prof. RNDr. Jiří Šponer, DrSc.

2011

• 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

• Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome

  BEŠŠEOVÁ Ivana REBLOVA Kamila NEOCLES Leontis SPONER Jiri

  Article in Periodical

  Nucleic Acids Research, year: 2010, volume: 38, edition: 18

• On the Role of the cis Hoogsteen:Sugar-Edge Family of Base Pairs in Platforms and Triplets: Quantum Chemical Insights into RNA Structural Biology

  SHARMA Purshotam SPONER Judit ŠPONER Jiří SHARMA Sitansh BHATTACHARYYA Dhananjay MITRA Abhijit

  Article in Periodical

  Jouranl of Physical Chemistry B, year: 2010, volume: 114, edition: -

• Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.

  MORGADO Claudio JUREČKA Petr SVOZIL Daniel HOBZA pavel ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2010, volume: 14, edition: -

• Structural Dynamics of the Box C/D RNA Kink-Turn and Its Complex with Proteins: The Role of the A-Minor 0 Interaction, Long-Residency Water Bridges, and Structural Ion-Binding Sites Revealed by Molecular Simulations

  ŠPAČKOVÁ Naděžda RÉBLOVÁ Kamila SPONER Jiri

  Article in Periodical

  Jouranl of Physical Chemistry B, year: 2010, volume: 114, edition: 32