2018

• QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

  POKORNÁ Pavlína KRUSE Holger KREPL Miroslav ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2018, volume: 14, edition: 10, DOI

2016

• 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

• 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

• Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

  PANECKA Joanna ŠPONER Jiří TRYLSKA Joanna

  Article in Periodical

  Biochimie, year: 2015, volume: 112, edition: May, 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

• Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

  KRUSE Holger MLÁDEK Arnošt GKIONIS Konstantinos HANSEN Andreas GRIMME Sstefan ŠPONER Jiří

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2015, volume: 11, edition: 10, DOI

• RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3 '-end extended forms of snRNAs

  HROŠŠOVÁ Dominika ŠIKORSKÝ Tomáš POTĚŠIL David BARTOŠOVIČ Marek PASULKA Josef ZDRÁHAL Zbyněk ŠTEFL Richard VAŇÁČOVÁ Štěpánka

  Article in Periodical

  Nucleic Acids Research, year: 2015, volume: 43, edition: 8, DOI

• Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions

  KRUSE Holger ŠPONER Jiří

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2015, volume: 17, edition: 2, DOI

2014

• Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation

  TUDEK Agnieszka FUERTE Odil Porrua KABZINSKI Tomasz LIDSCHREIBER Michael KUBÍČEK Karel FOŘTOVÁ Andrea LACROUTE Francoise VAŇÁČOVÁ Štěpánka CRAMER Patrick ŠTEFL Richard LIBRI Domenico

  Article in Periodical

  Molecular Cell, year: 2014, volume: 55, edition: 3, DOI