Stefl R - Search Results

1

Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding.

Csaszar K, Spacková N, Stefl R, Sponer J, Leontis NB. Csaszar K, et al. Among authors: stefl r. J Mol Biol. 2001 Nov 9;313(5):1073-91. doi: 10.1006/jmbi.2001.5100. J Mol Biol. 2001. PMID: 11700064

2

An A-type double helix of DNA having B-type puckering of the deoxyribose rings.

Trantírek L, Stefl R, Vorlícková M, Koca J, Sklenár V, Kypr J. Trantírek L, et al. Among authors: stefl r. J Mol Biol. 2000 Apr 7;297(4):907-22. doi: 10.1006/jmbi.2000.3592. J Mol Biol. 2000. PMID: 10736226

3

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

Stefl R, Spacková N, Berger I, Koca J, Sponer J. Stefl R, et al. Biophys J. 2001 Jan;80(1):455-68. doi: 10.1016/S0006-3495(01)76028-6. Biophys J. 2001. PMID: 11159416 Free PMC article.

4

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

Réblová K, Spacková N, Stefl R, Csaszar K, Koca J, Leontis NB, Sponer J. Réblová K, et al. Among authors: stefl r. Biophys J. 2003 Jun;84(6):3564-82. doi: 10.1016/S0006-3495(03)75089-9. Biophys J. 2003. PMID: 12770867 Free PMC article.

5

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates.

Stefl R, Cheatham TE 3rd, Spacková N, Fadrná E, Berger I, Koca J, Sponer J. Stefl R, et al. Biophys J. 2003 Sep;85(3):1787-804. doi: 10.1016/S0006-3495(03)74608-6. Biophys J. 2003. PMID: 12944293 Free PMC article.

6

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.

Fadrná E, Spacková N, Stefl R, Koca J, Cheatham TE 3rd, Sponer J. Fadrná E, et al. Among authors: stefl r. Biophys J. 2004 Jul;87(1):227-42. doi: 10.1529/biophysj.103.034751. Biophys J. 2004. PMID: 15240460 Free PMC article.

7

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: stefl r. 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

8

A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC).

Stefl R, Trantírek L, Vorlícková M, Koca J, Sklenár V, Kypr J. Stefl R, et al. J Mol Biol. 2001 Mar 23;307(2):513-24. doi: 10.1006/jmbi.2001.4484. J Mol Biol. 2001. PMID: 11254379

9

NMR methodology for the study of nucleic acids.

Zídek L, Stefl R, Sklenár V. Zídek L, et al. Among authors: stefl r. Curr Opin Struct Biol. 2001 Jun;11(3):275-81. doi: 10.1016/s0959-440x(00)00218-9. Curr Opin Struct Biol. 2001. PMID: 11406374 Review.

10

Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings.

Padrta P, Stefl R, Králík L, Zídek L, Sklenár V. Padrta P, et al. Among authors: stefl r. J Biomol NMR. 2002 Sep;24(1):1-14. doi: 10.1023/a:1020632900961. J Biomol NMR. 2002. PMID: 12449414

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