GROUP PUBLICATIONS SINCE 2008

B Bioinformatics P Biophysics C Cytokines D ssDNA S Solvation O Other
  • Jiří Zahradník, Lucie Kolářová, Hana Pařízková, Petr Kolenko, & Bohdan Schneider: Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function. Fish and Shellfish Immunology 79: 140-152 (2018).
    doi:org/10.1016/j.fsi.2018.05.008.
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  • Jiří Zahradník, Petr Kolenko, Andrea Palyzová, Jiří Černý, Lucie Kolářová, Eva Kyslíková, Helena Marešová, Michal Grulich, Jaroslav Nunvar, Miroslav Šulc, Pavel Kyslík & Bohdan Schneider: The crystal structure of XdpB, the bacterial old yellow Enzyme, in an FMN-free form. PLOS One 13: e0195299 (2018).
    doi:10.1371/journal.pone.0195299.
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  • Bohdan Schneider, Paulína Božíková, Iva Nečasová, Petr Čech, Daniel Svozil & Jiří Černý: A DNA structural alphabet provides a new insight into the DNA flexibility. Acta Crystallographica D74: 52-64 (2018).
    doi:10.1107/S2059798318000050.
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  • Bohdan Schneider, Paulína Božíková, Petr Čech, Daniel Svozil & Jiří Černý: A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes 8: 278 (2017).
    doi: 10.3390/genes8100278.
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  • Jiří Černý, Bohdan Schneider & Lada Biedermannová: WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations. Physical Chemistry & ChemicalPhysics 19: 17094-17102 (2017).
    doi: 10.1039/c7cp00187h.
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  • Pavel Mikulecký, Jiří Zahradník, Petr Kolenko, Jiří Černý, Tatsiana Charnavets, Lucie Kolářová, Iva Nečasová, Phuong Ngoc Pham & Bohdan Schneider: Crystal structure of human interferon-gamma receptor 2 reveals the structural basis for receptor specificity. Acta Crystallographica D72: 1017-1025 (2016).
    doi: 10.1107/S2059798316012237.
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  • Jiří Černý, Paulína Božíková & Bohdan Schneider: DNATCO: assignment of DNA conformers at dnatco.org. Nucleic Acids Research 44: W287-W287 (2016).
    doi: 10.1093/nar/gkw381.
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  • Lada Biedermannová & Bohdan Schneider: Hydration of proteins and nucleic acids: Advances in experiment and theory. A review. BBA - General Subjects 1860: 1821-1835 (2016).
    doi: 10.1016/j.bbagen.2016.05.036.
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  • Lada Biedermannová & Bohdan Schneider: Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. Acta Crystallographica D71: 2192-2202 (2015).
    doi: 10.1107/S1399004715015679.
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  • Tatsiana Charnavets, Jaroslav Nunvar, Iva Nečasová, Jens Völker, Kenneth J. Breslauer & Bohdan Schneider: Conformational Diversity of Single-stranded DNA from Bacterial Repetitive Extragenic Palindromes: Implications for the DNA Recognition Elements of Transposases. Biopolymers 103: 585-596 (2015).
    doi: 10.1002/bip.22666.
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  • Markéta Bocková, Tomáš Špringer, Iva Nečasová, Jaroslav Nunvar, Bohdan Schneider & Jiří Homola: Monitoring RAYT activity by surface plasmon resonance biosensor. Analytical and Bioanalytical Chemistry 407: 3985-3993 (2015).
    doi: 10.1007/s00216-015-8491-y.
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  • Pierrick Craveur, Agnel P. Joseph, Jeremy Esque, Tarun J. Narwani, Floriane Noel, Nicolas Shinada, Matthieu Goguet, Sylvain Leonard, Pierre Poulain, Olivier Bertrand, Guilhem Faure, Joseph Rebehmed, Amine Ghozlane, Lakshmipuram S. Swapna, Ramachandra M. Bhaskara, Jonathan Barnoud, Stéphane Téletchéa, Vincent Jallu, Jiří Černý, Bohdan Schneider, Catherine Etchebest, Narayanaswamy Srinivasan, Jean-Christophe Gelly & Alexandre G. de Brevern: Protein flexibility in the light of structural alphabets. Frontiers in Molecular Biosciences 2: (2015).
    doi: 10.3389/fmolb.2015.00020.
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  • Jiří Černý, Lada Biedermannová, Pavel Mikulecký, Jiří Zahradník, Tatsiana Charnavets, Peter Šebo & Bohdan Schneider: Redesigning protein cavities as a strategy for increasing affinity in protein-protein interaction. Interferon-γ receptor 1 as a model. BioMed Research International 2015: 716945 (2015).
    doi: 10.1155/2015/716945.
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  • Bohdan Schneider, Jean-Christophe Gelly, Alexandre G. de Brevern & Jiří Černý: Local dynamics of proteins and DNA evaluated from crystallographic B-factors. Acta Crystallographica D70: 2413-2419 (2014).
    doi: 10.1107/S1399004714014631.
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  • Bohdan Schneider, Jiří Černý, Petr Čech, Daniel Svozil, Jean-Christophe Gelly, & Alexandre G. de Brevern: Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Research 42: 3381-3394 (2014).
    doi: 10.1093/nar/gkt1273.
