J. Černý

发表

Bioinformatic analysis of the protein/DNA interface

Daniel Svozil, Jean-Christophe Gelly, Jiří Černý, 2011, Nucleic acids research.

Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.

J. Vymětal, J. Vondrášek, J. Černý, 2014, Protein engineering, design & selection : PEDS.

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

Jiří Vondrášek, Petr Malý, Lada Biedermannová, 2012, Proteins.

Non-covalent interactions in biomacromolecules.

J. Černý, P. Hobza, 2007, Physical chemistry chemical physics : PCCP.

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

J. Zahradník, B. Schneider, J. Černý, 2018, PloS one.

A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints

J. Černý, E. Peter, 2019, International journal of molecular sciences.

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

J. Černý, E. Peter, 2018, International journal of molecular sciences.

A unified dinucleotide alphabet describing both RNA and DNA structures

B. Schneider, J. Černý, Paulína Božíková, 2020, Nucleic acids research.

A deep phylogeny of viral and cellular right-hand polymerases.

J. Černý, D. Růžek, L. Grubhoffer, 2015, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

L. Vyklický, J. Černý, A. Balík, 2018, Front. Mol. Neurosci..

Development and characterization of recombinant tick-borne encephalitis virus expressing mCherry reporter protein: a new tool for high-throughput screening of antiviral compounds, and neutralizing antibody assays.

E. Gould, X. de Lamballerie, J. Černý, 2020, Antiviral research.

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

B. Schneider, J. Černý, L. Biedermannová, 2017, Physical chemistry chemical physics : PCCP.

Nucleoside Inhibitors of Tick-Borne Encephalitis Virus

E. De Clercq, J. Černý, J. Valdés, 2015, Antimicrobial Agents and Chemotherapy.

Evolution of Tertiary Structure of Viral RNA Dependent Polymerases

J. Černý, J. Valdés, D. Růžek, 2014, PloS one.

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

J. Černý, P. Hobza, P. Jurečka, 2007, The journal of physical chemistry. A.

Full genome sequences and molecular characterization of tick-borne encephalitis virus strains isolated from human patients.

J. Černý, B. Bolfíková, J. Valdés, 2015, Ticks and tick-borne diseases.

Escape of Tick-Borne Flavivirus from 2′-C-Methylated Nucleoside Antivirals Is Mediated by a Single Conservative Mutation in NS5 That Has a Dramatic Effect on Viral Fitness

E. De Clercq, R. Kizek, J. Černý, 2017, Journal of Virology.

Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B

D. Kavan, J. Černý, J. Cerny, 2017 .

Pregnane‐based steroids are novel positive NMDA receptor modulators that may compensate for the effect of loss‐of‐function disease‐associated GRIN mutations

L. Vyklický, J. Černý, M. Horak, 2022, British journal of pharmacology.

Palmitoylation Controls NMDA Receptor Function and Steroid Sensitivity

L. Vyklický, J. Černý, M. Korinek, 2021, The Journal of Neuroscience.

Motif orientation matters: structural characterization of TEAD1 recognition of genomic DNA.

D. Kavan, J. Černý, P. Man, 2020, Structure.

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

J. Vondrášek, J. Černý, P. Dobes, 2011 .

Roles of octabutoxy substitution and J-aggregation in stabilization of the excited state in nickel phthalocyanine.

J. Pfleger, J. Černý, D. Rais, 2014, The journal of physical chemistry. A.

Origin of the São Paulo Yellow Fever epidemic of 2017–2018 revealed through molecular epidemiological analysis of fatal cases

E. Holmes, Beatriz Perondi, P. Zanotto, 2019, Scientific Reports.

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

J. Lubkowski, J. Černý, C. Bařinka, 2016, The FEBS journal.

Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution

J. Zahradník, B. Schneider, J. Černý, 2021, Viruses.

Germline SUCLG2 Variants in Patients with Pheochromocytoma and Paraganglioma.

Jun Zhu, J. Černý, J. Neuzil, 2021, Journal of the National Cancer Institute.

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

J. Černý, R. Osicka, P. Šebo, 2015, eLife.

Ixodes scapularis saliva components that elicit responses associated with acquired tick-resistance.

