Krepl M - Search Results

1

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

Krepl M, Havrila M, Stadlbauer P, Banas P, Otyepka M, Pasulka J, Stefl R, Sponer J. Krepl M, et al. J Chem Theory Comput. 2015 Mar 10;11(3):1220-43. doi: 10.1021/ct5008108. Epub 2015 Feb 3. J Chem Theory Comput. 2015. PMID: 26579770

2

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. 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.

3

Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study.

Krepl M, Otyepka M, Banáš P, Šponer J. Krepl M, et al. J Phys Chem B. 2013 Feb 14;117(6):1872-9. doi: 10.1021/jp311180u. Epub 2013 Feb 5. J Phys Chem B. 2013. PMID: 23350675

4

Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

Krepl M, Réblová K, Koča J, Sponer J. Krepl M, et al. J Phys Chem B. 2013 May 9;117(18):5540-55. doi: 10.1021/jp401482m. Epub 2013 Apr 24. J Phys Chem B. 2013. PMID: 23534440

5

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: krepl m. Phys Chem Chem Phys. 2013 May 21;15(19):7295-310. doi: 10.1039/c3cp44383c. Phys Chem Chem Phys. 2013. PMID: 23575975

6

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations.

Stadlbauer P, Krepl M, Cheatham TE 3rd, Koca J, Sponer J. Stadlbauer P, et al. Among authors: krepl m. Nucleic Acids Res. 2013 Aug;41(14):7128-43. doi: 10.1093/nar/gkt412. Epub 2013 May 21. Nucleic Acids Res. 2013. PMID: 23700306 Free PMC article.

7

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.

Estarellas C, Otyepka M, Koča J, Banáš P, Krepl M, Šponer J. Estarellas C, et al. Among authors: krepl m. Biochim Biophys Acta. 2015 May;1850(5):1072-1090. doi: 10.1016/j.bbagen.2014.10.021. Epub 2014 Oct 24. Biochim Biophys Acta. 2015. PMID: 25450173

8

Extended molecular dynamics of a c-kit promoter quadruplex.

Islam B, Stadlbauer P, Krepl M, Koca J, Neidle S, Haider S, Sponer J. Islam B, et al. Among authors: krepl m. Nucleic Acids Res. 2015 Oct 15;43(18):8673-93. doi: 10.1093/nar/gkv785. Epub 2015 Aug 5. Nucleic Acids Res. 2015. PMID: 26245347 Free PMC article.

9

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

Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M. Šponer J, et al. Among authors: krepl m. J Phys Chem Lett. 2014 May 15;5(10):1771-82. doi: 10.1021/jz500557y. Epub 2014 May 7. J Phys Chem Lett. 2014. PMID: 26270382

10

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.

Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J. Havrila M, et al. Among authors: krepl m. J Phys Chem B. 2015 Dec 10;119(49):15176-90. doi: 10.1021/acs.jpcb.5b08876. Epub 2015 Nov 30. J Phys Chem B. 2015. PMID: 26548477

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