prof. RNDr. Jiří Šponer, DrSc.

2016

• Assessing the Current State of Amber Force Field Modifications for DNA

  GALINDO-MURILLO Rodrigo ROBERTSON James C. ZGARBOVÁ Marie ŠPONER Jiří OTYEPKA Michal JUREČKA Petr CHEATHAM Thomas E.

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2016, volume: 12, edition: 8, DOI

• Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?

  ISLAM Barira STADLBAUER Petr NEIDLE Stephen HAIDER Shozeb ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2016, volume: 120, edition: 11, DOI

• Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes

  STADLBAUER Petr MAZZANTI L CRAGNOLINI T WALES DJ DERREUMAUX P PASQUALI S ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2016, volume: 12, edition: 12, DOI

• Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective

  SZABLA Rafal HAVRILA Marek KRUSE Holger ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2016, volume: 120, edition: 41, DOI

• Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label

  ZHANG Xiaojun XU Cui-Xia DI FELICE Rosa ŠPONER Jiří ISLAM Barira STADLBAUER Petr DING Yuan MAO Lingling MAO Zong-Wan QIN Peter Z.

  Article in Periodical

  Biochemistry, year: 2016, volume: 55, edition: 2, DOI

• Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

  GKIONIS Konstantinos KRUSE Holger ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2016, volume: 12, edition: 4, DOI

• Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

  ŠPONEROVÁ Judit ŠPONER Jiří NOVÁKOVÁ Olga BRABEC Viktor ŠEDO Ondrej ZDRÁHAL Zbyněk COSTANZO Giovanna PINO Samanta SALADINO Raffaele DI MAURO Ernesto

  Article in Periodical

  Chemistry - A European Journal, year: 2016, volume: 22, edition: 11, DOI

• Four Ways to Oligonucleotides Without Phosphoimidazolides

  ŠPONEROVÁ Judit ŠPONER Jiří DI MAURO Ernesto

  Article in Periodical

  Journal of molecular evolution, year: 2016, volume: 82, edition: 1, DOI

• Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models

  REBIČ Matúš LAAKSONEN Aatto ŠPONER Jiří ULIČNÝ Jozef MOCCI Francesca

  Article in Periodical

  Journal of Physical Chemistry B, year: 2016, volume: 120, edition: 30, DOI

• Non-Enzymatic Oligomerization of 3 ', 5 ' Cyclic AMP

  COSTANZO Giovanna PINO Samanta TIMPERIO Anna Maria ŠPONEROVÁ Judit ŠPONER Jiří NOVAKOVA Olga ŠEDO Ondrej ZDRÁHAL Zbyněk DI MAURO Ernesto

  Article in Periodical

  Plos one, year: 2016, volume: 11, edition: 11, DOI