GROUP PUBLICATIONS SINCE 2008

B Bioinformatics P Biophysics C Cytokines D ssDNA S Solvation O Other
  • David Biedermann, Martina Hurtová, Oldřich Benada, Kateřina Valentová, Lada Biedermannová & Vladimír Křen: Continuous Diastereomeric Kinetic Resolution—Silybins A and B. Catalysts 11: (2021).
    doi.org/10.3390/catal11091106.
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  • Prokopis C. Andrikopoulos, Aditya S. Chaudhari, Yingliang Liu, Patrick E. Konold, John T. M. Kennis, Bohdan Schneider & Gustavo Fuertes: QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors. Physical Chemistry & Chemical Physics 23: (2021).
    doi.org/10.1039/D1CP00447F.
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  • Aditya S. Chaudhari, Catarina A. Oliveira, Yingliang Liu, Prokopis C. Andrikopoulos, Inger Andersson, Bohdan Schneider & Gustavo Fuertes: Site-Specific Photoinduced Dynamics of the LOV Protein EL222 Monitored by Multiple Genetically Encoded Infrared Probes. Biophysical Journal 120: (2021).
    doi.org/10.1016/j.bpj.2020.11.964.
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  • Phuong Ngoc Pham and Maroš Huličiak, Lada Biedermannová, Jiří Černý, Tatsiana Charnavets, Gustavo Fuertes, Štěpán Herynek, Lucie Kolářová, Petr Kolenko, Jiří Pavlíček, Jiří Zahradník, Pavel Mikulecký & Bohdan Schneider: Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. Viruses (2021)
    doi:10.3390/v13020190
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  • Petr Kolenko, Jakub Svoboda, Jiří Černý, Tatsiana Charnavets, & Bohdan Schneider: Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta Crysrallographica D76: 1233-1243 (2020).
    10.1107/S2059798320014151.
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  • Vitaly Polovinkin, Krishna Khakurel, Michal Babiak, Boris Angelov, Bohdan Schneider, Jan Dohnalek, Jakob Andreasson & Janos Hajdu: Demonstration of electron diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures. Journal of Applied Crystallography 53: 1416-1424 (2020)
    doi: 10.1107/S1600576720013096 ↓ PDF
  • Jiří Černý, Paulína Božíková, Michal Malý, Michal Tykač, Lada Biedermannová & Bohdan Schneider: Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org. Acta Crysrallographica D76: 805-813 (2020).
    doi.org/10.1107/S2059798320009389.
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  • Jiří Černý, Paulína Božíková, Jakub Svoboda & Bohdan Schneider: A unified dinucleotide alphabet describing both RNA and DNA structures. Nucleic Acids Research 48: 6367-6381 (2020).
    doi: 10.1093/nar/gkaa383.
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  • Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, ..., & Bohdan Schneider: A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000 Research 9(ELIXIR):278:(2020).
    doi:10.12688/f1000research.20559.1).
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  • Prokopis C. Andrikopoulos, Yingliang Liu, Alessandra Picchiotti, Nils Lenngren, Miroslav Kloz, Aditya S. Chaudhari, Martin Precek, Mateusz Rebarz, Jakob Andreasson, Janos Hajdu, Bohdan Schneider & Gustavo Fuertes: Femtosecond-to-nanosecond dynamics of flavin mononucleotide monitored by stimulated Raman spectroscopy and simulations. Physical Chemistry & Chemical Physics 22: 6538-6552 (2020).
    doi:10.1039/c9cp04918e.
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  • Gustavo Fuertes, Laura Nevola, Santiago Esteban-Martín: Chapter 9 - Perspectives on drug discovery strategies based on IDPs. Intrinsically Disordered Proteins : (2019), 275-327, ISBN 9780128163481.
    doi.org/10.1016/B978-0-12-816348-1.00009-0.
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  • Jiří Zahradník, Lucie Kolářová, Yoav Peleg, Petr Kolenko, Silvie Svidenska, Tatsiana Charnavets, Tamar Unger, Joel L. Sussman & Bohdan Schneider: Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1. FEBS Journal 286: 3858 (2019).
    doi:10.1111/febs.14945.
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  • Gustavo Fuertes, Niccolo Banterle, Kiersten M. Ruff, Aritra Chowdhury, Rohit V. Pappu, Dmitri I Svergun & Edward A. Lemke: Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”. Science 361: (2018).
    doi:10.1126/science.aau8230.
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  • 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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