prof. RNDr. Jiří Šponer, DrSc.

2009

• Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion

  SYCHROVSKÝ Vladimír FOLDÝNOVÁ-TRANTÍRKOVÁ Silvie ŠPAČKOVÁ Naděžda ROBEYNS Koen VAN MEERVELT Luc BLANKENFELDT Wulf VOKÁČOVÁ Zuzana ŠPONER Jiří TRANTÍREK Lukáš

  Article in Periodical

  Nucleic Acids Research, year: 2009, volume: 37, edition: 21

• Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

  FADRNÁ Eva ŠPAČKOVÁ Naděžda JOANNA Sarzynska KOČA Jaroslav OROZCO Modesto CHEATHAM Thomas KULINSKI Tadeusz SPONER Jiri

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2009, volume: 5, edition: 9

• Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies, and Stabilities from Quantum Chemical Calculations

  MLÁDEK Arnošt SHARMA Purshotam MITRA Abhijit BHATTACHARYYA Dhananjay ŠPONER Jiří ŠPONER Judit

  Article in Periodical

  Journal of Physical Chemistry B, year: 2009, volume: 113, edition: 6

2008

• Conformational Transitions of Flanking Purines in HIV-1 RNA Dimerization Initiation Site Kissing Complexes Studied by Charmm Explicit Solvent Molecular Dynamics

  SARZYNSKA Joanna REBLOVA Kamila SPONER Jiri KULINSKI Tadeusz

  Article in Periodical

  Biopolymers, year: 2008, volume: 89, edition: 9

• General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

  BANAS Pavel RULISEK Lubomir HANOSOVA Veronika SVOZIL Daniel WALTER Nils SPONER Jiri OTYEPKA Michal

  Article in Periodical

  Journal of Physical Chemistry B, year: 2008, volume: 112, edition: 35

• Geometrical and Electronic Structure Variability of the Sugar-phosphate Backbone in Nucleic Acids

  SVOZIL Daniel SPONER Judit MARCHAN Ivan PEREZ Alberto CHEATHAM Thomas FORTI Ferda LUQUE Javier OROZCO Modesto SPONER Jiri

  Article in Periodical

  Journal of Physical Chemistry B, year: 2008, volume: 112, edition: 27

• Tautomeric Equilibrium, Stability, and Hydrogen Bonding in 2-Deoxyguanosine Monophosphate Complexed with Mg2+

  KOSENKOV Dmytro GORB Leonid SHISHKIN Oleg SPONER Jiri LESZCZYNSKI Jerzy

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY B, year: 2008, volume: 112, edition: 1

• Theoretical Study on the Factors Controlling the Stability of the Borate Complexes of Ribose, Arabinose, Lyxose, and Xylose

  SPONER Judit E SUMPTER Bobby LESZCZYNSKI Jerzy ŠPONER Jiří FUENTES-CABRERA Miguel

  Article in Periodical

  Chemistry – A European Journal, year: 2008, volume: 32/2008, edition: 14

2007

• Computational studies of nucleic acids, advances and failures

  ŠPONER Jiří

  Article in Proceedings

  Modeling Interactions in Biomolecules III, year: 2007

• Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by Molecular Dynamics

  RÉBLOVÁ Kamila FADRNÁ Eva JOANNA Sarzynska KULINSKI Tadeusz KULHÁNEK Petr ENNIFAR Eric KOČA Jaroslav SPONER Jiri

  Article in Periodical

  Biophysical Journal, year: 2007, volume: 93, edition: 11