Selected Papers
Nucleic Acid Conformations
DNA Conformations and Their Sequence Preferences. Daniel Svozil, Jan Kalina, Marek Omelka, and Bohdan Schneider. Nucleic Acids Res. 36, 3690-3704 (2008). doi: 10.1093/nar/gkn260
RNA Conformational Classes. Bohdan Schneider, Zdenek Moravek, Helen M. Berman: Nucl.Acids Res. 32, 1666-1677 (2004).
RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature. Jane S. Richardson et al.: RNA, 14, 465-481 (2008). doi: 10.1261/rna.657708
Structure - Property Relationships of Nucleic Acids:
Calculation of electron density maps, calculation of NMR parameters,
measurements of electric conductivity of DNA
Calculation of Structural Behavior of Indirect NMR Spin-Spin Couplings in the Backbone of Nucleic Acids. Vladimir Sychrovsky, Zuzana Vokacova, Jiri Sponer, Nada Spackova, Bohdan Schneider: J.Phys.Chem.B 110, 22894-22902 (2006). PMID: 17092041, doi: 10.1021/jp065000l.
Building of RNA and DNA double helices into electron density. Frantisek Pavelcik and Bohdan Schneider: Acta Cryst. D64, 620-626 (2008). doi: 10.1107/S0907444908007075
Charge Transport in DNA Oligonucleotides with Various Base-Pairing
Patterns. Irena Kratochvílová, Tatiana Todorciuc, Karel Král, Hynek
Nemec, Martin Buncek, Jakub Šebera, Stanislav Záliš, Zuzana Vokáčová,
Vladimír Sychrovský, Lucie Bednárová, Peter Mojzeš & Bohdan
Schneider. J. Phys. Chem. B 114, 5196–5205 (2010).
doi: 10.1021/jp100264v.
Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking. Irena Kratochvilova, Karel Kral, Martin Buncek, Alena Viskova, Stanislav Nespurek, Anna Kochalska, Tatiana Todorciuc, Martin Weiter, and Bohdan Schneider. Biophys. Chem. 6, 422-426 (2008). doi: 10.1016/j.bpc.2008.08.005
Solvation of Nucleic Acids
Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with
Nucleic Acids. Wei Ge, Bohdan Schneider & Wilma.K. Olson:
Biophys. J. 88, 1166-1190 (2005).
Protein and Drug Interactions in the Minor Groove of B-DNA. Zdenek Moravek, Stephen Neidle, Bohdan Schneider: Nucl. Acids Res. 30, 1182-1191 (2002).
Hydration of the Phosphate Group in Double-Helical DNA. Bohdan
Schneider, Ketan Patel & Helen M. Berman: Biophys. J. 75, 2422-2434
(1998).
An Analysis of the Relationship between Hydration and Protein-DNA
Interactions. Julia Woda, Bohdan Schneider, Ketan Patel, K. Mistry &
Helen M. Berman: Biophys. J. 75, 2170-2177 (1998).
Hydration of the DNA Bases Is Local. Bohdan Schneider & Helen M. Berman: Biophys. J. 69, 2661-2669 (1995).
A Systematic Method to Study the Spatial Distribution of Water
Molecules around Nucleic Acid Bases. Bohdan Schneider, Dawn.M. Cohen,
Leo Schleifer, A.R. Srinivasan, Wilma K. Olson & Helen M. Berman:
Biophys .J. 65, 2291-2303 (1993).
Building and Maintaining Structural Databases, the PDB and NDB
A Biocurator Perspective: Annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. Kyle Burkhardt, Bohdan Schneider, Jeramia Ory: PLOS Comp.Biol. 2, 1186-1189 (2006).
The Nucleic Acid Database. Helen M. Berman et al.; Acta Cryst. D58, 889-898 (2002).
The Protein Data Bank. Helen M. Berman at al.: Acta Cryst. D58, 899-907 (2002).
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