Zgarbová M - Search Results

1

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

Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE 3rd, Jurečka P, Sponer J. Krepl M, et al. Among authors: zgarbova m. J Chem Theory Comput. 2012 Jul 10;8(7):2506-2520. doi: 10.1021/ct300275s. Epub 2012 Jun 5. J Chem Theory Comput. 2012. PMID: 23197943 Free PMC article.

2

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

Zgarbová M, Otyepka M, Sponer J, Hobza P, Jurecka P. Zgarbová M, et al. Phys Chem Chem Phys. 2010 Sep 21;12(35):10476-93. doi: 10.1039/c002656e. Epub 2010 Jul 5. Phys Chem Chem Phys. 2010. PMID: 20603660

3

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.

Zgarbová M, Jurečka P, Banáš P, Otyepka M, Sponer JE, Leontis NB, Zirbel CL, Sponer J. Zgarbová M, et al. J Phys Chem A. 2011 Oct 20;115(41):11277-92. doi: 10.1021/jp204820b. Epub 2011 Sep 12. J Phys Chem A. 2011. PMID: 21910417

4

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

Zgarbová M, Otyepka M, Sponer J, Mládek A, Banáš P, Cheatham TE 3rd, Jurečka P. Zgarbová M, et al. J Chem Theory Comput. 2011 Sep 13;7(9):2886-2902. doi: 10.1021/ct200162x. Epub 2011 Aug 2. J Chem Theory Comput. 2011. PMID: 21921995 Free PMC article.

5

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

Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. Šponer J, et al. Among authors: zgarbova m. Phys Chem Chem Phys. 2012 Nov 28;14(44):15257-77. doi: 10.1039/c2cp41987d. Epub 2012 Oct 16. Phys Chem Chem Phys. 2012. PMID: 23072945 Review.

6

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.

Mládek A, Krepl M, Svozil D, Cech P, Otyepka M, Banáš P, Zgarbová M, Jurečka P, Sponer J. Mládek A, et al. Among authors: zgarbova m. Phys Chem Chem Phys. 2013 May 21;15(19):7295-310. doi: 10.1039/c3cp44383c. Phys Chem Chem Phys. 2013. PMID: 23575975

7

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

Zgarbová M, Luque FJ, Sponer J, Cheatham TE 3rd, Otyepka M, Jurečka P. Zgarbová M, et al. J Chem Theory Comput. 2013 May 14;9(5):2339-2354. doi: 10.1021/ct400154j. J Chem Theory Comput. 2013. PMID: 24058302 Free PMC article.

8

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

Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F. Dršata T, et al. Among authors: zgarbova m. Nucleic Acids Res. 2014 Jun;42(11):7383-94. doi: 10.1093/nar/gku338. Epub 2014 May 14. Nucleic Acids Res. 2014. PMID: 24829460 Free PMC article.

9

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

Mlýnský V, Kührová P, Zgarbová M, Jurečka P, Walter NG, Otyepka M, Šponer J, Banáš P. Mlýnský V, et al. Among authors: zgarbova m. J Phys Chem B. 2015 Mar 19;119(11):4220-9. doi: 10.1021/jp512069n. Epub 2015 Mar 5. J Phys Chem B. 2015. PMID: 25692537

10

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

Zgarbová M, Rosnik AM, Luque FJ, Curutchet C, Jurečka P. Zgarbová M, et al. J Comput Chem. 2015 Sep 30;36(25):1874-84. doi: 10.1002/jcc.24012. Epub 2015 Jul 30. J Comput Chem. 2015. PMID: 26224547

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