Veronika Navrátilová, Jaroslav Koča, Karel Berka, Radka Svobodová Vařeková

Methods in Molecular Biology, 2019, 47-71

Channels

DOI Link
Article

Synthesis of novel galeterone derivatives and evaluation of their in vitro activity against prostate cancer cell lines

Radek Jorda, Eva Řezníčková, Urszula Kiełczewska, Jadwiga Maj, Jacek W. Morzycki, Leszek Siergiejczyk, Václav Bazgier, Karel Berka, Lucie Rárová, Agnieszka Wojtkielewicz

European Journal of Medicinal Chemistry, 2019, 179, 483-492

Drug Design

DOI Link
Article

Pokusnice - hub chemických pokusů

Karel Berka et al.

Preprint / Manuscript, 2019

Education & Outreach
Article

ChannelsDB: database of biomacromolecular tunnels and pores

Lukáš Pravda, David Sehnal, Radka Svobodová Vařeková, Veronika Navrátilová, Dominik Toušek, Karel Berka, Michal Otyepka, Jaroslav Koča

Nucleic Acids Research, 2018, 46(D1), D399-D405

DatabasesChannels

DOI Link GitHub
Article

Channelsdb and Moleonline - Database and Tool for Analysis of Biomacromolecular Tunnels and Pores

Lukáš Pravda, David Sehnal, Karel Berka, Veronika Navrátilová, Dominik Toušěk, Václav Bazgier, Radka Svobodová Vařeková, Michal Otyepka, Jaroslav Koča

Biophysical Journal, 2018, 114(3), 342a-343a

DatabasesToolsChannelsSelected

DOI Link GitHub
Article

Discovery of N-2-(4-Amino-cyclohexyl)-9-cyclopentyl-N-6-(4-morpholin-4-ylmethyl-phenyl)-9H-purine-2,6-diamine as a Potent FLT3 Kinase Inhibitor for Acute Myeloid Leukemia with FLT3 Mutations

Tomáš Gucký, Eva Řezníčková, Tereza Radošová Muchová, Radek Jorda, Zuzana Klejová, Veronika Malínková, Karel Berka, Václav Bazgier, Haresh Ajani, Martin Lepšík, Vladimír Divoký, Vladimír Kryštof

Journal of Medicinal Chemistry, 2018, 61(9), 3855-3869

Drug Design

DOI Link
Article

Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite

David Sehnal, Mandar Deshpande, Alexander Rose, Lukas Pravda, Adam Midlik, Radka Svobodová Vařeková, Saqib Mir, Karel Berka, Sameer Velankar, Jaroslav Koca

Biophysical Journal, 2018, 114(3), 47a

VisualizationChannels

DOI Link
Article

Is Machine Learning the Future of Theoretical Chemistry?

Karel Berka et al.

Chemicke Listy, 2018

Other / General
Article

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

Lukáš Pravda, David Sehnal, Dominik Toušek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vařeková, Jaroslav Koča, Michal Otyepka

Nucleic Acids Research, 2018, 46(W1), W368-W373

ChannelsDatabasesLipid MembranesSelectedToolsVisualization

DOI Link
Article

Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners.

Martin Šrejber, Veronika Navrátilová, Markéta Paloncýová, Václav Bazgier, Karel Berka, Pavel Anzenbacher, Michal Otyepka

Journal of Inorganic Biochemistry, 2018, 183, 117-136

Drug DesignLipid MembranesChannels

DOI Link
Article

Protein structures - a challenge of data delivery, visualization and annotation

Karel Berka et al.

FEBS Open Bio, 2018

Visualization
Article

Secondary Structure Elements - Annotations and Schematic 2D Visualizations Stable for Individual Protein Families

Radka Svobodova Varekova, Adam Midlik, Ivana Hutarova Varekova, Jan Hutar, Veronika Navratilova, Jaroslav Koca, Karel Berka

Biophysical Journal, 2018, 114(3), 46a-47a

Visualization

DOI Link
Article

Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms.

