prof. RNDr. Jiří Šponer, DrSc.

2014

• Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

  ZGARBOVÁ Marie OTYEPKA Michal ŠPONER Jiří LANKAŠ Filip JUREČKA Petr

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2014, volume: 10, edition: 8, DOI

• Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

  MLÝNSKÝ Vojtěch BANÁŠ Pavel ŠPONER Jiří VAN DER KAMP Marc W. MULHOLLAND Adrian J. OTYEPKA Michal

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2014, volume: 10, edition: 4, DOI

• Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

  SRIPATHI Kamali N. TAY Wendy W. BANÁŠ Pavel OTYEPKA Michal ŠPONER Jiří WALTER Nils G.

  Article in Periodical

  RNA, year: 2014, volume: 20, edition: 7, DOI

• Energies and 2 '-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations

  MLÁDEK Arnošt BANÁŠ Pavel JUREČKA Petr OTYEPKA Michal ZGARBOVÁ Marie ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2014, volume: 10, edition: 1, DOI

• High-Energy Chemistry of Formamide: A Simpler Way for Nucleobase Formation

  FERUS Martin MICHALČÍKOVÁ Regina SHESTIVSKÁ Violetta ŠPONER Jiří ŠPONEROVÁ Judit CIVIŠ Svatopluk

  Article in Periodical

  Journal of Physical Chemistry A, year: 2014, volume: 118, edition: 4, DOI

• Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

  GKIONIS Konstantinos KRUSE Holger PLATTS James MLÁDEK Arnošt KOČA Jaroslav ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2014, volume: 10, edition: 3, DOI

• Mechanical Model of DNA Allostery

  DRŠATA Tomáš ZGARBOVÁ Marie ŠPAČKOVÁ Naděžda JUREČKA Petr ŠPONER Jiří LANKAŠ Filip

  Article in Periodical

  Journal of Physical Chemistry Letters, year: 2014, volume: 5, edition: 21, DOI

• Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

  DRSATA Tomáš ŠPAČKOVÁ Naďa JUREČKA Petr ZGARBOVÁ Marie ŠPONER Jiří LANKAŠ Filip

  Article in Periodical

  Nucleic Acids Research, year: 2014, volume: 42, edition: 11, DOI

• Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

  ŠPONER Jiří BANÁŠ Pavel JUREČKA Petr ZGARBOVÁ Marie KÜHROVÁ Petra HAVRILA Marek KREPL Miroslav STADLBAUER Petr OTYEPKA Michal

  Article in Periodical

  The Journal of Physical Chemistry Letters, year: 2014, volume: 5, edition: 10, DOI

• Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases

  SZABLA Rafal Kazimierz GÓRA Robert W. ŠPONER Jiří ŠPONEROVÁ Judit

  Article in Periodical

  Chemistry - A European Journal, year: 2014, volume: 20, edition: 9, DOI