prof. RNDr. Jiří Šponer, DrSc.

2012

• The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

  ŠPONER Jiří MLÁDEK Arnošt ŠPONEROVÁ Judit SVOZIL Daniel ZGARBOVÁ Marie BANÁŠ Pavel JUREČKA Petr OTYEPKA Michal

  Article in Periodical

  PHYSICAL CHEMISTRY CHEMICAL PHYSICS, year: 2012, volume: 14, edition: 44, DOI

• Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

  MORGADO Claudio A SVOZIL Daniel TURNER Douglas H ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2012, volume: 14, edition: 36, DOI

• Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

  MLÁDEK Arnošt ŠPONEROVÁ Judit KULHÁNEK Petr LU Xiang-Jun OLSON Wilma K. ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2012, volume: 8, edition: 1, DOI

2011

• A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis

  RÉBLOVÁ Kamila ŠPONEROVÁ Judit ŠPAČKOVÁ Naděžda BEŠŠEOVÁ Ivana ŠPONER Jiří

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY B, year: 2011, volume: 115, edition: 47, DOI

• NMR cross-­correlated relaxation rates reveal ion coordination sites in DNA

  FIALA Radovan ŠPAČKOVÁ Naděžda FOLDYNOVÁ-TRANTÍRKOVÁ Silvie ŠPONER Jiří SKLENÁŘ Vladimír TRANTÍREK Lukáš

  Article in Periodical

  Journal of the American Chemical Society, year: 2011, volume: 133, edition: 35, DOI

• Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base-Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

  ZGARBOVA Marie JUREČKA Petr BANÁŠ Pavel OTYEPKA Michal ŠPONEROVÁ Judit LEONTIS Neocles B. ZIRBEL Craig L. ŠPONER Jiří

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY A, year: 2011, volume: 115, edition: 41, DOI

• QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

  MLÝNSKÝ Vojtěch BANÁŠ Pavel WALTER Nils G. ŠPONER Jiří OTYEPKA Michal

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY B, year: 2011, volume: 115, edition: 47, DOI

2010

• An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods

  RÉBLOVÁ Kamila STŘELCOVÁ Zora KULHÁNEK Petr BEŠŠEOVÁ Ivana MATHEWS David H. VAN NOSTRAND Keith YILDIRIM Ilyas TURNER Douglas H. ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2010, volume: 2010, edition: 6

• Conformational Energies of DNA Sugar Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

  MLÁDEK Arnošt ŠPONEROVÁ Judit JUREČKA Petr BANÁŠ Pavel OTYEPKA Michal SVOZIL Daniel ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2010, volume: 6/2010, edition: 12

• Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.

  RÉBLOVÁ Kamila RÁZGA Filip LI Wen GAO Haixiao FRANK Joachim ŠPONER Jiří

  Article in Periodical

  Nucleic Acids Research, year: 2010, volume: 38, edition: 4