Karel Berka

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publications

Impact Indicators

citations

h-index

i10-index

+ 15 missing works

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List of works

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113 results (4 pages)

Foldify: Web Application for Protein Structure Prediction

Romana Ďuráčiová; Michaela Capandová; Karel Berka; Radka Svobodová; Terézia Slanináková; Kr (...)

Journal of Chemical Information and Modeling · 2026

Open Access

Publication

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

Císařová, Terezie; Balouch, Martin; Hanuš, Jaroslav; Kouba, Vojtech; Berka, Karel; Stepanek, Fra (...)

Physical Chemistry Chemical Physics · 2026

Open Access

Publication

The impact of FDM infill parameters on tensile mechanical properties

Jan Urbánek; Karel Berka

N/A · 2026

Unknown Access

Publication

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

Tomáš Raček; Martin Pilát; Ondřej Schindler; Gabriela Bučeková; Dominik Tichý; Karel Berka; (...)

Nucleic Acids Research · 2026

Open Access

Publication

PROPTIMUS LIVE: local constrained α-carbon optimization of proteins

Tomáš Svoboda; Michal Mikuš; Lukáš Bohuš; Tomáš Raček; Gabriela Bučeková; Dominik Tichý; (...)

Nucleic Acids Research · 2026

Open Access

Publication

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Ondřej Schindler; Tomáš Svoboda; Adrián Rošinec; Tomáš Raček; Gabriela Bučeková; Dominik T (...)

Nucleic Acids Research · 2025

Enzyme Structure and Function | Mass Spectrometry Techniques and Applications | Protein Structure and Dynamics |

Open Access

Publication

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

Tomáš Raček; Dušan Vel’ký; Gabriela Bučeková; Ondřej Schindler; Ivana Hutařová Vařekov� (...)

Bioinformatics · 2025

Advanced Proteomics Techniques and Applications | Mass Spectrometry Techniques and Applications | Enzyme Structure and Function |

Open Access

Publication

Gromacs MetaDump: a tool for extracting GROMACS simulation metadata

Adrián Rosinec; Terézia Slanináková; Tomás Pavlík; Róbert Randiak; Tomás Svoboda; Tomás Rac (...)

Journal of Cheminformatics · 2025

Research Data Management Practices | Scientific Computing and Data Management | Data Quality and Management |

Open Access

Publication

Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs

Klára Odehnalová; Martin Balouch; Kateřina Storchmannová; Eliška Petrová; Magdalena Konefał; (...)

Molecular Pharmaceutics · 2024

Lipid Membrane Structure and Behavior | Nanoparticle-Based Drug Delivery | Protein Interaction Studies and Fluorescence Analysis |

Conceptualization Resources Writing - original draft Writing - review and editing

Open Access

Publication

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; Hel (...)

Scientific Reports · 2024

SARS-CoV-2 and COVID-19 Research | SARS-CoV-2 detection and testing | COVID-19 Clinical Research Studies |

Open Access

Publication

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

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

Molecular Pharmaceutics · 2024

Microbial Natural Products and Biosynthesis | Synthetic Organic Chemistry Methods | Microbial bioremediation and biosurfactants |

Conceptualization Resources Supervision Writing - original draft Writing - review and editing

Open Access

Publication

Pathogenicity Patterns in Cytochrome P450 Family

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

Bioinformatics Advances · 2024

Biosimilars and Bioanalytical Methods | Pharmacogenetics and Drug Metabolism |

Open Access

Publication

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

Vonka, Petr; Rarova, Lucie; Bazgier, Vaclav; Tichy, Vlastimil; Kolarova, Tamara; Holcakova, Jitka; B (...)

The Journal of Steroid Biochemistry and Molecular Biology · 2023

Estrogen and related hormone effects | Bioactive Compounds and Antitumor Agents | Computational Drug Discovery Methods |

Methodology

Open Access

Publication

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

Martin Balouch; Kateřina Storchmannová; František Štěpánek; Karel Berka

Molecular Pharmaceutics · 2023

RNA Interference and Gene Delivery | Advanced biosensing and bioanalysis techniques | Nanoparticle-Based Drug Delivery |

Open Access

Publication

αCharges: partial atomic charges for AlphaFold structures in high quality

Ondrej Schindler; Karel Berka; Alessio Cantara; Ales Krenek; Dominik Tichý; Tomás Racek; Radka Svo (...)

Nucleic Acids Research · 2023

Enzyme Structure and Function | Protein Structure and Dynamics | Mass Spectrometry Techniques and Applications |

Open Access

Publication

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 (...)

Nucleic Acids Research · 2023

Cell Image Analysis Techniques | Genomics and Phylogenetic Studies | Advanced Electron Microscopy Techniques and Applications |

Open Access

Publication

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 V (...)

Bioorganic & Medicinal Chemistry · 2023

ATP Synthase and ATPases Research | Cancer therapeutics and mechanisms | Biochemical and Molecular Research |

Open Access

Publication

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; (...)