B. Chantemargue, F. Di Meo, K. Berka, N. Picard, H. Arnion, M. Essig, P. Marquet, M. Otyepka, P. Trouillas

Pharmacological Research, 2018, 133, 318-327

ToolsLipid MembranesDrug DesignChannels

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Article

ALK5 kinase inhibitory activity and synthesis of 2,3,4-substituted 5,5-dimethyl-5,6-dihydro-4H-pyrrolo[1,2-b]pyrazoles.

Eva Řezníčková, Lukáš Tenora, Pavlína Pospíšilová, Juraj Galeta, Radek Jorda, Karel Berka, Pavel Majer, Milan Potáček, Vladimír Kryštof

European Journal of Medicinal Chemistry, 2017, 127, 632-642

Drug DesignChannels

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Article

Acetylated deoxycholic (DCA) and cholic (CA) acids are potent ligands of pregnane X (PXR) receptor.

Alejandro Carazo, Lucie Hyrsova, Jan Dusek, Hana Chodounska, Alzbeta Horvatova, Karel Berka, Vaclav Bazgier, Hongying Gan-Schreier, Waleé Chamulitrat, Eva Kudova, Petr Pavek

Toxicology Letters, 2017, 265, 86-96

Drug Design

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Article

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.

David Sehnal, Mandar Deshpande, Radka Svobodová Vařeková, Saqib Mir, Karel Berka, Adam Midlik, Lukáš Pravda, Sameer Velankar, Jaroslav Koča

Nature Methods, 2017, 14(12), 1121-1122

VisualizationChannels

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Article

Molecular insights into the role of a distal F240A mutation that alters CYP1A1 activity towards persistent organic pollutants.

Veronika Navrátilová, Markéta Paloncýová, Karel Berka, Shintaro Mise, Yuki Haga, Chisato Matsumura, Toshiyuki Sakaki, Hideyuki Inui, Michal Otyepka

Biochimica et Biophysica Acta (BBA) - General Subjects, 2017, 1861(11), 2852-2860

Drug DesignChannels

DOI Link
Article

RH421 binds into the ATP-binding site on the Na⁺/K⁺-ATPase.

Miroslav Huličiak, Václav Bazgier, Karel Berka, Martin Kubala

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2017, 1859(10), 2113-2122

ToolsLipid MembranesChannels

DOI Link
Article

Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution

David Sehnal, Mandar Deshpande, Radka Svobodova Varekova, Saquib Mir, Karel Berka, Adam Midlik, Lukas Pravda, Sameer Velankar, Jaroslav Koca

Biophysical Journal, 2017, 112(3), 178a

Channels

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Article

Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases

Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal, Michal Otyepka

SpringerBriefs in Biochemistry and Molecular Biology, 2017

DatabasesToolsDrug DesignChannels

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Article

Surface properties of MoS₂ probed by inverse gas chromatography and their impact on electrocatalytic properties.

Eva Otyepková, Petr Lazar, Jan Luxa, Karel Berka, Klára Čépe, Zdeněk Sofer, Martin Pumera, Michal Otyepka

Nanoscale, 2017, 9(48), 19236-19244

Tools

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Article

Arabidopsis histidine kinase 4 cytokinin receptor - The object of interest in ligand-receptor study

Lucia Gallová, Zoila Gándara Barreiro, Václav Bazgier, Karel Berka, Pavel Mazura, Lukáš Spíchal, Miroslav Strnad

New Biotechnology, 2016, 33, S165

Drug Design

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Article

Design, synthesis and biological activities of new brassinosteroid analogues with a phenyl group in the side chain.

M. Kvasnica, J. Oklestkova, V. Bazgier, L. Rárová, P. Korinkova, J. Mikulík, M. Budesinsky, T. Béres, K. Berka, Q. Lu, E. Russinova, M. Strnad

Organic & Biomolecular Chemistry, 2016, 14(37), 8691-8701

Drug DesignChannels

DOI Link
Article

Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4.

