prof. RNDr. Jiří Šponer, DrSc.

2012

• Molecular Dynamics Simulations of RNA Molecules

  ŠPONER Jiří OTYEPKA Michal BANÁŠ Pavel RÉBLOVÁ Kamila WALTER Nils

  Chapter of a book

  Innovations in Biomolecular Modeling and Simulations, edition: 1. vydání, year: 2012, number of pages: 27 s.

• Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study

  BANÁŠ Pavel SKLENOVSKY Petr WEDEKIND Joseph E ŠPONER Jiří OTYEPKA Michal

  Article in Periodical

  Journal of Physical Chemistry B, year: 2012, volume: 116, edition: 42, DOI

• On the Road from Formamide Ices to Nucleobases: IR-Spectroscopic Observation of a Direct Reaction between Cyano Radicals and Formamide in a High-Energy Impact Event

  FERUS Martin CIVIS Svatopluk MLÁDEK Arnošt ŠPONER Jiří JUHA Libor ŠPONEROVÁ Judit

  Article in Periodical

  Journal of the American Chemical Society, year: 2012, volume: 134, edition: 51, DOI

• Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

  KREPL Miroslav ZGARBOVA Marie STADLBAUER Petr OTYEPKA Michal BANÁŠ Pavel KOČA Jaroslav CHEATHAM Thomas E. JURECKA Petr ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2012, volume: 8, edition: 7, DOI

• Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

  BEŠŠEOVÁ Ivana BANÁŠ Pavel KUEHROVA Petra KOSINOVA Pavlina OTYEPKA Michal ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2012, volume: 116, edition: 33, DOI

• Structure and mechanical properties of the ribosomal L1 stalk three-way junction

  RÉBLOVÁ Kamila ŠPONER Jiří LANKAŠ Filip

  Article in Periodical

  Nucleic Acids Research, year: 2012, volume: 40, edition: 13, DOI

• The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

  ŠPONER Jiří MLÁDEK Arnošt ŠPONEROVÁ Judit SVOZIL Daniel ZGARBOVÁ Marie BANÁŠ Pavel JUREČKA Petr OTYEPKA Michal

  Article in Periodical

  PHYSICAL CHEMISTRY CHEMICAL PHYSICS, year: 2012, volume: 14, edition: 44, DOI

• Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

  MORGADO Claudio A SVOZIL Daniel TURNER Douglas H ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2012, volume: 14, edition: 36, DOI

• Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform

  MLÁDEK Arnošt ŠPONEROVÁ Judit KULHÁNEK Petr LU Xiang-Jun OLSON Wilma K. ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2012, volume: 8, edition: 1, DOI

2011

• A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis

  RÉBLOVÁ Kamila ŠPONEROVÁ Judit ŠPAČKOVÁ Naděžda BEŠŠEOVÁ Ivana ŠPONER Jiří

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY B, year: 2011, volume: 115, edition: 47, DOI