Nucleic Acids Research · 2023

Advanced Proteomics Techniques and Applications | Protein Structure and Dynamics | Enzyme Structure and Function |

Open Access

Publication

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

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

N/A · 2023

Machine Learning in Bioinformatics | Advanced Proteomics Techniques and Applications | Protein Structure and Dynamics |

Open Access

Publication

OverProt: secondary structure consensus for protein families

Adam Midlik; Ivana Hutarová Vareková; Jan Hutar; Aliaksei Chareshneu; Karel Berka; Radka Svobodov� (...)

Bioinformatics · 2022

Enzyme Structure and Function | Protein Structure and Dynamics | Advanced Proteomics Techniques and Applications |

Open Access

Publication

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; L (...)

European Journal of Medicinal Chemistry · 2022

Tuberculosis Research and Epidemiology | Biochemical and Molecular Research | Pneumocystis jirovecii pneumonia detection and treatment |

Restricted/Closed access

Publication

High-performance macromolecular data delivery and visualization for the web. Corrigendum

David Sehnal; Radka Svobodová; Karel Berka; Alexander S. Rose; Stephen K. Burley; Sameer Velankar; (...)

Acta Crystallographica Section D Structural Biology · 2021

Cell Image Analysis Techniques | Advanced Electron Microscopy Techniques and Applications | Advanced Biosensing Techniques and Applications |

Open Access

Publication

Optimized SQE atomic charges for peptides accessible via a web application

3 D

Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová (...)

Journal of Cheminformatics · 2021

Mass Spectrometry Techniques and Applications | Computational Drug Discovery Methods | Protein Structure and Dynamics |

Dataset 5

Open Access

Publication

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

3 D

David Sehnal; Sebastian Bittrich; Mandar S. Deshpande; Radka Svobodová Vareková; Karel Berka; Vác (...)

Nucleic Acids Research · 2021

Protein Structure and Dynamics | Enzyme Structure and Function | Genetics, Bioinformatics, and Biomedical Research |

Dataset 2

Open Access

Publication

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

Ivana Hutarová Vareková; Jan Hutar; Adam Midlik; Vladimír Horský; Eva Hladká; Radka Svobodová (...)

Bioinformatics · 2021

Enzyme Structure and Function | Protein Structure and Dynamics | Advanced Proteomics Techniques and Applications |

Open Access

Publication

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

Varadi, Mihaly; Anyango, Stephen; Armstrong, David; Berrisford, John; Choudhary, Preeti; Deshpande, (...)

Nucleic Acids Research · 2021

Enzyme Structure and Function | Protein Structure and Dynamics | Bioinformatics and Genomic Networks |

Open Access

Publication

ELIXIR and Toxicology: a community in development

Marvin Martens; Rob Stierum; Emma L. Schymanski; Chris T. Evelo; Reza Aalizadeh; Hristo Aladjov; Kas (...)

F1000Research · 2021

Metabolomics and Mass Spectrometry Studies | Computational Drug Discovery Methods | Health, Environment, Cognitive Aging |

Open Access

Publication

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 (...)

The FEBS Journal · 2021

Alzheimer's disease research and treatments | Cholinesterase and Neurodegenerative Diseases | Neuroscience and Neuropharmacology Research |

Open Access

Publication

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 · 2020

Lipid Membrane Structure and Behavior | Advanced Drug Delivery Systems | Nanoparticle-Based Drug Delivery |

Open Access

Publication

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

Veronika Šlachtová; Marek Šebela; Eveline Torfs; Lauren Oorts; Davie Cappoen; Karel Berka; Václa (...)

European Journal of Medicinal Chemistry · 2020

Tuberculosis Research and Epidemiology | Biochemical and Molecular Research | HIV/AIDS drug development and treatment |

Restricted/Closed access

Publication

Missing works

Mapping pathogenic patterns in membrane transporters from the GLUT transporter family

N/A · 2026

2025 Ownership and Maintenance of FAIRsharing record: MolMeDB

N/A · 2025

MOLEonline

N/A · 2025

2024 Ownership and Maintenance of FAIRsharing record: ValidatorDB

N/A · 2024

ChannelsDB 2.0

N/A · 2023

Dextrans as Permeation Markers and Carriers for Oral Transmucosal Drug Delivery

N/A · 2020

Molmedb - database about interactions of molecules with membranes

N/A · 2020

Pokusnice - hub chemických pokusů

N/A · 2019

Je strojové učení budoucností teoretické chemie?

N/A · 2018

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

N/A · 2018

Cytochrome P450 Oxidoreductase Simulations: Cofactors Movement and Structural Changes

N/A · 2015

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

N/A · 2015

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

N/A · 2013

Korespondenční seminář inspirovaný chemickou tematikou (KSICHT)

N/A · 2012

Structural properties of CYP2D6: Requirements for substrates and inhibitors

N/A · N/A

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List of works

Missing works

Karel Berka