prof. RNDr. Jiří Šponer, DrSc.

2015

• Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions

  KRUSE Holger ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2015, volume: 17, edition: 2, DOI

• Untemplated Nonenzymatic Polymerization of 3 ',5 ' cGMP: A Plausible Route to 3 ',5 '-Linked Oligonucleotides in Primordia

  ŠPONEROVÁ Judit ŠPONER Jiří GIORGI Alessandra DI MAURO Ernesto PINO Samanta COSTANZO Giovanna

  Article in Periodical

  Journal of Physical Chemistry B, year: 2015, volume: 119, edition: 7, DOI

• Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

  SRIPATHI Kamali N. BANÁŠ Pavel RÉBLOVÁ Kamila ŠPONER Jiří OTYEPKA Michal WALTER Nils G.

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2015, volume: 17, edition: 8, DOI

2014

• Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations

  KUEHROVA Petra OTYEPKA Michal ŠPONER Jiří BANÁŠ Pavel

  Article in Periodical

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

• 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