E. Fikrig, S. Narasimhan, J. Černý, 2020, Ticks and tick-borne diseases.

Redesigning Protein Cavities as a Strategy for Increasing Affinity in Protein-Protein Interaction: Interferon-γ Receptor 1 as a Model

J. Zahradník, B. Schneider, J. Černý, 2015, BioMed research international.

Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.

M. Pomper, J. Lubkowski, J. Černý, 2014, Bioorganic & medicinal chemistry letters.

Structure and base catalysed cyclization of methyl (2,6-disubstituted-4-nitrophenylsulphanyl)ethanoates

J. Černý, V. Bertolasi, P. Šimůnek, 2003 .

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

B. Schneider, D. Svozil, J. Černý, 2017, Genes.

Mitochondrial Targeting of Metformin Enhances Its Activity against Pancreatic Cancer

J. Černý, J. Neuzil, J. Štursa, 2016, Molecular Cancer Therapeutics.

Fractionation of tick saliva reveals proteins associated with the development of acquired resistance to Ixodes scapularis.

E. Fikrig, S. Narasimhan, J. Černý, 2020, Vaccine.

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

J. Vymětal, J. Vondrášek, J. Černý, 2009, The Journal of organic chemistry.

Myomedin replicas of gp120 V3 loop glycan epitopes recognized by PGT121 and PGT126 antibodies as non-cognate antigens for stimulation of HIV-1 broadly neutralizing antibodies

J. Černý, M. Kuchař, H. Petroková, 2022, Frontiers in Immunology.

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

J. Vondrášek, J. Černý, P. Hobza, 2009, The journal of physical chemistry. B.

Double-helical --> ladder structural transition in the B-DNA is induced by a loss of dispersion energy.

J. Černý, P. Hobza, M. Kabelác, 2008, Journal of the American Chemical Society.

Guanine quadruplexes in the RNA genome of the tick-borne encephalitis virus: their role as a new antiviral target and in virus biology

J. Černý, E. Bouřa, D. Růžek, 2022, Nucleic acids research.

Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein

J. Černý, L. Rulíšek, Zahra Aliakbar Tehrani, 2021, Journal of biomolecular structure & dynamics.

Cadmium hyperaccumulating mushroom Cystoderma carcharias has two metallothionein isoforms usable for cadmium and copper storage.

J. Borovička, J. Černý, J. Šantrůček, 2021, Fungal genetics and biology : FG & B.

Automatic workflow for the classification of local DNA conformations

Bohdan Schneider, Petr Cech, Jaromir Kukal, 2013, BMC Bioinformatics.

Vertebrate viruses in polar ecosystems

J. Černý, D. Růžek, L. Grubhoffer, 2020 .

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

L. Vyklický, J. Černý, M. Horak, 2018, Front. Mol. Neurosci..

Structure, function, and pharmacology of NMDA receptor channels.

L. Vyklický, J. Černý, A. Balík, 2014, Physiological research.

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

J. Černý, K. Müller-Dethlefs, A. Armentano, 2011, Physical chemistry chemical physics : PCCP.

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

L. Vyklický, J. Černý, K. Valeš, 2016, The Journal of Neuroscience.

Preparation and characterization of novel double-decker rare-earth phthalocyanines substituted with 5-bromo-2-thienyl groups

J. Černý, A. Lyčka, F. Bureš, 2017, Chemistry Central Journal.

Management Options for Ixodes ricinus-Associated Pathogens: A Review of Prevention Strategies

J. Černý, M. Golovchenko, L. Grubhoffer, 2020, International journal of environmental research and public health.

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

Jirí Cerný, Pavel Hobza, Dennis R. Salahub, 2007, J. Comput. Chem..

Role of Zoo-Housed Animals in the Ecology of Ticks and Tick-Borne Pathogens—A Review

J. Černý, L. Grubhoffer, N. Rudenko, 2021, Pathogens.

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

P. Ježek, J. Černý, J. Neuzil, 2017, Antioxidants & redox signaling.

MAIA, Fc receptor–like 3, supersedes JUNO as IZUMO1 receptor during human fertilization

M. Ikawa, J. Černý, A. Pacey, 2022, Science advances.

Addressing the Compartmentalization of Specific Integrin Heterodimers in Mouse Sperm

J. Černý, N. Sebková, K. Dvorakova-Hortova, 2019, International journal of molecular sciences.

Effect of noncovalent interactions on conformers of the n-butylbenzene monomer studied by mass analyzed threshold ionization spectroscopy and basis-set convergent ab initio computations.