Veronika Navrátilová, Markéta Paloncýová, Karel Berka, Michal Otyepka

The Journal of Physical Chemistry B, 2016, 120(43), 11205-11213

ToolsLipid MembranesDrug DesignChannels

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Article

Exponential repulsion improves structural predictability of molecular docking.

Václav Bazgier, Karel Berka, Michal Otyepka, Pavel Banáš

Journal of Computational Chemistry, 2016, 37(28), 2485-2494

ToolsDrug DesignChannels

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Article

In silico pharmacology: Drug membrane partitioning and crossing.

Florent Di Meo, Gabin Fabre, Karel Berka, Tahani Ossman, Benjamin Chantemargue, Markéta Paloncýová, Pierre Marquet, Michal Otyepka, Patrick Trouillas

Pharmacological Research, 2016, 111, 471-486

Drug DesignLipid MembranesChannels

DOI Link
Article

Ion Pathways in the Na⁺/K⁺-ATPase.

Petra Čechová, Karel Berka, Martin Kubala

Journal of Chemical Information and Modeling, 2016, 56(12), 2434-2444

ToolsLipid MembranesChannels

DOI Link
Article

Novel thidiazuron-derived inhibitors of cytokinin oxidase/dehydrogenase.

Jaroslav Nisler, David Kopečný, Radka Končitíková, Marek Zatloukal, Václav Bazgier, Karel Berka, David Zalabák, Pierre Briozzo, Miroslav Strnad, Lukáš Spíchal

Plant Molecular Biology, 2016, 92(1-2), 235-248

Drug DesignChannels

DOI Link
Article

Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4.

Markéta Paloncýová, Veronika Navrátilová, Karel Berka, Alessandro Laio, Michal Otyepka

Journal of Chemical Theory and Computation, 2016, 12(4), 2101-2109

ToolsLipid MembranesDrug DesignChannels

DOI Link
Article

Synthesis, biological evaluation and molecular modeling of a novel series of 7-azaindole based tri-heterocyclic compounds as potent CDK2/Cyclin E inhibitors.

Christine B. Baltus, Radek Jorda, Christophe Marot, Karel Berka, Václav Bazgier, Vladimír Kryštof, Gildas Prié, Marie-Claude Viaud-Massuard

European Journal of Medicinal Chemistry, 2016, 108, 701-719

ToolsDrug DesignChannels

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Article

The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function.

Emily E. Scott, C. Roland Wolf, Michal Otyepka, Sara C. Humphreys, James R. Reed, Colin J. Henderson, Lesley A. McLaughlin, Markéta Paloncýová, Veronika Navrátilová, Karel Berka, Pavel Anzenbacher, Upendra P. Dahal, Carlo Barnaba, James A. Brozik, Jeffrey P. Jones, D. Fernando Estrada, Jennifer S. Laurence, Ji Won Park, Wayne L. Backes

Drug Metabolism and Disposition, 2016, 44(4), 576-590

ToolsLipid MembranesDrug DesignChannels

DOI Link
Article

2,6,9-Trisubstituted purines as CRK3 kinase inhibitors with antileishmanial activity in vitro.

Eva Řezníčková, Alexandr Popa, Tomáš Gucký, Marek Zatloukal, Libor Havlíček, Václav Bazgier, Karel Berka, Radek Jorda, Igor Popa, Abdelmajeed Nasereddin, Charles L. Jaffe, Vladimír Kryštof, Miroslav Strnad

Bioorganic & Medicinal Chemistry Letters, 2015, 25(11), 2298-2301

Drug DesignChannels

DOI Link
Article

Characterization of a Pyrazolo[4,3-d]pyrimidine Inhibitor of Cyclin-Dependent Kinases 2 and 5 and Aurora A With Pro-Apoptotic and Anti-Angiogenic Activity In Vitro.

Eva Řezníčková, Sabine Weitensteiner, Libor Havlíček, Radek Jorda, Tomáš Gucký, Karel Berka, Václav Bazgier, Stefan Zahler, Vladimír Kryštof, Miroslav Strnad

Chemical Biology & Drug Design, 2015, 86(6), 1528-1540

ToolsDrug Design

DOI Link
Article

Chrysin, baicalein and galangin are indirect activators of the human constitutive androstane receptor (CAR).

