Karel Berka

Palacký University Olomouc — Czech Republic

Biochemistry, Genetics and Molecular Biology · Life Sciences

39h-index6.9kcitations229works0.92yr avg
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Research Topics

Protein Structure and Dynamics(35), Computational Drug Discovery Methods(24), Enzyme Structure and Function(23), Pharmacogenetics and Drug Metabolism(22), Lipid Membrane Structure and Behavior(14)

Publications229 total

MolMeDB RDF
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
MolMeDB RDF
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata
Zenodo (CERN European Organization for Nuclear Research)·2026Open Access
METRICS - Monitoring of Key Performance Indicators for ELIXIR Services
2026Open Access
METRICS - Monitoring of Key Performance Indicators for ELIXIR Services
BioHackrXiv (OSF Preprints)·2026Open Access
METRICS - Monitoring of Key Performance Indicators for ELIXIR Services
BioHackrXiv (OSF Preprints)·2026Open Access
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
Journal of Cheminformatics·2025Open Access
MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update)
Bioinformatics·2025· 1 citedOpen Access
Review for "AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold-Based Kinase Structures"
2025
Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021–2022)
Scientific Reports·2025Open Access
PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures
Nucleic Acids Research·2025· 1 citedOpen Access
Review for "AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold-Based Kinase Structures"
2025
Pathogenicity Patterns in Cytochrome P450 Family
2025Open Access
Meta-Analysis of Permeability Literature Data Shows Possibilities and Limitations of Popular Methods
Molecular Pharmaceutics·2025· 10 citedOpen Access
ELIXIR CZ Structural bioinformatics
Faculty of 1000 Research Ltd·2025Open Access
ELIXIR CZ: Chemical Biology
Faculty of 1000 Research Ltd·2025Open Access
Pathogenicity patterns in cytochrome P450 family
Bioinformatics Advances·2024Open Access
Meta-analysis of permeability literature data shows possibilities and limitations of popular methods
2024· 1 citedOpen Access
Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs
Molecular Pharmaceutics·2024· 3 citedOpen Access
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Frequent Co-authors

Michal Otyepka(26), Markéta Paloncýová(14), Radka Svobodová Vařeková(12), Václav Bazgier(10), Veronika Navrátilová(10), Jaroslav Koča(9), David Sehnal(7), Lukáš Pravda(7), Pavel Anzenbacher(6), Pavel Hobza(5), Mandar Deshpande(4), Sameer Velankar(4), Roman A. Laskowski(4), Jiřı́ Vondrášek(4), Patrick Trouillas(4), Russell DeVane(4), Vladimı́r Kryštof(4), Christine Orengo(3), Dominik Toušěk(3), Pavel Banáš(3)