Jurečka P - Search Results

1

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

Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M. Šponer J, et al. Among authors: jurecka p. Wiley Interdiscip Rev RNA. 2017 May;8(3). doi: 10.1002/wrna.1405. Epub 2016 Nov 10. Wiley Interdiscip Rev RNA. 2017. PMID: 27863061 Review.

2

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs.

Sponer J, Jurecka P, Hobza P. Sponer J, et al. Among authors: jurecka p. J Am Chem Soc. 2004 Aug 18;126(32):10142-51. doi: 10.1021/ja048436s. J Am Chem Soc. 2004. PMID: 15303890

3

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

Pérez A, Sponer J, Jurecka P, Hobza P, Luque FJ, Orozco M. Pérez A, et al. Among authors: jurecka p. Chemistry. 2005 Aug 19;11(17):5062-6. doi: 10.1002/chem.200500255. Chemistry. 2005. PMID: 15977281

4

Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.

Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M, Hobza P. Sponer J, et al. Among authors: jurecka p. Chemistry. 2006 Mar 20;12(10):2854-65. doi: 10.1002/chem.200501239. Chemistry. 2006. PMID: 16425171

5

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.

Jurecka P, Sponer J, Cerný J, Hobza P. Jurecka P, et al. Phys Chem Chem Phys. 2006 May 7;8(17):1985-93. doi: 10.1039/b600027d. Epub 2006 Mar 7. Phys Chem Chem Phys. 2006. PMID: 16633685

6

Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.

Kubar T, Jurecka P, Cerný J, Rezac J, Otyepka M, Valdés H, Hobza P. Kubar T, et al. Among authors: jurecka p. J Phys Chem A. 2007 Jul 5;111(26):5642-7. doi: 10.1021/jp068858j. Epub 2007 Apr 6. J Phys Chem A. 2007. PMID: 17411021

7

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: jurecka p. 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.

8

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.

Morgado CA, Jurecka P, Svozil D, Hobza P, Sponer J. Morgado CA, et al. Among authors: jurecka p. Phys Chem Chem Phys. 2010 Apr 14;12(14):3522-34. doi: 10.1039/b924461a. Epub 2010 Feb 12. Phys Chem Chem Phys. 2010. PMID: 20336251

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: jurecka p. 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: jurecka p. 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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