Selected Papers

  • Computer-Aided Modulation of Protein Activity
  • Pavel Mikulecky, Jiri Cerny, Lada Biedermannova, Hana Petrokova, Milan Kuchar, Jiri Vondrasek, Petr Maly, Peter Sebo & Bohdan Schneider: Increasing affinity of interferon-γ receptor 1 to interferon-γ by computer-aided design. BioMed Research International 2013, 12 pages, (2013). doi: 10.1155/2013/752514.

    Milan Kuchar, Lucie Vankova, Hana Petrokova, Jiri Cerny, Radim Osicka, Ondrej Pelak, Hana Sipova, Bohdan Schneider, Jiri Homola, Peter Sebo, Tomas Kalina & Petr Maly: 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 82, 975-989 (2014). doi:10.1002/prot.24472.

  • Nucleic Acid Conformations and Dynamics
  • Bohdan Schneider, Jiri Cerny, Daniel Svozil, Petr Cech, Jean-Christophe Gelly & Alexandre G. de Brevern: Bioinformatic analysis of the protein/DNA interface. Nucleic Acids Res. 42, 3381-3394 (2014). doi: 10.1093/nar/gkt1273

    Petr Cech, Jaromir Kukal, Jiri Cerny, 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

    Bohdan Schneider, Jean-Christophe Gelly, Alexandre G. de Brevern & Jiri Cerny: Local dynamics of proteins and DNA evaluated from crystallographic B-factors. Acta Crystallographica D 70: 2413 (2014). doi:10.1107/S1399004714014631.

    Daniel Svozil, Jan Kalina, Marek Omelka & Bohdan Schneider: DNA Conformations and Their Sequence Preferences. Nucleic Acids Res. 36, 3690-3704 (2008). doi: 10.1093/nar/gkn260

    Bohdan Schneider, Zdenek Moravek & Helen M. Berman: RNA Conformational Classes. Nucleic Acids Res. 32, 1666-1677 (2004).

    Jane S. Richardson et al.: RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature. RNA, 14, 465-481 (2008). doi: 10.1261/rna.657708

    Jaroslav Nunvar, Dana Elhottova, Alena Chronakova, 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 Announc. 2: e00134-14 (2014). doi: 10.1128/genomeA.00134-14.

    Jaroslav Nunvar, Irena Licha & Bohdan Schneider: Evolution of REP diversity: a comparative study. BMC Genomics 14:385m (2013). doi:10.1186/1471-2164-14-385.

  • Structure - Property Relationships of Nucleic Acids:
    Calculation of electron density maps, calculation of NMR parameters, measurements of electric conductivity of DNA
  • Vladimir Sychrovsky, Zuzana Vokacova, Jiri Sponer, Nada Spackova & Bohdan Schneider: Calculation of Structural Behavior of Indirect NMR Spin-Spin Couplings in the Backbone of Nucleic Acids. J.Phys.Chem.B 110, 22894-22902 (2006). PMID: 17092041, doi: 10.1021/jp065000l.

    Frantisek Pavelcik & Bohdan Schneider: Building of RNA and DNA double helices into electron density. Acta Cryst. D64, 620-626 (2008). doi: 10.1107/S0907444908007075

    Irena Kratochvilova, Tatiana Todorciuc, Karel Kral, Hynek Nemec, Martin Buncek, Jakub Sebera, Stanislav Zalis, Zuzana Vokacova, Vladimir Sychrovsky, Lucie Bednarova, Peter Mojzes & Bohdan Schneider: Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns. J. Phys. Chem. B 114, 5196–5205 (2010). doi: 10.1021/jp100264v.

    Irena Kratochvilova, Karel Kral, Martin Buncek, Alena Viskova, Stanislav Nespurek, 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. Biophys. Chem. 6, 422-426 (2008). doi: 10.1016/j.bpc.2008.08.005

  • Solvation of Nucleic Acids
  • Bohdan Schneider, Ketan Patel & Helen M. Berman: Hydration of the Phosphate Group in Double-Helical DNA. Biophys. J. 75, 2422-2434 (1998).

    B. Schneider & M. Kabelac: Stereochemistry of Binding of Metal Cations and Water to a Phosphate Group. J. Am. Chem. Soc. 120, 161-165 (1998).

    Julia Woda, Bohdan Schneider, Ketan Patel, K. Mistry & Helen M. Berman: An Analysis of the Relationship between Hydration and Protein-DNA Interactions. Biophys. J. 75, 2170-2177 (1998).

    Zdenek Moravek, Stephen Neidle & Bohdan Schneider: Protein and Drug Interactions in the Minor Groove of B-DNA. Nucleic Acids Res. 30, 1182-1191 (2002).

    Bohdan Schneider & Helen M. Berman: Hydration of the DNA Bases Is Local. Biophys. J. 69, 2661-2669 (1995).

    Wei Ge, Bohdan Schneider & Wilma.K. Olson: Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with Nucleic Acids. Biophys. J. 88, 1166-1190 (2005).

    B. Schneider, M. Kabelac & P. Hobza: Geometry of the Phosphate Group and Its Interactions with Metal Cations in Crystals and ab Initio Calculations. J. Am. Chem. Soc. 118, 12207-12217 (1996).

    Bohdan Schneider, Dawn.M. Cohen, Leo Schleifer, A.R. Srinivasan, Wilma K. Olson & Helen M. Berman: A Systematic Method to Study the Spatial Distribution of Water Molecules around Nucleic Acid Bases. Biophys .J. 65, 2291-2303 (1993).

  • Building and Maintaining Structural Databases, the PDB and NDB
  • Kyle Burkhardt, Bohdan Schneider & Jeramia Ory: A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PLOS Comp.Biol. 2, 1186-1189 (2006).

    Helen M. Berman et al.: The Nucleic Acid Database. Acta Cryst. D58, 889-898 (2002).

    Helen M. Berman at al.: The Protein Data Bank. Acta Cryst. D58, 899-907 (2002).

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    © Bohdan Schneider 2008-2014