List of works - Jiri Cerny

A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle.

scientific article published on 18 October 2017

A DNA structural alphabet provides new insight into DNA flexibility

scientific article

A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints

scientific article published on 16 January 2019

A unified dinucleotide alphabet describing both RNA and DNA structures

scientific article published on 14 May 2020

ABD-Derived Protein Blockers of Human IL-17 Receptor A as Non-IgG Alternatives for Modulation of IL-17-Dependent Pro-Inflammatory Axis

scientific article published on 09 October 2018

Addressing the Compartmentalization of Specific Integrin Heterodimers in Mouse Sperm ⬇️

scientific article published on 26 February 2019

Affinity of vitamin E analogues for the ubiquinone complex II site correlates with their toxicity to cancer cells

scientific article published on 8 June 2011

Automatic workflow for the classification of local DNA conformations

scientific article

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

article

Bioinformatic analysis of the protein/DNA interface.

scientific article published on 11 December 2013

Block of NMDA receptor channels by endogenous neurosteroids: implications for the agonist induced conformational states of the channel vestibule

scientific article published on 18 June 2015

Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3

scientific article

CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization.

scientific article

Cation–π complexes between alkali metal cation andpara-halogenophenols. Structures, binding energies and thermodynamic properties: DFT study and CCSD(T) complete basis set limit calculations

Chemical Cross-Linking and H/D Exchange for Fast Refinement of Protein Crystal Structure

scientific article published on 23 December 2011

Competition between stacking and hydrogen bonding: theoretical study of the phenol⋯Ar cation and neutral complex and comparison to experiment

article

Complete Basis Set Extrapolation and Hybrid Schemes for Geometry Gradients of Noncovalent Complexes

article

Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity

scientific article published on 18 August 2016

DNATCO: assignment of DNA conformers at dnatco.org.

scientific article published on 05 May 2016

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

scientific article published on 30 January 2007

Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.

scientific article published on 06 April 2007

Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities

scientific article

Dispersion Interactions Govern the Strong Thermal Stability of a Protein

scientific article published on 01 January 2007

Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy

scientific article published on 01 November 2008

Effect of noncovalent interactions on the n-butylbenzene...Ar cluster studied by mass analyzed threshold ionization spectroscopy and ab initio computations.

scientific article published on 6 June 2008

Energy barriers between H-bonded and stacked structures of 9-methyladenine...1-methylthymine and 9-methylguanine...1-methylcytosine complexes.

scientific article published on 13 November 2009

Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank

scientific article published on 30 October 2018

Expression and distribution of CD151 as a partner of alpha6 integrin in male germ cells

scientific article published on 09 March 2020

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

scientific article published in 2011

Human interleukin-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells

scientific article

Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design.

scientific article published on 2 October 2013

Local dynamics of proteins and DNA evaluated from crystallographic B factors

scientific article

Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein.

scientific article

Mitochondrial Targeting of Metformin Enhances Its Activity against Pancreatic Cancer

scientific article published on 07 October 2016

Mitochondrial targeting of vitamin E succinate enhances its pro-apoptotic and anti-cancer activity via mitochondrial complex II

scientific article

NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics

scientific article published on 28 September 2019

Non-covalent interactions in biomacromolecules.

scientific article published on 14 June 2007

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G.

scientific article

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations

scientific article published on 9 December 2009

Palmitoylation Controls NMDA Receptor Function and Steroid Sensitivity

scientific article published on 01 February 2021

Preferential Inhibition of Tonically over Phasically Activated NMDA Receptors by Pregnane Derivatives

scientific article published in February 2016

Protein flexibility in the light of structural alphabets

scientific article

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

Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction: interferon- γ receptor 1 as a model

scientific article published on 28 April 2015

Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): a promising tool for studying isolated small peptides.

scientific article

Rigid duplex alpha-cyclodextrin reversibly connected with disulfide bonds. Synthesis and inclusion complexes.

scientific article

Selective Disruption of Respiratory Supercomplexes as a New Strategy to Suppress Her2high Breast Cancer

scientific article published on 08 July 2016

Site of action of brain neurosteroid pregnenolone sulfate at the N-methyl-D-aspartate receptor

scientific article published on 02 July 2020

Spectral shifts and structures of phenol...Ar(n) clusters.

scientific article

State of the art theoretical study and comparison to experiment for the phenol...argon complex.

scientific article

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

scientific article published on 17 August 2020

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

scientific article published on 24 November 2020

Study of the Origin of the Hindered Rotation of an Aryl Ring in Chromium Aminocarbene Complexes Bearing an Aromatic Ring Attached to the Carbene Carbon Atom

scientific article published in November 2006

Surface Expression, Function, and Pharmacology of Disease-Associated Mutations in the Membrane Domain of the Human GluN2B Subunit.

scientific article published on 6 April 2018

The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate.

scientific article published on 6 April 2018

The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine

scientific article published in December 2008

The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.

scientific article

Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment

scientific article published on 09 May 2006

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.

scientific article published in August 2006

Threshold ionization spectroscopic investigation of supersonic jet-cooled, laser-desorbed Tryptophan

scientific article published in July 2016

Ubiquinone-binding site mutagenesis reveals the role of mitochondrial complex II in cell death initiation

scientific article

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

scientific article

When will RNA get its AlphaFold moment?

scientific article published on 13 September 2023

p19-Targeting ILP Protein Blockers of IL-23/Th-17 Pro-Inflammatory Axis Displayed on Engineered Bacteria of Food Origin

scientific article published in July 2018

p19-targeted ABD-derived protein variants inhibit IL-23 binding and exert suppressive control over IL-23-stimulated expansion of primary human IL-17+ T-cells

scientific article

List of works by Jiri Cerny

A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle.

