prof. RNDr. Michal Otyepka, Ph.D.

2014

• 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

• MOLE: Pokročilý nástroj pro vyhledávání a charakterizaci tunelů

  PRAVDA Lukáš SVOBODOVÁ VAŘEKOVÁ Radka SEHNAL David IONESCU Crina-Maria BERKA Karel OTYEPKA Michal KOČA Jaroslav

  Appeared in Conference without Proceedings

  Year: 2014, type: Appeared in Conference without Proceedings

• 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

2013

• Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory

  MLÁDEK Arnošt KREPL Miroslav SVOZIL Daniel CECH Petr OTYEPKA Michal BANÁŠ Pavel ZGARBOVA Marie JURECKA Petr ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2013, volume: 15, edition: 19, DOI

• Computer Folding of RNA Tetraloops? Are We There Yet?

  KUHROVA Petra BANÁŠ Pavel BEST Robert B ŠPONER Jiří OTYEPKA Michal

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2013, volume: 9, edition: 4, DOI

• Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study

  KREPL Miroslav OTYEPKA Michal BANÁŠ Pavel ŠPONER Jiří

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY B, year: 2013, volume: 117, edition: 6, DOI

• How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

  ŠPONER Jiří ŠPONEROVÁ Judit MLÁDEK Arnošt BANÁŠ Pavel JURECKA Petr OTYEPKA Michal

  Article in Periodical

  Methods, year: 2013, volume: 64, edition: 1, DOI

• MOLE 2.0: advanced approach for analysis of biomacromolecular channels

  SEHNAL David SVOBODOVÁ VAŘEKOVÁ Radka BERKA Karel PRAVDA Lukáš NAVRÁTILOVÁ Veronika BANÁŠ Pavel IONESCU Crina-Maria OTYEPKA Michal KOČA Jaroslav

  Article in Periodical

  Journal of Cheminformatics, year: 2013, volume: 5, edition: 39, DOI

• MOLE 2.0: Improved Approach for Analysis of Biomacromolecular Channels and Pores

  PRAVDA Lukáš SVOBODOVÁ VAŘEKOVÁ Radka SEHNAL David BERKA Karel OTYEPKA Michal KOČA Jaroslav

  Appeared in Conference without Proceedings

  Year: 2013, type: Appeared in Conference without Proceedings