prof. RNDr. Jiří Šponer, DrSc.

2010

• 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

• Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

  ŠPONER Judit VAZQUEZ-MAYAGOITIA Alvaro SUMPTER Bobby LESZCZYNSKI Jerzy ŠPONER Jiří OTYEPKA Michal BANÁŠ Pavel FUENTES-CABRERA Miguel

  Article in Periodical

  Chemistry – A European Journal, year: 2010, volume: 16, edition: 10

2009

• Balance of Attraction and Repulsion in Nucleic Acid Base Stacking: CCSD(T)/Complete Basis Set Limit Calculations on Uracil Dimer and a Comparison with the Force Field Description

  MORGADO Claudio JUREČKA Petr SVOZIL Daniel HOBZA Pavel ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2009, volume: 5, edition: 1

• Classification and energetics of the base-phosphate interactions in RNA

  ZIRBEL Craig ŠPONER Judit ŠPONER Jiří STOMBAUGH Jesse LEONTIS Neocles

  Article in Periodical

  Nucleic Acids Research, year: 2009, volume: 37, edition: 15

• Dependence of A-RNA simulations on the choice of the force field and salt strength

  BEŠŠEOVÁ Ivana OTYEPKA Michal RÉBLOVÁ Kamila ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2009, volume: 11, edition: -

• Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCIG Base Pairs

  YILDIRIM Ilyas STERN Harry ŠPONER Jiří ŠPAČKOVÁ Naděžda TURNER Douglas

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2009, volume: 5, edition: 8

• Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2OH Group of Ribose

  ŠPONER Jiří ZGARBOVÁ Marie JUREČKA Petr RILEY Kevin ŠPONER Judit HOBZA Pavel

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2009, volume: 5, edition: 4

• 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