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Employment (2)

University of Ostrava: Ostrava, CZ

2024-03 to present (Department of Physics)
Employment
Source: Self-asserted source
Marie Zgarbova

Palacký University, Olomouc: Olomouc, CZ

2009-01-01 to present
Employment
Source: Self-asserted source
Marie Zgarbova

Works (41)

Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field

Journal of Chemical Theory and Computation
2025-01-28 | Journal article
DOI: 10.1021/acs.jctc.4c01100
Contributors: Marie Zgarbová; Jiří Šponer; Petr Jurečka
Source: check_circle
Crossref

Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field

2024-08-22 | Preprint
DOI: 10.1101/2024.08.21.609021
Contributors: Marie Zgarbova; Jiri Sponer; Petr Jurecka
Source: check_circle
Crossref

Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition

Journal of Chemical Theory and Computation
2023-07-11 | Journal article
DOI: 10.1021/acs.jctc.3c00233
Contributors: Olivia Love; Rodrigo Galindo-Murillo; Marie Zgarbová; Jiří Šponer; Petr Jurečka; Thomas E. Cheatham, III
Source: check_circle
Crossref

Probabilistic Interpretation of NMR J-Couplings Determines BI-BII State Equilibria in DNA

Journal of Chemical Theory and Computation
2022 | Journal article
DOI: 10.1021/acs.jctc.2c00733
Part of ISSN: 1549-9618
Contributors: Fukal, J.; Zgarbova, M.; Jurecka, P.; Sebera, J.; Sychrovsky, V.
Source: Self-asserted source
Marie Zgarbova
grade
Preferred source (of 2)‎

The Ad-MD method to calculate NMR shift including effects due to conformational dynamics: The P-31 NMR shift in DNA

Journal of Computational Chemistry
2022 | Journal article
DOI: 10.1002/jcc.26778
Part of ISSN: 0192-8651
Contributors: Fukal, J.; Budesinsky, M.; Pav, O.; Jurecka, P.; Zgarbova, M.; Sebera, J.; Sychrovsky, V.
Source: Self-asserted source
Marie Zgarbova

Continuous B- to A-Transition in Protein-DNA Binding - How Well Is It Described by Current AMBER Force Fields?

2022-01-13 | Preprint
DOI: 10.1101/2022.01.13.476176
Contributors: Petr Jurečka; Marie Zgarbová; Filip Černý; Jan Salomon
Source: check_circle
Crossref

Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

Journal of Chemical Theory and Computation
2021 | Journal article
DOI: 10.1021/acs.jctc.1c00697
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Sponer, J.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova
grade
Preferred source (of 2)‎

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions (vol 15, pg 3288, 2019)

Journal of Chemical Theory and Computation
2020 | Journal article
DOI: 10.1021/acs.jctc.9b01189
Part of ISSN: 1549-9618
Contributors: Kuhrova, P.; Mlynsky, V.; Zgarbova, M.; Krepl, M.; Bussi, G.; Best, R. B.; Otyepka, M.; Sponer, J.; Banas, P.
Source: Self-asserted source
Marie Zgarbova

Evaluation of the current state of AMBER DNA force fields

Journal of Biomolecular Structure & Dynamics
2019 | Conference abstract
Part of ISSN: 0739-1102
Contributors: Zgarbova, M.; Otyepka, M.; Sponer, J.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

Force fields in trouble-what could our DNA and RNA potentials do better?

Journal of Biomolecular Structure & Dynamics
2019 | Conference abstract
Part of ISSN: 0739-1102
Contributors: Jurecka, P.; Zgarbova, M.; Sponer, J.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

Journal of Chemical Theory and Computation
2019 | Journal article
DOI: 10.1021/acs.jctc.8b00955
Part of ISSN: 1549-9618
Contributors: Kuhrova, P.; Mlynsky, V.; Zgarbova, M.; Krepl, M.; Bussi, G.; Best, R. B.; Otyepka, M.; Sponer, J.; Banas, P.
Source: Self-asserted source
Marie Zgarbova

Tuning the hydrogen-bonding interactions of the AMBER RNA force field

Journal of Biomolecular Structure & Dynamics
2019 | Conference abstract
Part of ISSN: 0739-1102
Contributors: Kuhrova, P.; Mlynsky, V.; Zgarbova, M.; Krepl, M.; Bussi, G.; Best, R. B.; Otyepka, M.; Sponer, J.; Banas, P.
Source: Self-asserted source
Marie Zgarbova

A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker

Journal of Chemical Theory and Computation
2018 | Journal article
DOI: 10.1021/acs.jctc.7b00926
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Jurecka, P.; Sponer, J.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Improving The Performance Of The Amber Rna Force Field By Tuning The Hydrogen-Bonding Interactions