Alejandro Carazo Fernández, Tomas Smutny, Lucie Hyrsová, Karel Berka, Petr Pavek

Toxicology Letters, 2015, 233(2), 68-77

Drug Design

DOI Link
Article

Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase.

Žofie Sovová, Karel Berka, Michal Otyepka, Petr Jurečka

The Journal of Physical Chemistry B, 2015, 119(10), 3988-3998

Lipid Membranes

DOI Link
Article

Cytochrome P450 Oxidoreductase Simulations: Cofactors Movement and Structural Changes

Karel Berka et al.

Protein Science, 2015

ToolsDrug Design
Article

Effect of cholesterol on the structure of membrane-attached cytochrome P450 3A4.

Veronika Navrátilová, Markéta Paloncýová, Michaela Kajšová, Karel Berka, Michal Otyepka

Journal of Chemical Information and Modeling, 2015, 55(3), 628-635

ToolsLipid MembranesDrug DesignChannels

DOI Link
Article

Effect of Membrane Composition on the Structure of Membrane-Attached Cytochrome P450 3A4

Karel Berka et al.

Protein Science, 2015

Drug DesignLipid Membranes
Article

Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane.

Gabin Fabre, Anne Hänchen, Claude-Alain Calliste, Karel Berka, Srinivas Banala, Michal Otyepka, Roderich D. Süssmuth, Patrick Trouillas

Bioorganic & Medicinal Chemistry, 2015, 23(15), 4866-4870

Drug DesignLipid MembranesChannels

DOI Link
Article

Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails.

Markéta Paloncýová, Kateřina Vávrová, Žofie Sovová, Russell DeVane, Michal Otyepka, Karel Berka

The Journal of Physical Chemistry B, 2015, 119(30), 9811-9819

ToolsLipid MembranesDrug DesignChannels

DOI Link
Article

Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes.

Gabin Fabre, Imene Bayach, Karel Berka, Markéta Paloncýová, Marcelina Starok, Claire Rossi, Jean-Luc Duroux, Michal Otyepka, Patrick Trouillas

Chemical Communications, 2015, 51(36), 7713-7716

Lipid MembranesChannels

DOI Link
Article

Tools and data services registry: a community effort to document bioinformatics resources.

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan 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 Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić, Rune Møllegaard Friborg, Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen, Søren Brunak

Nucleic Acids Research, 2015, 44(D1), D38-D47

DatabasesTools

DOI Link
Article

Amphiphilic drug-like molecules accumulate in a membrane below the head group region.

Markéta Paloncýová, Russell DeVane, Bruce Murch, Karel Berka, Michal Otyepka

The Journal of Physical Chemistry B, 2014, 118(4), 1030-1039

Drug DesignLipid MembranesChannels

DOI Link
Article

Anatomy of enzyme channels.

Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča, Michal Otyepka

BMC Bioinformatics, 2014, 15(1)

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Article

Benchmarking of Force Fields for Molecule-Membrane Interactions.

Markéta Paloncýová, Gabin Fabre, Russell H. DeVane, Patrick Trouillas, Karel Berka, Michal Otyepka

Journal of Chemical Theory and Computation, 2014, 10(9), 4143-4151

ToolsLipid MembranesDrug DesignChannels

DOI Link
Article

Biological activities of new monohydroxylated brassinosteroid analogues with a carboxylic group in the side chain.

Miroslav Kvasnica, Jana Oklestkova, Vaclav Bazgier, Lucie Rarova, Karel Berka, Miroslav Strnad

Steroids, 2014, 85, 58-64

Drug Design

DOI Link
Article

LiteMol: web-based 3D visualization of macromolecular structure data

Karel Berka et al.

Acta Crystallographica Section A: Foundations and Advances, 2014

VisualizationChannels
Article

PDBsum additions.

