Stadlbauer P - Search Results

1

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: stadlbauer p. 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.

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. Among authors: stadlbauer p. 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

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. 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.

4

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations.

Stadlbauer P, Trantírek L, Cheatham TE 3rd, Koča J, Sponer J. Stadlbauer P, et al. Biochimie. 2014 Oct;105:22-35. doi: 10.1016/j.biochi.2014.07.009. Epub 2014 Jul 17. Biochimie. 2014. PMID: 25038568 Free article.

5

Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides.

Stadlbauer P, Šponer J, Costanzo G, Di Mauro E, Pino S, Šponer JE. Stadlbauer P, et al. Chemistry. 2015 Feb 23;21(9):3596-604. doi: 10.1002/chem.201406140. Epub 2015 Jan 29. Chemistry. 2015. PMID: 25640446

6

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: stadlbauer p. 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

7

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.

Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J. Stadlbauer P, et al. Nucleic Acids Res. 2015 Nov 16;43(20):9626-44. doi: 10.1093/nar/gkv994. Epub 2015 Oct 3. Nucleic Acids Res. 2015. PMID: 26433223 Free PMC article.

8

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. Among authors: stadlbauer p. 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

9

Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.

Zhang X, Xu CX, Di Felice R, Sponer J, Islam B, Stadlbauer P, Ding Y, Mao L, Mao ZW, Qin PZ. Zhang X, et al. Among authors: stadlbauer p. Biochemistry. 2016 Jan 19;55(2):360-72. doi: 10.1021/acs.biochem.5b01189. Epub 2015 Dec 31. Biochemistry. 2016. PMID: 26678746 Free PMC article.

10

Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?

Islam B, Stadlbauer P, Neidle S, Haider S, Sponer J. Islam B, et al. Among authors: stadlbauer p. J Phys Chem B. 2016 Mar 24;120(11):2899-912. doi: 10.1021/acs.jpcb.6b01059. Epub 2016 Mar 11. J Phys Chem B. 2016. PMID: 26918369 Free article.

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