RNDr. Miroslav Krepl, Ph.D.

2015

• Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

  HAVRILA Marek ZGARBOVÁ Marie JUREČKA Petr BANÁŠ Pavel KREPL Miroslav OTYEPKA Michal ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2015, volume: 119, edition: 49, DOI

• Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

  ESTARELLAS MARTIN Carolina OTYEPKA Michal KOČA Jaroslav BANÁŠ Pavel KREPL Miroslav ŠPONER Jiří

  Article in Periodical

  BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, year: 2015, volume: 1850, edition: 5, DOI

2014

• 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

• Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-turns, Loops, and Tetraloops

  KREPL Miroslav RÉBLOVÁ Kamila KOČA Jaroslav ŠPONER Jiří

  Article in Periodical

  JOURNAL OF PHYSICAL CHEMISTRY B, year: 2013, volume: 117, edition: 18, 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

• Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

  STADLBAUER Petr KREPL Miroslav CHEATHAM Thomas E. KOČA Jaroslav ŠPONER Jiří

  Article in Periodical

  Nucleic Acids Research, year: 2013, volume: 41, edition: 14, DOI

• Study of protein/RNA systems utilizing NMR structural data

  KREPL Miroslav HAVRILA Marek

  Conference abstract

  Year: 2013, type: Conference abstract

2012

• 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

2011

• Molecular dynamics of ribosomal L1 stalk

  KREPL Miroslav RÉBLOVÁ Kamila ŠPONER Jiří

  Conference abstract

  Year: 2011, type: Conference abstract