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

Nucleic Acids Research, 2014, 42(D1), D292-D296

ToolsChannels

DOI Link
Article

Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO- induced red-shift emission

Katerina Hola, Athanasios B. Bourlinos, Ondrej Kozak, Karel Berka, Karolina M. Siskova, Marketa Havrdova, Jiri Tucek, Klara Safarova, Michal Otyepka, Emmanuel P. Giannelis, Radek Zboril

Carbon, 2014, 70, 279-286

Other / General

DOI Link
Article

Rationalization of reduced penetration of drugs through ceramide gel phase membrane.

Markéta Paloncýová, Russell H. DeVane, Bruce P. Murch, Karel Berka, Michal Otyepka

Langmuir, 2014, 30(46), 13942-13948

Drug DesignLipid MembranesChannels

DOI Link
Article

Structural properties of CYP2D6: Requirements for substrates and inhibitors

Eva Anzenbacherová, Karel Berka, Michal Otyepka, Pavel Anzenbacher

CYP2D6: Genetics, Pharmacology and Clinical Relevance, 2014, 68-78

ToolsDrug Design

DOI Link
Article

Synthesis and kinase inhibitory activity of new sulfonamide derivatives of pyrazolo[4,3-e][1,2,4]triazines.

Mariusz Mojzych, Veronika Šubertová, Anna Bielawska, Krzysztof Bielawski, Václav Bazgier, Karel Berka, Tomáš Gucký, Emilia Fornal, Vladimír Kryštof

European Journal of Medicinal Chemistry, 2014, 78, 217-224

Drug Design

DOI Link
Article

A novel series of highly potent 2,6,9-trisubstituted purine cyclin-dependent kinase inhibitors.

Tomáš Gucký, Radek Jorda, Marek Zatloukal, Václav Bazgier, Karel Berka, Eva Řezníčková, Tibor Béres, Miroslav Strnad, Vladimír Kryštof

Journal of Medicinal Chemistry, 2013, 56(15), 6234-6247

Drug Design

DOI Link
Article

Antiallergic effects of pigments isolated from green sea urchin (Strongylocentrotus droebachiensis) shells.

Olga Pozharitskaya, Alexander Shikov, Marina Makarova, Svetlana Ivanova, Vera Kosman, Valery Makarov, Václav Bazgier, Karel Berka, Michal Otyepka, Jitka Ulrichová

Planta Medica, 2013, 79(18), 1698-1704

Drug DesignChannels

DOI Link
Article

Behavior of human cytochromes P450 on lipid membranes.

Karel Berka, Markéta Paloncýová, Pavel Anzenbacher, Michal Otyepka

The Journal of Physical Chemistry B, 2013, 117(39), 11556-11564

Drug DesignLipid MembranesChannels

DOI Link
Article

Fluorone dyes binding to extracellular and cytoplasmic domains of Na, K-ATPase

Karel Berka et al.

The FEBS Journal, 2013

Other / General
Article

Fluorone dyes have binding sites on both cytoplasmic and extracellular domains of Na,K-ATPase.

Marika Havlíková, Miroslav Huličiak, Václav Bazgier, Karel Berka, Martin Kubala

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2013, 1828(2), 568-576

ToolsLipid MembranesChannels

DOI Link
Article

Lipid bilayer membrane affinity rationalizes inhibition of lipid peroxidation by a natural lignan antioxidant.

Pavlína Podloucká, Karel Berka, Gabin Fabre, Markéta Paloncýová, Jean-Luc Duroux, Michal Otyepka, Patrick Trouillas

The Journal of Physical Chemistry B, 2013, 117(17), 5043-5049

Drug DesignLipid Membranes

DOI Link
Article

MOLE 2.0: advanced approach for analysis of biomacromolecular channels.

David Sehnal, Radka Svobodová Vařeková, Karel Berka, Lukáš Pravda, Veronika Navrátilová, Pavel Banáš, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koča

Journal of Cheminformatics, 2013, 5(1)

ToolsDrug DesignChannels

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Article

Molecular insight into affinities of drugs and their metabolites to lipid bilayers.

