RNDr. Miroslav Krepl, Ph.D.

2017

• How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

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

  Article in Periodical

  Wiley Interdisciplinary Reviews: RNA, year: 2017, volume: 8, edition: 3, DOI

• MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, L-Histidine Ligand, and Mg2+

  POKORNÁ Pavlína KREPL Miroslav KRUSE Holger ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2017, volume: 13, edition: 11, DOI

• MD Simulations of HIV‐1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases

  HAVRILA Marek ZGARBOVÁ Marie JURECKA Petr BANÁŠ Pavel KREPL Miroslav OTYEPKA Michal ŠPONER Jiri

  Conference abstract

  Year: 2017, type: Conference abstract

• Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.

  KREPL Miroslav BLATTER Markus CLERY Antoine DAMBERGER Fred F ALLAIN Frederic H T ŠPONER Jiří

  Article in Periodical

  Nucleic acids research, year: 2017, DOI

• Study of Fox-1 and SRSF1 RRMs - the molecular recognition and hydration

  KREPL Miroslav CLERY Antoine BLATTER Markus ALLAIN Frederic ŠPONER Jiří

  Conference abstract

  Year: 2017, type: Conference abstract

2016

• Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

  KREPL Miroslav CLERY Antoine BLATTER Markus ALLAIN Frederic H. T. ŠPONER Jiří

  Article in Periodical

  Nucleic Acids Research, year: 2016, volume: 44, edition: 13, DOI

2015

• Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

  KREPL Miroslav HAVRILA Marek STADLBAUER Petr BANÁŠ Pavel OTYEPKA Michal PASULKA Josef ŠTEFL Richard ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2015, volume: 11, edition: 3, DOI

• Extended molecular dynamics of a c-kit promoter quadruplex

  ISLAM Barira STADLBAUER Petr KREPL Miroslav KOČA Jaroslav NEIDLE Stephen HAIDER Shozeb ŠPONER Jiří

  Article in Periodical

  Nucleic Acids Research, year: 2015, volume: 43, edition: 18, DOI

• 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