2018-09-07 | Preprint
DOI: 10.1101/410993
Contributors: Petra Kührová; Vojtěch Mlýnský; Marie Zgarbová; Miroslav Krepl; Giovanni Bussi; Robert B. Best; Michal Otyepka; Jiří Šponer; Pavel Banáš
Source: check_circle
Crossref

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

Wiley Interdisciplinary Reviews-Rna
2017 | Journal article
DOI: ARTN e1405 10.1002/wrna.1405
Part of ISSN: 1757-7004
Contributors: Sponer, J.; Krepl, M.; Banas, P.; Kuhrova, P.; Zgarbova, M.; Jurecka, P.; Havrila, M.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Journal of Chemical Information and Modeling
2017 | Journal article
DOI: 10.1021/acs.jcim.6b00621
Part of ISSN: 1549-9596
Contributors: Zgarbova, M.; Jurecka, P.; Lankas, F.; Cheatham, T. E.; Sponer, J.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Noncanonical alpha/gamma Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field

Journal of Physical Chemistry B
2017 | Journal article
DOI: 10.1021/acs.jpcb.7b00262
Part of ISSN: 1520-6106
Contributors: Zgarbova, M.; Jurecka, P.; Banas, P.; Havrila, M.; Sponer, J.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Assessing the Current State of Amber Force Field Modifications for DNA

Journal of Chemical Theory and Computation
2016 | Journal article
DOI: 10.1021/acs.jctc.6b00186
Part of ISSN: 1549-9618
Contributors: Galindo-Murillo, R.; Robertson, J. C.; Zgarbova, M.; Sponer, J.; Otyepka, M.; Jurecka, P.; Cheatham, T. E.
Source: Self-asserted source
Marie Zgarbova

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Biophysical Journal
2016 | Journal article
DOI: 10.1016/j.bpj.2015.12.039
Part of ISSN: 0006-3495
Contributors: Drsata, T.; Zgarbova, M.; Jurecka, P.; Sponer, J.; Lankas, F.
Source: Self-asserted source
Marie Zgarbova

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

Journal of Physical Chemistry B
2015 | Journal article
DOI: 10.1021/acs.jpcb.5b08876
Part of ISSN: 1520-6106
Contributors: Havrila, M.; Zgarbova, M.; Jurecka, P.; Banas, P.; Krepl, M.; Otyepka, M.; Sponer, J.
Source: Self-asserted source
Marie Zgarbova

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

Journal of Physical Chemistry B
2015 | Journal article
DOI: 10.1021/jp512069n
Part of ISSN: 1520-6106
Contributors: Mlynsky, V.; Kuhrova, P.; Zgarbova, M.; Jurecka, P.; Walter, N. G.; Otyepka, M.; Sponer, J.; Banas, P.
Source: Self-asserted source
Marie Zgarbova

Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Journal of Chemical Theory and Computation
2015 | Journal article
DOI: 10.1021/acs.jctc.5b00716
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Sponer, J.; Otyepka, M.; Cheatham, T. E.; Galindo-Murillo, R.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields

Journal of Computational Chemistry
2015 | Journal article
DOI: 10.1002/jcc.24012
Part of ISSN: 0192-8651
Contributors: Zgarbova, M.; Rosnik, A. M.; Luque, F. J.; Curutchet, C.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Journal of Chemical Theory and Computation
2014 | Journal article
DOI: 10.1021/ct500120v
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Otyepka, M.; Sponer, J.; Lankas, F.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

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

Journal of Chemical Theory and Computation
2014 | Journal article
DOI: 10.1021/ct400837p
Part of ISSN: 1549-9618
Contributors: Mladek, A.; Banas, P.; Jurecka, P.; Otyepka, M.; Zgarbova, M.; Sponer, J.
Source: Self-asserted source
Marie Zgarbova

Mechanical Model of DNA Allostery

Journal of Physical Chemistry Letters
2014 | Journal article
DOI: 10.1021/jz501826q
Part of ISSN: 1948-7185
Contributors: Drsata, T.; Zgarbova, M.; Spackova, N.; Jurecka, P.; Sponer, J.; Lankas, F.
Source: Self-asserted source
Marie Zgarbova

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

Nucleic Acids Research
2014 | Journal article
DOI: 10.1093/nar/gku338
Part of ISSN: 0305-1048
Contributors: Drsata, T.; Spackova, N.; Jurecka, P.; Zgarbova, M.; Sponer, J.; Lankas, F.
Source: Self-asserted source
Marie Zgarbova