Markéta Paloncýová, Karel Berka, Michal Otyepka

The Journal of Physical Chemistry B, 2013, 117(8), 2403-2410

Drug DesignLipid MembranesChannels

DOI Link
Article

Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site.

Karel Berka, Eva Anzenbacherová, Tereza Hendrychová, Reinhard Lange, Vlastimil Mašek, Pavel Anzenbacher, Michal Otyepka

Journal of Inorganic Biochemistry, 2012, 110, 46-50

Drug DesignChannels

DOI Link
Article

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer.

Markéta Paloncýová, Karel Berka, Michal Otyepka

Journal of Chemical Theory and Computation, 2012, 8(4), 1200-1211

ToolsLipid MembranesDrug DesignChannels

DOI Link
Article

Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations

Karel Berka et al.

Current Drug Metabolism, 2012

Drug DesignChannels
Article

Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?

Michal Otyepka, Karel Berka, Pavel Anzenbacher

Current Drug Metabolism, 2012, 13(2), 130-142

ToolsDrug DesignChannels

DOI Link
Article

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels.

K. Berka, O. Hanak, D. Sehnal, P. Banas, V. Navratilova, D. Jaiswal, C.-M. Ionescu, R. Svobodova Varekova, J. Koca, M. Otyepka

Nucleic Acids Research, 2012, 40(W1), W222-W227

ChannelsSelected

DOI Link
Article

Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition.

Pavlína Košinová, Karel Berka, Michael Wykes, Michal Otyepka, Patrick Trouillas

The Journal of Physical Chemistry B, 2012, 116(4), 1309-1318

ToolsLipid MembranesChannels

DOI Link
Article

Korespondenční seminář inspirovaný chemickou tematikou (KSICHT)

Karel Berka et al.

Chemické listy, 2012

Education & Outreach
Article

Insenstivity to Close Contacts and Inability to Predict Protein Foldability

Karel Berka et al.

Journal of Biomolecular Structure & Dynamics, 2011

Channels
Article

Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site.

Karel Berka, Tereza Hendrychová, Pavel Anzenbacher, Michal Otyepka

The Journal of Physical Chemistry A, 2011, 115(41), 11248-11255

Drug DesignLipid MembranesChannels

DOI Link
Article

Novel covalent bond in proteins: calculations on model systems question the bond stability.

Milan Ončák, Karel Berka, Petr Slavíček

ChemPhysChem, 2011, 12(17), 3449-3457

Tools

DOI Link
Article

Energy matrix of structurally important side-chain/side-chain interactions in proteins

Karel Berka et al.

Journal of Chemical Theory and Computation, 2010

Tools
Article

On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes

Karel Berka et al.

ChemPhysChem, 2010

Other / General
Article

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.

Karel Berka, Roman Laskowski, Kevin E. Riley, Pavel Hobza, Jiří Vondrášek

Journal of Chemical Theory and Computation, 2009, 5(4), 982-992

ToolsChannels

DOI Link
Article

Analysis of energy stabilization inside the hydrophobic core of rubredoxin.

Karel Berka, Pavel Hobza, Jiří Vondrášek

ChemPhysChem, 2009, 10(3), 543-548

Tools

DOI Link
Article

The stabilization energy of the Glu-Lys salt bridge in the protein/water environment: Correlated quantum chemical ab initio, DFT and empirical potential studies

Jan Řezáč, Karel Berka, Dominik Horinek, Pavel Hobza, Jiří Vondrášek

Collection of Czechoslovak Chemical Communications, 2008, 73(6-7), 921-936

Other / General

DOI Link
Article

Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane.

