Mgr. Petra Kührová, Ph.D.
Tel: 58 563 4766, E-mail: petra.kuhrova@upol.cz, Room: 3.007

Research interests
- Structure and dynamics of proteins and nucleic acids (MD)
- Folding of biomolecules (REMD, REST2, WT-metaD)
Education
- 2002 – 07 Mgr. – Education of Mathematic and Chemistry, Palacký University, Olomouc
- 2007 – 11 Ph.D. – Department of Physical chemistry, Palacký University, Olomouc
Employment
- 2009 – 2011 Junior Researcher, Department of Physical chemistry, Palacký University, Olomouc
- 2012 – Junior Researcher, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, Olomouc
- 2013 – Assistant Professor, Department of Physical chemistry, Palacký University, Olomouc
International experience
- 2010, 2011, 2012, 2013 – Department of Chemistry, University of Cambridge, UK; group of Dr. Robert Best
- 2014, 2015 – NIH, Washington DC, USA; group of Dr. Robert Best
Cooperation
- Dr. Robert Best, NIH, Washington DC, USA – folding of biomelcules, coarse-grained model of protein/DNA complexes
Publications
2020
- Mlýnský V, Kührová P, Kühr T, Otyepka M, Bussi G, Banáš P, Šponer J: Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. J. Chem. Theory Comput., 16(6), 3936-3946, 2020. (DOI)
2019
- Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P: Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. J. Chem. Theory Comput., 15(5), 3288-3305, 2019. (DOI)
- Stadlbauer P, Kührová P, Vicherek L, Banáš P, Otyepka M, Trantírek L, Šponer J: Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic Acids Res., 47(14), 7276–7293, 2019. (DOI)
- Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG: Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat. Commun., 10, 4304, 2019. (DOI)
2018
- Havrila M, Stadlbauer P, Kührová P, Banáš P, Mergny J, Otyepka M, Šponer J: Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. Nucleic Acids Res., 46(17), 8754–8771, 2018. (DOI)
2017
- Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P: Mapping the Chemical Space of the RNA Cleavage and its Implications for Ribozyme Catalysis. J. Phys. Chem. B, 121(48), 10828–10840, 2017. (DOI)
- Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M: Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim. Biophys. Acta, Gen. Subj., 1861(5), 1246–1263, 2017. (DOI)
- Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M: How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes? WIREs RNA, 8(3), e1405, 2017. (DOI)
2016
- Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P: Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. J. Chem. Theory Comput., 12(9), 4534–4548, 2016. (DOI)
2015
- Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M: Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. J. Chem. Theory Comput., 11(8), 3866-3877, 2015. (DOI)
- Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P: Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with $epsilon$/$zeta$ Force Field Reparametrizations. J. Phys. Chem. B., 119(11), 4220-4229, 2015. (DOI)
- Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J: Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic. Acids Res., 43(20), 9626-9644, 2015. (DOI)
2014
- Kührová P, Otyepka M, Šponer J, Banáš P: Are Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics Simulations. J. Chem. Theory Comput., 10(1), 401-411, 2014. (DOI)
- Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett., 5(10), 1771-1782, 2014. (DOI)
2013
- Kührová P, Banáš P, Best RB, Šponer J, Otyepka M: Computer Folding of RNA Tetraloops? Are We There Yet?. J. Chem. Theory Comput., 9(4), 2115-2125, 2013. (DOI)
2012
- Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J: Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J. Phys. Chem. B, 116(33), 9899-9916, 2012. (DOI)
- Kührová P, De Simone A, Otyepka M, Best RB: Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign. Biophys. J., 102(8), 1897-1906, 2012. (DOI)
2011
- Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J: Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J. Chem. Theory Comput., 7(9), 2963-2980, 2011. (DOI)
2010
- Florová P, Sklenovský P, Banáš P, Otyepka M: Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact. J. Chem. Theory Comput., 6(11), 3569-3579, 2010. (DOI)