Karel Berka

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Associate Professor

Palacký University, Olomouc

Czech Republic

Research Interests

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About

Karel Berka is an Associate Professor at Palacký University, Olomouc, Czech Republic. His research focuses on computational biology, particularly in areas such as protein channels, tunnels, and pores analysis, as well as drug interactions and prodrug design methodologies. Recent publications include works on MOLEonline, ChannelsDB, and the development of innovative synthetic pathways for biological evaluation.

Recent Grants

Grant: Close

Czech National Infrastructure for Biological data (acronym ELIXIR CZ)

Open Date: 2020-01-01

Close Date: 2022-12-01

Grant: Close

MolMeDB - Validated Predictions of Small Molecule Interactions with Biological Membranes

Open Date: 2017-01-01

Close Date: 2019-12-01

Grant: Close

Czech National Infrastructure for Biological data (acronym ELIXIR CZ)

Open Date: 2016-01-01

Close Date: 2019-12-31

Grant: Close

Mechanism of ligand access/egress to/from active site of microsomal drug-metabolising cytochromes P450

Open Date: 2012-01-01

Close Date: 2014-12-31

Articles (19)

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2021

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2021

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2021

Collaborators (15)

Jaroslav Koca

Professor

Masaryk University

CZECH REPUBLIC

Karel Berka

Research Interests

Contact this professor

About

Recent Grants

Articles (19)

Meta-Analysis of Permeability Literature Data Shows Possibilities and Limitations of Popular Methods

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

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

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

αCharges: partial atomic charges for AlphaFold structures in high quality

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

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

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

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

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

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

OverProt: secondary structure consensus for protein families

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

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

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

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

Collaborators (15)

Jaroslav Koca

Pathmanaban Ramasamy

Franca Fraternali

Paweł Rubach

Frantisek Stepanek

Petr Škoda

Nathalie Reuter

Tomáš Raček

Ondrej Vavra

Margherita Romeo

Martin Balouch

Antonio Rosato

Magdalena Konefał

Lucie Brulíková

Jose Maria Carazo Garcia

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