Lada Biedermannova, Kevin E. Riley, Karel Berka, Pavel Hobza, Jiri Vondrasek

Physical Chemistry Chemical Physics, 2008, 10(42), 6350

Tools

DOI Link
Article

Quantum chemical benchmark energy and geometry database for molecular clusters and complex molecular systems (www.begdb.com): A users manual and examples

Jan Řezáč, Petr Jurečka, Kevin E. Riley, Jiří Černý, Haydee Valdes, Kristýna Pluháčková, Karel Berka, Tomáš Řezáč, Michal Pitoňák, Jiří Vondrášek, Pavel Hobza

Collection of Czechoslovak Chemical Communications, 2008, 73(10), 1261-1270

DatabasesChannels

DOI Link
Article

Ligand binding to the human MT2 melatonin receptor: the role of residues in transmembrane domains 3, 6, and 7.

Petr Mazna, Karel Berka, Irena Jelinkova, Ales Balik, Petr Svoboda, Veronika Obsilova, Tomas Obsil, Jan Teisinger

Biochemical and Biophysical Research Communications, 2005, 332(3), 726-734

Lipid Membranes

DOI Link
Article

Molecular modeling of human MT2 melatonin receptor: the role of Val204, Leu272 and Tyr298 in ligand binding.

Petr Mazna, Veronika Obsilova, Irena Jelinkova, Ales Balik, Karel Berka, Zofie Sovova, Rüdiger Ettrich, Petr Svoboda, Tomas Obsil, Jan Teisinger

Journal of Neurochemistry, 2004, 91(4), 836-842

Lipid MembranesChannels

DOI Link
Article

Molecular modeling of human MT2 melatonin receptor: the role of Val204, Leu272 and Tyr298 in ligand binding (vol 91, pg 836, 2004)

Petr Mazna, Veronika Obsilova, Irena Jelinkova, Ales Balik, Karel Berka, Zofie Sovova, Rüdiger Ettrich, Petr Svoboda, Tomas Obsil, Jan Teisinger

Journal of Neurochemistry, 2004, 91(6), 1505-1505

Channels

DOI Link
Article

Detection of Channels

Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal, Michal Otyepka

SpringerBriefs in Biochemistry and Molecular Biology, 59-69

Channels

DOI Link
Article

Structural Bioinformatics Databases of General Use

Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal, Michal Otyepka

SpringerBriefs in Biochemistry and Molecular Biology, 17-30

DatabasesToolsChannels

DOI Link

Get in TouchKontakt

Reach out for academic collaborations, research queries, or student projects

Office & Laboratory Address Adresa kanceláře a laboratoře

Department of Physical Chemistry

Faculty of Science, Palacký University Olomouc

17. listopadu 12, 771 46 Olomouc, Czech Republic

Room 3.009

karel.berka@upol.cz

+420 585 634 756

Send a Message Napište mi zprávu

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Prof. RNDr. Karel Berka, Ph.D.

ChemData Lab ChemData Lab

Our Focus Náš výzkum

🎓 Thesis Opportunities (2026/2027) 🎓 Témata vysokoškolských prací (2026/2027)

TeachingVýuka

OutreachPopularizace vědy

Key Collaborators Klíčoví spolupracovníci

Prof. Jiří Vondrášek, CSc.

Prof. RNDr. Radka Svobodová, Ph.D.

Prof. Ing. František Štěpánek, Ph.D.

RNDr. Marian Novotný, Ph.D.

Dr. David Sehnal, Ph.D.

ELIXIR Europe & PDB Nodes

Publications Publikace

PROPTIMUS LIVE: local constrained α-carbon optimization of proteins

Atomic Charge Calculator III: a modern platform for calculating partial atomic charges

The impact of FDM infill parameters on tensile mechanical properties

Dense yet flexible: how ladderanes found in anammox bacteria impact phospholipid membrane structure and properties

MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update)

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021-2022)

Gromacs MetaDump: a tool for extracting GROMACS simulation metadata

Pathogenicity patterns in cytochrome P450 family

2025 Ownership and Maintenance of FAIRsharing record: MolMeDB

Meta-analysis of permeability literature data shows possibilities and limitations of popular methods

Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0

2024 Ownership and Maintenance of FAIRsharing record: ValidatorDB

ChannelsDB 2.0

Computational Prodrug Design Methodology for Liposome Formulability Enhancement of Small-Molecule APIs

