Otyepka M - Search Results

1

Formic Acid, a Ubiquitous but Overlooked Component of the Early Earth Atmosphere.

Mohammadi E, Petera L, Saeidfirozeh H, Knížek A, Kubelík P, Dudžák R, Krůs M, Juha L, Civiš S, Coulon R, Malina O, Ugolotti J, Ranc V, Otyepka M, Šponer J, Ferus M, Šponer JE. Mohammadi E, et al. Among authors: otyepka m. Chemistry. 2020 Sep 16;26(52):12075-12080. doi: 10.1002/chem.202000323. Epub 2020 Aug 11. Chemistry. 2020. PMID: 32293757

2

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.

Banás P, Rulísek L, Hánosová V, Svozil D, Walter NG, Sponer J, Otyepka M. Banás P, et al. Among authors: otyepka m. J Phys Chem B. 2008 Sep 4;112(35):11177-87. doi: 10.1021/jp802592z. Epub 2008 Aug 8. J Phys Chem B. 2008. PMID: 18686993 Free PMC article.

3

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

Banás P, Jurecka P, Walter NG, Sponer J, Otyepka M. Banás P, et al. Among authors: otyepka m. Methods. 2009 Oct;49(2):202-16. doi: 10.1016/j.ymeth.2009.04.007. Epub 2009 May 4. Methods. 2009. PMID: 19398008 Free PMC article. Review.

4

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Ditzler MA, Otyepka M, Sponer J, Walter NG. Ditzler MA, et al. Among authors: otyepka m. Acc Chem Res. 2010 Jan 19;43(1):40-7. doi: 10.1021/ar900093g. Acc Chem Res. 2010. PMID: 19754142 Free PMC article.

5

Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues.

Sponer JE, Vázquez-Mayagoitia A, Sumpter BG, Leszczynski J, Sponer J, Otyepka M, Banás P, Fuentes-Cabrera M. Sponer JE, et al. Among authors: otyepka m. Chemistry. 2010 Mar 8;16(10):3057-65. doi: 10.1002/chem.200902068. Chemistry. 2010. PMID: 20119984

6

Dependence of A-RNA simulations on the choice of the force field and salt strength.

Besseová I, Otyepka M, Réblová K, Sponer J. Besseová I, et al. Among authors: otyepka m. Phys Chem Chem Phys. 2009 Dec 7;11(45):10701-11. doi: 10.1039/b911169g. Epub 2009 Sep 24. Phys Chem Chem Phys. 2009. PMID: 20145814

7

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

Mlýnský V, Banás P, Hollas D, Réblová K, Walter NG, Sponer J, Otyepka M. Mlýnský V, et al. Among authors: otyepka m. J Phys Chem B. 2010 May 20;114(19):6642-52. doi: 10.1021/jp1001258. J Phys Chem B. 2010. PMID: 20420375 Free PMC article.

8

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.

Banás P, Walter NG, Sponer J, Otyepka M. Banás P, et al. Among authors: otyepka m. J Phys Chem B. 2010 Jul 8;114(26):8701-12. doi: 10.1021/jp9109699. J Phys Chem B. 2010. PMID: 20536206 Free PMC article.

9

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. Among authors: otyepka m. 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

10

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. Among authors: otyepka m. 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

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