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

Journal of Physical Chemistry Letters
2014 | Journal article
DOI: 10.1021/jz500557y
Part of ISSN: 1948-7185
Contributors: Sponer, J.; Banas, P.; Jurecka, P.; Zgarbova, M.; Kuhrova, P.; Havrila, M.; Krepl, M.; Stadlbauer, P.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

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

Physical Chemistry Chemical Physics
2013 | Journal article
DOI: 10.1039/c3cp44383c
Part of ISSN: 1463-9076
Contributors: Mladek, A.; Krepl, M.; Svozil, D.; Cech, P.; Otyepka, M.; Banas, P.; Zgarbova, M.; Jurecka, P.; Sponer, J.
Source: Self-asserted source
Marie Zgarbova

Deriving force field dihedral angle parameters that account for conformation-dependent solvation effects

Journal of Biomolecular Structure & Dynamics
2013 | Conference abstract
DOI: 10.1080/07391102.2013.786348
Part of ISSN: 0739-1102
Contributors: Jurecka, P.; Zgarbova, M.; Luque, F. J.; Sponer, J.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Refinement of force field torsion parameters for nucleic acids based on inclusion of conformation-dependent solvation effects

Journal of Biomolecular Structure & Dynamics
2013 | Conference abstract
DOI: 10.1080/07391102.2013.786352
Part of ISSN: 0739-1102
Contributors: Zgarbova, M.; Otyepka, M.; Banas, P.; Luque, F. J.; Cheatham, T. E.; Sponer, J.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

Journal of Chemical Theory and Computation
2013 | Journal article
DOI: 10.1021/ct400154j
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Luque, F. J.; Sponer, J.; Cheatham, T. E.; Otyepka, M.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects

Journal of Chemical Theory and Computation
2012 | Journal article
DOI: 10.1021/ct3001987
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Luque, F. J.; Sponer, J.; Otyepka, M.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

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

Journal of Chemical Theory and Computation
2012 | Journal article
DOI: 10.1021/ct3001238
Part of ISSN: 1549-9618
Contributors: Banas, P.; Mladek, A.; Otyepka, M.; Zgarbova, M.; Jurecka, P.; Svozil, D.; Lankas, F.; Sponer, J.
Source: Self-asserted source
Marie Zgarbova

Reference Simulations of Noncanonical Nucleic Acids with Different chi Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

Journal of Chemical Theory and Computation
2012 | Journal article
DOI: 10.1021/ct300275s
Part of ISSN: 1549-9618
Contributors: Krepl, M.; Zgarbova, M.; Stadlbauer, P.; Otyepka, M.; Banas, P.; Koca, J.; Cheatham, T. E.; Jurecka, P.; Sponer, J.
Source: Self-asserted source
Marie Zgarbova

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

Physical Chemistry Chemical Physics
2012 | Journal article
DOI: 10.1039/c2cp41987d
Part of ISSN: 1463-9076
Contributors: Sponer, J.; Mladek, A.; Sponer, J. E.; Svozil, D.; Zgarbova, M.; Banas, P.; Jurecka, P.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

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

Journal of Physical Chemistry A
2011 | Journal article
DOI: 10.1021/jp204820b
Part of ISSN: 1089-5639
Contributors: Zgarbova, M.; Jurecka, P.; Banas, P.; Otyepka, M.; Sponer, J. E.; Leontis, N. B.; Zirbel, C. L.; Sponer, J.
Source: Self-asserted source
Marie Zgarbova

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

Journal of Chemical Theory and Computation
2011 | Journal article
DOI: 10.1021/ct200162x
Part of ISSN: 1549-9618
Contributors: Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T. E.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

Physical Chemistry Chemical Physics
2010 | Journal article
DOI: 10.1039/c002656e
Part of ISSN: 1463-9076
Contributors: Zgarbova, M.; Otyepka, M.; Sponer, J.; Hobza, P.; Jurecka, P.
Source: Self-asserted source
Marie Zgarbova

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

Journal of Chemical Theory and Computation
2010 | Journal article
DOI: 10.1021/ct100481h
Part of ISSN: 1549-9618
Contributors: Banas, P.; Hollas, D.; Zgarbova, M.; Jurecka, P.; Orozco, M.; Cheatham, T. E.; Sponer, J.; Otyepka, M.
Source: Self-asserted source
Marie Zgarbova

Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2 '-OH Group of Ribose

Journal of Chemical Theory and Computation
2009 | Journal article
DOI: 10.1021/ct800547k
Part of ISSN: 1549-9618
Contributors: Sponer, J.; Zgarbova, M.; Jurecka, P.; Riley, K. E.; Sponer, J. E.; Hobza, P.
Source: Self-asserted source
Marie Zgarbova

Peer review (2 reviews for 2 publications/grants)

Review activity for Biophysical chemistry. (1)
Review activity for Journal of chemical theory and computation : (1)
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