Expanding the squaramide library as mycobacterial ATP synthase inhibitors: innovative synthetic pathway and biological evaluation

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations

Small change – big consequence: The impact of C15-C16 double bond in a D‑ring of estrone on estrogen receptor activity

αCharges: partial atomic charges for AlphaFold structures in high quality

Antitumour drugs targeting tau R3 VQIVYK and Cys322 prevent seeding of endogenous tau aggregates by exogenous seeds

Novel heterocyclic hydroxamates as inhibitors of the mycobacterial zinc metalloprotease Zmp1 to probe its mechanism of function

OverProt: secondary structure consensus for protein families

PDBe-KB: collaboratively defining the biological context of structural data

ELIXIR and Toxicology: a community in development

2DProts: database of family-wide protein secondary structure diagrams

CATH: increased structural coverage of functional space

In silico screening of drug candidates for thermoresponsive liposome formulations

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Optimized SQE atomic charges for peptides accessible via a web application

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Cytokinin fluoroprobe and receptor CRE1/AHK4 localize to both plasma membrane and endoplasmic reticulum

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

Dextrans as Permeation Markers and Carriers for Oral Transmucosal Drug Delivery

High-performance macromolecular data delivery and visualization for the web

Molmedb - database about interactions of molecules with membranes

Novel thiazolidinedione-hydroxamates as inhibitors of Mycobacterium tuberculosis virulence factor Zmp1

PDBe-KB: a community-driven resource for structural and functional annotations

Visualization and Analysis of Protein Structures with LiteMol Suite

In vitro testing of flash-frozen sublingual membranes for storage and reproducible permeability studies of macromolecular drugs from solution or nanofiber mats

MolMeDB: Molecules on Membranes Database

Automated Family-Wide Annotation of Secondary Structure Elements.

Synthesis of novel galeterone derivatives and evaluation of their in vitro activity against prostate cancer cell lines

Pokusnice - hub chemických pokusů

ChannelsDB: database of biomacromolecular tunnels and pores

Channelsdb and Moleonline - Database and Tool for Analysis of Biomacromolecular Tunnels and Pores

Discovery of N-2-(4-Amino-cyclohexyl)-9-cyclopentyl-N-6-(4-morpholin-4-ylmethyl-phenyl)-9H-purine-2,6-diamine as a Potent FLT3 Kinase Inhibitor for Acute Myeloid Leukemia with FLT3 Mutations

Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite

Is Machine Learning the Future of Theoretical Chemistry?

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners.

Protein structures - a challenge of data delivery, visualization and annotation

Secondary Structure Elements - Annotations and Schematic 2D Visualizations Stable for Individual Protein Families

Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms.

ALK5 kinase inhibitory activity and synthesis of 2,3,4-substituted 5,5-dimethyl-5,6-dihydro-4H-pyrrolo[1,2-b]pyrazoles.

Acetylated deoxycholic (DCA) and cholic (CA) acids are potent ligands of pregnane X (PXR) receptor.

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data.

Molecular insights into the role of a distal F240A mutation that alters CYP1A1 activity towards persistent organic pollutants.

RH421 binds into the ATP-binding site on the Na+/K+-ATPase.

Real-Time Interactive Visualisation of Large Macromolecular Assemblies and Molecular Machines at Atomic Resolution

Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases

Surface properties of MoS2 probed by inverse gas chromatography and their impact on electrocatalytic properties.

Arabidopsis histidine kinase 4 cytokinin receptor - The object of interest in ligand-receptor study

Design, synthesis and biological activities of new brassinosteroid analogues with a phenyl group in the side chain.

Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4.

🎓 Thesis Opportunities (2026/2027)

RH421 binds into the ATP-binding site on the Na⁺/K⁺-ATPase.

Surface properties of MoS₂ probed by inverse gas chromatography and their impact on electrocatalytic properties.

Ion Pathways in the Na⁺/K⁺-ATPase.