Mgr. Marie Zgarbová, Ph.D.

Tel: 58 563 4766, E-mail: marie.zgarbova@upol.cz, Room: 3.007

Research interests Education Employment International experience Cooperation Grants, projects

Publications

2017

  1. 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)
  2. Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M: Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J. Phys. Chem. B, 121(11), 2420–2433, 2017. (DOI)
  3. Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M: Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for all 136 Distinct Tetranucleotide Sequences. J. Chem. Inf. Model., 57(2), 275–287, 2017. (DOI)

2016

  1. Dršata T, Zgarbová M, Jurečka P, Šponer J, Lankaš F: On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA. Biophys. J., 110(4), 874–876, 2016. (DOI)
  2. Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE: Assessing the current state of AMBER force field modifications for DNA. J. Chem. Theory Comput., 12(8), 4114–4127, 2016. (DOI)

2015

  1. Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J: 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. J. Phys. Chem. B, 119, 15176−15190, 2015. (DOI)
  2. 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)
  3. Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P: Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields. J. Comput. Chem., 36(25), 1874-1884, 2015. (DOI)
  4. Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P: Refinement of the Sugar-Phosphate Backbone Torsion Beta for the AMBER Force Fields Improves the Description of Z-DNA and B-DNA. J. Chem. Theory Comput., 11(12), 5723–5736, 2015. (DOI)

2014

  1. Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F: Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res., 42(11), 7383-7394, 2014. (DOI)
  2. Dršata T, Zgarbová M, Špačková N, Jurečka P, Šponer J, Lankaš F: Mechanical Model of DNA Allostery. J. Phys. Chem. Lett., 5(21), 3831-3835, 2014. (DOI)
  3. Mládek A, Banáš P, Jurečka P, Otyepka M, Zgarbová M, Šponer J: Energies and 2′-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations. J. Chem. Theory Comput., 10(1), 463-480, 2014. (DOI)
  4. 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)
  5. Zgarbová M, Otyepka M, Šponer J, Lankaš F, Jurečka P: Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA. J. Chem. Theory Comput., 10(8), 3177-3189, 2014. (DOI)

2013

  1. Mládek A, Krepl M, Svozil D, Čech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Šponer J: 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. Phys. Chem. Chem. Phys., 15(19), 7295-7310, 2013. (DOI)
  2. Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P: Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J. Chem. Theory Comput., 9(5), 2339-2354, 2013. (DOI)

2012

  1. Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J: Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J. Chem. Theory Comput., 8(7), 2448-2460, 2012. (DOI)
  2. Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J: Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA. J. Chem. Theory Comput., 8(7), 2506-2520, 2012. (DOI)
  3. Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M: The DNA and RNA sugar–phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys. Chem. Chem. Phys., 14(44), 15257-15277, 2012. (DOI)
  4. Zgarbová M, Luque FJ, Šponer J, Otyepka M, Jurečka P: A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. J. Chem. Theory Comput., 8(9), 3232-3242, 2012. (DOI)

2011

  1. Zgarbová M, Jurečka P, Banáš P, Otyepka M, Šponer JE, Leontis NB, Zirbel CL, Šponer J: Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations. J. Phys. Chem. A, 115(41), 11277-11292, 2011. (DOI)
  2. Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P: Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 7(9), 2886-2902, 2011. (DOI)

2010

  1. Banáš P, Hollas D, Zgarbová M, Jurečka P, Orozco M, Cheatham TE, Šponer J, Otyepka M: Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput., 6(12), 3836-3849, 2010. (DOI)
  2. Zgarbová M, Otyepka M, Šponer J, Hobza P, Jurečka P: Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys. Chem. Chem. Phys., 12(35), 10476-10493, 2010. (DOI)

2009

  1. Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J. Chem. Theory Comput., 5(4), 1166-1179, 2009. (DOI)