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  • Milan Kuchař, Lucie Vaňková, Hana Petroková, Jiří Černý, Radim Osička, Ondřej Pelák, Hana Šípová, Bohdan Schneider, Jiří Homola, Peter Šebo, Tomáš Kalina & Petr Malý: 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. Proteins: Structure, Function and Bioinformatics 82: 975-989 (2014).
    doi: 10.1002/prot.24472.
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  • Jaroslav Nunvář, Dana Elhottová, Alena Chronáková, Bohdan Schneider & Irena Licha: Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage. Genome Announcements 2: e00134-14 (2014).
    doi: 10.1128/genomeA.00134-14.
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  • Petr Čech, Jaromír Kukal, Jiří Černý, Bohdan Schneider & Daniel Svozil: Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics 14: 205 (2013).
    doi: 10.1186/1471-2105-14-205.
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  • Pavel Mikulecký, Jiří Černý, Lada Biedermannová, Hana Petroková, Milan Kuchař, Jiří Vondrášek, Petr Malý, Peter Šebo & Bohdan Schneider: Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design. BioMed Research International 2013: 752514 (2013).
    doi: 10.1155/2013/752514.
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  • Jaroslav Nunvář, Irena Lichá & Bohdan Schneider: Evolution of REP diversity: a comparative study. BMC Genomics 14: 385m (2013).
    doi: 10.1186/1471-2164-14-385.
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  • Irena Kratochvílová, Martin Vala, Martin Weiter, Miroslava Špérová, Bohdan Schneider, Ondřej Páv, Jakub Šebera, Ivan Rosenberg & Vladimír Sychrovský: Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: Complex theoretical and experimental studies. Biophysical Chemistry 180-181: 127-134 (2013).
    doi: 0.1016/j.bpc.2013.07.009.
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  • Ladislav Benda, Bohdan Schneider, Vladimir Sychrovský: Calculating the Response of NMR Shielding Tensor σ((31)P) and (2)J((31)P,(13)C) Coupling Constants in Nucleic Acid Phosphate to Coordination of the Mg(2+) Cation. J. Physical Chemistry A 115: 2385-2395 (2011).
    doi: 10.1021/jp8105452.
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  • Agnel Praveen Joseph, Garima Agarwal, Swapnil Mahajan, Jean-Christophe Gelly, Lakshmipuram S. Swapna, Bernard Offmann, Frédéric Cadet, Aurélie Bornot, Manoj Tyagi, Hélène Valadié, Bohdan Schneider, Catherine Etchebest, Narayanaswamy Srinivasan, Alexandre G. de Brevern: A short survey on protein blocks. Biophysical Reviews 2: 137-145 (2010).
    doi: 10.1007/s12551-010-0036-1.
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  • Irena Kratochvílová, Tatiana Todorciuc, Karel Král, Hynek Němec, Martin Bunček, Jakub Šebera, Stanislav Záliš, Zuzana Vokáčová, Vladimír Sychrovský, Lucie Bednárová, Peter Mojzeš & Bohdan Schneider: Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns. J. Physical Chemistry B 114: 5196–5205 (2010).
    doi: 10.1021/jp100264v.
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  • Zuzana Vokáčová, Miloš Budĕsínský, Ivan Rosenberg, Bohdan Schneider, Jiří Šponer & Vladimír Sychrovský: Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings. J. Physical Chemistry B 113: 1182-1191 (2009).
    doi: 10.1021/jp809762b.
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  • Daniel Svozil, Jan Kalina, Marek Omelka & Bohdan Schneider: DNA Conformations and Their Sequence Preferences. Nucleic Acids Research 36: 3690-3704 (2008).
    doi: 10.1093/nar/gkn260.
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  • Jane S. Richardson, Bohdan Schneider, Laura W. Murray, Gary J. Kapral, Robert M. Immormino, Jeffrey J. Headd, David C. Richardson, Daniela Ham, Eli Hershkovits, Loren Dean Williams, Kevin S. Keating, Anna Marie Pyle, David Micallef, John Westbrook & Helen M. Berman: RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature. RNA 14: 465-481 (2008).
    doi: 10.1261/rna.657708.
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  • František Pavelčík & Bohdan Schneider: Building of RNA and DNA double helices into electron density. Acta Crystallographica D 64: 620-626 (2008).
    doi: 10.1107/S0907444908007075.
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  • Irena Kratochvílová, Karel Král, Martin Bunček, Alena Víšková, Stanislav Nešpůrek, Anna Kochalska, Tatiana Todorciuc, Martin Weiter & Bohdan Schneider: Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking. Biophysical Chemistry 6: 422-426 (2008).
    doi: 10.1016/j.bpc.2008.08.005.
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  • Irena Kratochvílová, Karel Král, Martin Bunček, Stanislav Nešpůrek, Tatiana Todorciuc, Martin Weiter, Jiři Navrátil, Bohdan Schneider & Jiři Pavluch: Scanning tunneling spectroscopy study of DNA conductivity. Central European J. Physics 6: 422-426 (2008).
    doi: 10.2478/s11534-008-0072-7.
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  • Eva Brumovská, Vladimír Sychrovský, Zuzana Vokáčová, Jiří Šponer, Bohdan Schneider & Lukáš Trantírek: Effect of local sugar and base geometry on (13)C and (15)N magnetic shielding anisotropy in DNA nucleosides. J. Biomolecular NMR 42: 209-223 (2008).
    doi: 10.1007/s10858-008-9278-7.
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