J. Černý, C. Dessent, K. Müller-Dethlefs, 2008, The journal of physical chemistry. A.

Expression of a second open reading frame present in the genome of tick-borne encephalitis virus strain Neudoerfl is not detectable in infected cells

J. Černý, D. Růžek, L. Grubhoffer, 2016, Virus Genes.

Site of Action of Brain Neurosteroid Pregnenolone Sulfate at the N-Methyl-D-Aspartate Receptor

L. Vyklický, J. Černý, A. Balík, 2020, The Journal of Neuroscience.

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

J. Černý, J. Jankovičová, J. Antalíková, 2018, International journal of molecular sciences.

Mitochondrial Targeting of Vitamin E Succinate Enhances Its Pro-apoptotic and Anti-cancer Activity via Mitochondrial Complex II*

R. Moreno-Sánchez, S. Rodríguez-Enríquez, J. Černý, 2010, The Journal of Biological Chemistry.

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

J. Černý, P. Hobza, K. Müller-Dethlefs, 2008, The Journal of chemical physics.

Characterization and in vitro assembly of tick‐borne encephalitis virus C protein

R. Hrabal, T. Ruml, J. Černý, 2020, FEBS letters.

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

Bohdan Schneider, Jiří Černý, Paulína Božíková, 2020, Acta crystallographica. Section D, Structural biology.

Hard ticks and tick-borne pathogens in Mongolia-A review.

J. Černý, T. Needham, Gantulga Gankhuyag, 2019, Ticks and tick-borne diseases.

Genetic and phylogenetic characterization of novel bocaparvovirus infecting chimpanzee.

J. Černý, D. Modrý, K. Hrazdilová, 2016, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Search for tick-borne pathogens in the Svalbard Archipelago and Jan Mayen

J. Černý, L. Grubhoffer, S. Coulson, 2015 .

Protein flexibility in the light of structural alphabets

Bohdan Schneider, L. S. Swapna, Pierrick Craveur, 2015, Front. Mol. Biosci..

A human secretome library screen reveals a role for Peptidoglycan Recognition Protein 1 in Lyme borreliosis

E. Fikrig, C. Jacobs-Wagner, J. Černý, 2020, PLoS pathogens.

Increasing Affinity of Interferon-γ Receptor 1 to Interferon-γ by Computer-Aided Design

Jiří Vondrášek, Petr Malý, Jiří Černý, 2013, BioMed research international.

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

Jirí Cerný, Pavel Hobza, J. Černý, 2005, Physical chemistry chemical physics : PCCP.

A DNA structural alphabet provides new insight into DNA flexibility

Bohdan Schneider, Daniel Svozil, Jiří Černý, 2018, Acta crystallographica. Section D, Structural biology.

An Ixodes scapularis Protein Disulfide Isomerase Contributes to Borrelia burgdorferi Colonization of the Vector

E. Fikrig, S. Narasimhan, J. Černý, 2020, Infection and Immunity.

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

J. Černý, R. Osicka, M. Kuchař, 2018, International journal of molecular sciences.

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

T. Kalina, Ondřej Pelák, J. Černý, 2017, Autoimmunity.

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

J. Homola, T. Kalina, Ondřej Pelák, 2013, Proteins.

Evidence for the Association between the Intronic Haplotypes of Ionotropic Glutamate Receptors and First-Episode Schizophrenia

V. Beneš, T. Rausch, L. Vyklický, 2021, Journal of personalized medicine.

Historia de la lingüística

J. Černý, 1998 .

Proteins mimicking epitope of HIV-1 virus neutralizing antibody induce virus-neutralizing sera in mice

J. Černý, M. Kuchař, H. Petroková, 2019, EBioMedicine.

Myomedin scaffold variants targeted to 10E8 HIV-1 broadly neutralizing antibody mimic gp41 epitope and elicit HIV-1 virus-neutralizing sera in mice

J. Černý, J. Dušková, J. Dohnálek, 2021, Virulence.

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.

Jirí Cerný, Pavel Hobza, Petr Jurecka, 2006, Physical chemistry chemical physics : PCCP.

