List of works - Karel Berka

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

scientific article published on 16 April 2015

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

scientific article published on 24 July 2013

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

scientific article published on 12 January 2017

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

scientific article

Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region

article by Markéta Paloncýová et al published 21 January 2014 in Journal of Physical Chemistry

Analysis of energy stabilization inside the hydrophobic core of rubredoxin.

scientific article

Anatomy of enzyme channels

scientific article

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

scientific article

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

scientific article

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

scientific article published on 13 May 2020

Automated Family-Wide Annotation of Secondary Structure Elements

scientific article published on 01 January 2019

Behavior of human cytochromes P450 on lipid membranes

scientific article published on 13 September 2013

Benchmarking of Force Fields for Molecule-Membrane Interactions

scientific article published on 8 July 2014

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

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

scientific article published on 21 April 2014

Biomacromolecular Fragments and Patterns

CATH: increased structural coverage of functional space

scientific article published on 25 November 2020

Channel Characteristics

ChannelsDB: database of biomacromolecular tunnels and pores

scientific article published on 3 October 2017

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

scientific article published on 22 July 2015

Characterization via Charges

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

scientific article

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

scientific article published on 25 February 2015

Complete Process of Data Extraction and Analysis

Concluding Remarks

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer ⬇️

scientific article published on February 24, 2012

Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum

scientific article published on 27 August 2020

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

scientific article published in September 2016

Detection and Extraction of Fragments

Detection of Channels

Discovery of N2-(4-Amino-cyclohexyl)-9-cyclopentyl- N6-(4-morpholin-4-ylmethyl-phenyl)- 9H-purine-2,6-diamine as a Potent FLT3 Kinase Inhibitor for Acute Myeloid Leukemia with FLT3 Mutations

scientific article published on 19 April 2018

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

article

ELIXIR and Toxicology: a community in development

scientific article published on 3 October 2023

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

article published in 2015

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

scientific article

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

scientific article published on July 2010

Exercises Solution

Exponential repulsion improves structural predictability of molecular docking

scientific article published on 13 September 2016

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

scientific article published on 8 November 2012

High-performance macromolecular data delivery and visualization for the web

scientific article published on 26 November 2020

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

scientific article published on 01 January 2021

In silico pharmacology: Drug membrane partitioning and crossing

scientific article

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

scientific article published on 05 October 2019

Insenstivity to Close Contacts and Inability to Predict Protein Foldability ⬇️

scientific article published on February 1, 2011

Introduction

Ion Pathways in the Na+/K+-ATPase.

scientific article

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

scientific article published on February 2012

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

scientific article

Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant

article published in 2013

Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane

scholarly article by Gabin Fabre published in August 2015

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

scientific article published in November 2017

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

scientific article (publication date: 16 August 2013)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

scientific article

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

scientific article published in July 2018

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

scientific article

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

scientific article published on 5 March 2018

MolMeDB: Molecules on Membranes Database

scientific article published on 19 November 2018

MolMeDB: Molecules on Membranes Database

scientific article published on 01 January 2019

Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

scholarly article by Karel Berka et al published February 2017 in Biophysical Journal

Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers ⬇️

scientific article published on February 19, 2013

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

scientific article published on 2 August 2017

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

scientific article

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

scientific article

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

scientific article published on 05 November 2019

Novel thidiazuron-derived inhibitors of cytokinin oxidase/dehydrogenase

scientific article

On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes.

scientific article published on August 2010

PDBsum additions

scientific article

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

article by Katerina Hola et al published April 2014 in Carbon

Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

scholarly article by Jan Řezáč et al published 2008 in Collection of Czechoslovak Chemical Communications

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

scientific article published on 31 July 2017

Rationalization of reduced penetration of drugs through ceramide gel phase membrane

scientific article

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

scientific article published on April 2009

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.

scientific article published on 11 March 2016

Structural Bioinformatics Databases of General Use

Structural Bioinformatics Tools for Drug Design

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

scientific article

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

scientific article published on 10 March 2018

Structural properties of CYP2D6: requirements for substrates and inhibitors

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

scientific article published on 30 November 2017

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

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

scientific article published on 18 March 2014

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

scientific article published on 18 June 2019

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

scientific article published on 19 December 2015

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

scientific article (publication date: April 2016)

The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies

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

scientific article

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

scientific article published on 11 June 2021

Validation

book chapter in Structural Bioinformatics Tools for Drug Design (2016)

Visualization and Analysis of Protein Structures with LiteMol Suite

scientific article published on 01 January 2020

List of works by Karel Berka

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

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

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

Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region

Analysis of energy stabilization inside the hydrophobic core of rubredoxin.

Anatomy of enzyme channels

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

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

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

Automated Family-Wide Annotation of Secondary Structure Elements

Behavior of human cytochromes P450 on lipid membranes

Benchmarking of Force Fields for Molecule-Membrane Interactions

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

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

Biomacromolecular Fragments and Patterns

CATH: increased structural coverage of functional space

Channel Characteristics

ChannelsDB: database of biomacromolecular tunnels and pores

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

Characterization via Charges

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

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

Complete Process of Data Extraction and Analysis

Concluding Remarks

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer ⬇️

Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum

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

Detection and Extraction of Fragments

Detection of Channels

Discovery of N2-(4-Amino-cyclohexyl)-9-cyclopentyl- N6-(4-morpholin-4-ylmethyl-phenyl)- 9H-purine-2,6-diamine as a Potent FLT3 Kinase Inhibitor for Acute Myeloid Leukemia with FLT3 Mutations

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

ELIXIR and Toxicology: a community in development

ELIXIR and Toxicology: a community in development

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

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

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

Exercises Solution

Exponential repulsion improves structural predictability of molecular docking

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

High-performance macromolecular data delivery and visualization for the web

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

In silico pharmacology: Drug membrane partitioning and crossing

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

Insenstivity to Close Contacts and Inability to Predict Protein Foldability ⬇️

Introduction

Ion Pathways in the Na+/K+-ATPase.

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

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

Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant

Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane

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

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

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

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

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

MolMeDB: Molecules on Membranes Database

MolMeDB: Molecules on Membranes Database

MolMeDB: Molecules on Membranes Database

Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers ⬇️

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

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

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

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

Novel thidiazuron-derived inhibitors of cytokinin oxidase/dehydrogenase

On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes.

PDBsum additions

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

Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

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

Rationalization of reduced penetration of drugs through ceramide gel phase membrane

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

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.

Structural Bioinformatics Databases of General Use

Structural Bioinformatics Tools for Drug Design

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