- Zgarbova, M.; Luque, F. J.; Sponer, J.; Otyepka, M.; Jurecka, P., A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects. J. Chem. Theory Comput. 2012, 8 (9), 3232-3242.
- Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A., A 2nd Generation Force-Field for the Simulation of Proteins, Nucleic-Acids, and Organic-Molecules. J. Am. Chem. Soc. 1995, 117 (19), 5179-5197.
- Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J., The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26 (16), 1668-1688.
- Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T. E.; Jurecka, 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. 2011, 7 (9), 2886-2902.
- Banas, P.; Hollas, D.; Zgarbova, M.; Jurecka, P.; Orozco, M.; Cheatham, T. E.; Sponer, J.; Otyepka, M., Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins. J. Chem. Theory Comput. 2010, 6 (12), 3836-3849.
- Krepl, M.; Zgarbova, M.; Stadlbauer, P.; Otyepka, M.; Banas, P.; Koca, J.; Cheatham, T. E.; Jurecka, P.; Sponer, 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. 2012, 8 (7), 2506-2520.
- Zgarbova, M.; Luque, F. J.; Sponer, J.; Cheatham, T. E.; Otyepka, M.; Jurecka, P., Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J. Chem. Theory Comput. 2013, 9 (5), 2339-2354.
- Zgarbova, M.; Sponer, J.; Otyepka, M.; Cheatham, T. E.; Galindo-Murillo, R.; Jurecka, 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. 2015, 11 (12), 5723-5736.
- Wang, J. M.; Cieplak, P.; Kollman, P. A., How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21 (12), 1049-1074.
- Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M., Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys. J. 2007, 92 (11), 3817-3829.
- Mlynsky, V.; Banas, P.; Hollas, D.; Reblova, K.; Walter, N. G.; Sponer, J.; Otyepka, M., Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme. J. Phys. Chem. B 2010, 114 (19), 6642-6652.
- Sponer, J.; Banas, P.; Jurecka, P.; Zgarbova, M.; Kuehrova, P.; Havrila, M.; Krepl, M.; Stadlbauer, P.; Otyepka, M., Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome J. Phys. Chem. Lett. 2014, 5, 1771-1782.
- Mlynsky, V.; Kuehrova, P.; Zgarbova, M.; Jurecka, P.; Walter, N. G.; Otyepka, M.; Sponer, J.; Banas, P., Reactive Conformation of the Active Site in the Hairpin Rybozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations J. Phys. Chem. B 2015, 119, 4220-4229.
- Maier, J.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K.; Simmerling, C., ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB J. Chem. Theory Comput. 2015, 11, 3696-3713.
- Allner, O.; Nilsson, L.; Villa, A., Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations J. Chem. Theory Comput. 2012, 8, 1493-1502.
- Zgarbova, M.; Sponer, J.; Jurecka, P., Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER J. Chem. Theory Comput. 2021, https://doi.org/10.1021/acs.jctc.1c00697