A DNA structural alphabet provides new insight into DNA flexibility

A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints

A unified dinucleotide alphabet describing both RNA and DNA structures

ABD-Derived Protein Blockers of Human IL-17 Receptor A as Non-IgG Alternatives for Modulation of IL-17-Dependent Pro-Inflammatory Axis

Addressing the Compartmentalization of Specific Integrin Heterodimers in Mouse Sperm ⬇️

Affinity of vitamin E analogues for the ubiquinone complex II site correlates with their toxicity to cancer cells

Automatic workflow for the classification of local DNA conformations

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

Bioinformatic analysis of the protein/DNA interface.

Block of NMDA receptor channels by endogenous neurosteroids: implications for the agonist induced conformational states of the channel vestibule

Bordetella adenylate cyclase toxin is a unique ligand of the integrin complement receptor 3

CD9 and CD81 Interactions and Their Structural Modelling in Sperm Prior to Fertilization.

Cation–π complexes between alkali metal cation andpara-halogenophenols. Structures, binding energies and thermodynamic properties: DFT study and CCSD(T) complete basis set limit calculations

Chemical Cross-Linking and H/D Exchange for Fast Refinement of Protein Crystal Structure

Competition between stacking and hydrogen bonding: theoretical study of the phenol⋯Ar cation and neutral complex and comparison to experiment

Complete Basis Set Extrapolation and Hybrid Schemes for Geometry Gradients of Noncovalent Complexes

Crystal structure of human interferon-γ receptor 2 reveals the structural basis for receptor specificity

DNATCO: assignment of DNA conformers at dnatco.org.

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.

Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities

Dispersion Interactions Govern the Strong Thermal Stability of a Protein

Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy

Effect of noncovalent interactions on the n-butylbenzene...Ar cluster studied by mass analyzed threshold ionization spectroscopy and ab initio computations.

Energy barriers between H-bonded and stacked structures of 9-methyladenine...1-methylthymine and 9-methylguanine...1-methylcytosine complexes.

Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank

Expression and distribution of CD151 as a partner of alpha6 integrin in male germ cells

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

Human interleukin-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells

Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design.

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein.

Mitochondrial Targeting of Metformin Enhances Its Activity against Pancreatic Cancer

Mitochondrial targeting of vitamin E succinate enhances its pro-apoptotic and anti-cancer activity via mitochondrial complex II

NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics

Non-covalent interactions in biomacromolecules.

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G.

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations

Palmitoylation Controls NMDA Receptor Function and Steroid Sensitivity

Preferential Inhibition of Tonically over Phasically Activated NMDA Receptors by Pregnane Derivatives

Protein flexibility in the light of structural alphabets

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

Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction: interferon- γ receptor 1 as a model

Resolution of identity density functional theory augmented with an empirical dispersion term (RI-DFT-D): a promising tool for studying isolated small peptides.

Rigid duplex alpha-cyclodextrin reversibly connected with disulfide bonds. Synthesis and inclusion complexes.

Selective Disruption of Respiratory Supercomplexes as a New Strategy to Suppress Her2high Breast Cancer

Site of action of brain neurosteroid pregnenolone sulfate at the N-methyl-D-aspartate receptor

Spectral shifts and structures of phenol...Ar(n) clusters.

State of the art theoretical study and comparison to experiment for the phenol...argon complex.

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

Study of the Origin of the Hindered Rotation of an Aryl Ring in Chromium Aminocarbene Complexes Bearing an Aromatic Ring Attached to the Carbene Carbon Atom

Surface Expression, Function, and Pharmacology of Disease-Associated Mutations in the Membrane Domain of the Human GluN2B Subunit.

The LILI Motif of M3-S2 Linkers Is a Component of the NMDA Receptor Channel Gate.

The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine

The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.

Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.

Threshold ionization spectroscopic investigation of supersonic jet-cooled, laser-desorbed Tryptophan

Ubiquinone-binding site mutagenesis reveals the role of mitochondrial complex II in cell death initiation

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

When will RNA get its AlphaFold moment?

p19-Targeting ILP Protein Blockers of IL-23/Th-17 Pro-Inflammatory Axis Displayed on Engineered Bacteria of Food Origin

p19-targeted ABD-derived protein variants inhibit IL-23 binding and exert suppressive control over IL-23-stimulated expansion of primary human IL-17+ T-cells