Pavel Banáš

发表

Promoting transparency and reproducibility in enhanced molecular simulations

Jakub Rydzewski, Toni Giorgino, Massimiliano Bonomi, 2019, Nature Methods.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2014, The journal of physical chemistry letters.

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

Jaroslav Koča, Michal Otyepka, Carolina Estarellas, 2015, Biochimica et biophysica acta.

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Physical chemistry chemical physics : PCCP.

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

Michal Otyepka, Arnošt Mládek, Petr Jurečka, 2013, Methods.

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Physical chemistry chemical physics : PCCP.

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.

Michal Otyepka, Modesto Orozco, Thomas E. Cheatham, 2010, Journal of chemical theory and computation.

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

Michal Otyepka, Marek Havrila, Petr Jurečka, 2017, Wiley interdisciplinary reviews. RNA.

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self‐cleavage

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Biopolymers.

Free Energy Landscape of GAGA and UUCG RNA Tetraloops.

Giovanni Bussi, Sandro Bottaro, Pavel Banáš, 2016, The journal of physical chemistry letters.

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

Giovanni Bussi, Michal Otyepka, Sandro Bottaro, 2016, Journal of chemical theory and computation.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

Michal Otyepka, Arnošt Mládek, Petr Jurečka, 2013, Biopolymers.

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2012, The journal of physical chemistry. B.

Computer Folding of RNA Tetraloops? Are We There Yet?

Michal Otyepka, Robert B Best, Pavel Banáš, 2013, Journal of chemical theory and computation.

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

Michal Otyepka, Pavel Hobza, Vojtěch Spiwok, 2015, Journal of chemical theory and computation.

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

Alessandra Magistrato, Michal Otyepka, Jiří Damborský, 2008, Proteins.

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics.

Daniel Svozil, Michal Otyepka, Arnošt Mládek, 2012, Journal of chemical theory and computation.

Chapter 6:Molecular Dynamics Simulations of RNA Molecules

Michal Otyepka, Nils G. Walter, Pavel Banáš, 2012 .

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.

Adrian J Mulholland, Michal Otyepka, Pavel Banáš, 2014, Journal of chemical theory and computation.

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.

Michal Otyepka, Marek Havrila, Petr Jurečka, 2015, The journal of physical chemistry. B.