Local dynamics of proteins and DNA evaluated from crystallographic B factors

Jean-Christophe Gelly, Jiří Černý, Alexandre G. de Brevern, 2014, Acta crystallographica. Section D, Biological crystallography.

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

J. Černý, P. Hobza, D. Michalska, 2006 .

Spiroplasma Isolated From Third-Generation Laboratory Colony Ixodes persulcatus Ticks

J. Černý, D. Růžek, L. Bell-Sakyi, 2021, Frontiers in Veterinary Science.

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.

J. Černý, P. Hobza, D. Michalska, 2008, The journal of physical chemistry. B.

Preparation, characterization and investigation of photo-physical properties of thiophene-substituted rare-earth bisphthalocyanines

J. Černý, A. Lyčka, F. Bureš, 2017 .

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

J. Zahradník, B. Schneider, J. Černý, 2016, Acta crystallographica. Section D, Structural biology.

Effects of Pregnanolone Glutamate and Its Metabolites on GABAA and NMDA Receptors and Zebrafish Behavior.

L. Vyklický, J. Černý, K. Valeš, 2023, ACS chemical neuroscience.

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

J. Černý, J. Neuzil, J. C. Dyason, 2011, Molecular nutrition & food research.

Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data.

Jirí Cerný, Pavel Hobza, Stefan Grimme, 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.

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

Karel Berka, Pavel Hobza, Kevin E. Riley, 2008 .

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

J. Černý, D. Nachtigallová, P. Hobza, 2006, Physical chemistry chemical physics : PCCP.

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

J. Černý, P. Hobza, K. Müller-Dethlefs, 2008, Physical chemistry chemical physics : PCCP.

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

J. Černý, K. Müller-Dethlefs, A. Armentano, 2016 .

Engineered Lactococcus lactis Secreting IL-23 Receptor-Targeted REX Protein Blockers for Modulation of IL-23/Th17-Mediated Inflammation

J. Černý, A. Berlec, M. Kuchař, 2019, Microorganisms.

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

J. Černý, Katja Škrlec, A. Berlec, 2018, International journal of molecular sciences.

Toward designed singlet fission: electronic states and photophysics of 1,3-diphenylisobenzofuran.

M. Ratner, J. Černý, J. Michl, 2010, The journal of physical chemistry. A.

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

L. Vyklický, J. Černý, A. Balík, 2019, Biomolecules.

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

Pavel Hobza, Kevin E. Riley, Jiří Černý, 2010, Journal of chemical theory and computation.

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

E. Gottlieb, J. Černý, J. Neuzil, 2015, Cell Death and Disease.

Dispersion interactions govern the strong thermal stability of a protein.

J. Vondrášek, J. Černý, V. Sklenar, 2007, Chemistry.

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

L. Vyklický, J. Černý, M. Zapotocky, 2015, Scientific Reports.

No indication of arthropod-vectored viruses in mosquitoes (Diptera: Culicidae) collected on Greenland and Svalbard

J. Černý, D. Růžek, L. Grubhoffer, 2018, Polar Biology.

Chemical cross-linking and H/D exchange for fast refinement of protein crystal structure.

D. Kavan, J. Černý, P. Man, 2012, Analytical chemistry.

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

Pavel Hobza, Kevin E. Riley, Jiří Černý, 2011, Journal of chemical theory and computation.

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

B. Schneider, J. Černý, P. Kolenko, 2020, Acta crystallographica. Section D, Structural biology.

Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia

J. Stránský, J. Černý, T. Skálová, 2023, Acta crystallographica. Section F, Structural biology communications.

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

J. Černý, J. Jankovičová, J. Antalíková, 2020, Scientific Reports.

DNATCO: assignment of DNA conformers at dnatco.org

Bohdan Schneider, Jirí Cerný, Paulína Bozíková, 2016, Nucleic Acids Res..

Nucleoside Inhibitors of Tick-Borne Encephalitis Virus

E. De Clercq, J. Černý, J. Valdés, 2015, Antimicrobial Agents and Chemotherapy.

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

P. Ježek, J. Černý, J. Neuzil, 2017, Antioxidants and Redox Signaling.

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

Jirí Cerný, Agnieszka Bronowska, Jirí Vondrásek, 2006, Journal of molecular biology.