Marie Zgarbová

发表

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. Šponer, M. Otyepka, P. Banáš, 2014, Journal of chemical theory and computation.

Assessing the Current State of Amber Force Field Modifications for DNA

James C. Robertson, J. Šponer, T. Cheatham, 2016, Journal of chemical theory and computation.

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

J. Šponer, G. Bussi, R. Best, 2018, bioRxiv.

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

J. Šponer, T. Cheatham, M. Otyepka, 2011, Journal of chemical theory and computation.

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

J. Šponer, T. Cheatham, J. Koča, 2012, Journal of chemical theory and computation.

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

F. J. Luque, J. Šponer, T. Cheatham, 2013, Journal of chemical theory and computation.

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

J. Šponer, T. Cheatham, M. Otyepka, 2015, Journal of chemical theory and computation.

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

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

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

J. Šponer, M. Otyepka, P. Jurečka, 2012, Journal of chemical theory and computation.

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

P. Jurečka, Marie Zgarbová, V. Sychrovský, 2022, Journal of chemical theory and computation.

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

Michal Otyepka, Thomas E. Cheatham, Jirí Sponer, 2017, J. Chem. Inf. Model..

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

J. Šponer, G. Bussi, R. Best, 2019, Journal of chemical theory and computation.

Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.

J. Šponer, M. Otyepka, P. Banáš, 2017, The journal of physical chemistry. B.

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.

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.

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.

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.

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

P. Jurečka, Marie Zgarbová, J. Salomón, 2022, bioRxiv.

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

J. Šponer, P. Jurečka, Marie Zgarbová, 2021, Journal of chemical theory and computation.

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

J. Šponer, P. Jurečka, Marie Zgarbová, 2021, bioRxiv.

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

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

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

F. Javier Luque, F. J. Luque, Carles Curutchet, 2015, J. Comput. Chem..

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

J. Šponer, M. Otyepka, F. Lankaš, 2014, Journal of chemical theory and computation.

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.

J. Šponer, M. Otyepka, P. Banáš, 2013, Physical chemistry chemical physics : PCCP.

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

F. J. Luque, J. Šponer, T. Cheatham, 2013 .

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions".

J. Šponer, G. Bussi, R. Best, 2019, Journal of chemical theory and computation.

Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.

J. Šponer, N. Walter, M. Otyepka, 2015, The journal of physical chemistry. B.

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

Michal Otyepka, Pavel Hobza, Petr Jurecka, 2010, Physical chemistry chemical physics : PCCP.

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

P. Jurečka, Marie Zgarbová, M. Buděšínský, 2021, J. Comput. Chem..

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

J. Šponer, N. Špačková, Tomáš Dršata, 2014, Nucleic acids research.

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.

Craig L. Zirbel, J. Šponer, N. Leontis, 2011, The journal of physical chemistry. A.

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

Kevin E. Riley, J. Šponer, J. Šponer, 2009, Journal of chemical theory and computation.

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

J. Šponer, M. Otyepka, P. Jurečka, 2018, Journal of chemical theory and computation.

Mechanical Model of DNA Allostery.

J. Šponer, N. Špačková, Tomáš Dršata, 2014, The journal of physical chemistry letters.

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

J. Šponer, T. Cheatham, R. Galindo-Murillo, 2023, Journal of Chemical Theory and Computation.

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

J. Šponer, M. Otyepka, F. Lankaš, 2014, Journal of chemical theory and computation.

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

J. Šponer, M. Otyepka, P. Hobza, 2010, Physical chemistry chemical physics : PCCP.

J. Šponer, M. Otyepka, P. Banáš, 2015, The journal of physical chemistry. B.

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.

Craig L. Zirbel, N. Leontis, M. Otyepka, 2011, The journal of physical chemistry. A.