Výpis publikací

ŠPAČKOVÁ, Naděžda, Zuzana TROŠANOVÁ, F. SEBESTA, Séverine JANSEN, J.V. BURDA, Pavel SRB, Milan ZACHRDLA, Lukáš ŽÍDEK a Jiří KOZELKA. Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants. Physical Chemistry Chemical Physics. CAMBRIDGE: Royal Society of Chemistry, 2018, roč. 20, č. 18, s. 12664-12677. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/c7cp08623g.

ŠPAČKOVÁ, Naděžda a Kamila RÉBLOVÁ. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. GENES. BASEL: MDPI AG, 2018, roč. 9, č. 7, s. 324-337. ISSN 2073-4425. Dostupné z: https://dx.doi.org/10.3390/genes9070324.

RŮŽIČKA, Michal, Petr KULHÁNEK, Lenka RADOVÁ, Andrea ČECHOVÁ, Naděžda ŠPAČKOVÁ, Lenka FAJKUSOVÁ a Kamila RÉBLOVÁ. DNA mutation motifs in the genes associated with inherited diseases. Plos one. San Francisco: Public Library of Science, 2017, roč. 12, č. 8, s. nestránkováno, 16 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0182377.

RÉBLOVÁ, Kamila, Lenka RADOVÁ, Andrea ČECHOVÁ, Michal RŮŽIČKA, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK a Lenka FAJKUSOVÁ. Analysis of intrinsic properties of mutation motifs (coldspots-hotspots) in genes associated with inherited disorders using molecular dynamics methods. In 21st EuroQSAR. 2016.

ŠPAČKOVÁ, Naděžda a Kamila RÉBLOVÁ. Effect of a modified base on stability and flexibility of RNA duplexes: molecular dynamics and thermodynamics study. In 21st EuroQSAR. 2016.

DRŠATA, Tomáš, Marie ZGARBOVÁ, Naděžda ŠPAČKOVÁ, Petr JUREČKA, Jiří ŠPONER a Filip LANKAŠ. Mechanical Model of DNA Allostery. Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2014, roč. 5, č. 21, s. 3831-3835. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz501826q.

ŠPONER, Jiří, Arnošt MLÁDEK, Naděžda ŠPAČKOVÁ, Xiaohui H. CANG, Thomas E. CHEATHAM a Stefan GRIMME. Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations. Journal of the American Chemical Society. WASHINGTON: American Chemical Society, 2013, roč. 135, č. 26, s. 9785-9796. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja402525c.

RÉBLOVÁ, Kamila, Judit ŠPONEROVÁ, Naděžda ŠPAČKOVÁ, Ivana BEŠŠEOVÁ a Jiří ŠPONER. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2011, roč. 115, č. 47, s. 13897-13910. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp2065584.

FIALA, Radovan, Naděžda ŠPAČKOVÁ, Silvie FOLDYNOVÁ-TRANTÍRKOVÁ, Jiří ŠPONER, Vladimír SKLENÁŘ a Lukáš TRANTÍREK. NMR cross-­correlated relaxation rates reveal ion coordination sites in DNA. Journal of the American Chemical Society. Washington, DC., USA: American Chemical Society, 2011, roč. 133, č. 35, s. 13790-13793. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/ja202397p.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Daniel SVOZIL, Jiří ŠPONER a Jaroslav KOČA. Human telomeric G-DNA - a test example for force field adjustment. In Journal Of Biomolecular Structure and Dynamics. Albany: Adenine Press, 2007, s. 709-709. ISSN 0006-3525.

MCDOWELL, Elizabeth, Naďa ŠPAČKOVÁ, Jiří ŠPONER a Nils WALTER. Molecular dynamics simulations of RNA: An in silico single molecule approach. BIOPOLYMERS. 2007, roč. 85, č. 2, s. 169-184. ISSN 0006-3525.

ŠPONER, Jiří, Ali MOKDAD, Filip RÁZGA, Kamila RÉBLOVÁ a Naděžda ŠPAČKOVÁ. Ribosomal RNA motifs and segments have salient flexibilities. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007, s. 632-633. ISSN 0006-3525.

ŠPAČKOVÁ, Naděžda, Thomas E CHEATHAM a Jiří ŠPONER. Molecular dynamics simulations of nucleic acids: MD simulations of G-DNA and functional RNAs. In Challenges and advances in computational chemistry and physics. Computational studies of RNA and DNA. Netherlands: Springer, 2006, s. 301-326. Volume 2. ISBN 1-4020-4794-0.

ŠPAČKOVÁ, Naděžda a Jiří ŠPONER. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Research. Oxford University Press, 2006, roč. 34, č. 2, s. 697-708. ISSN 0006-3465.

ŠPONER, Judit E, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK, Jerzy LESZCZYNSKI a Jiří ŠPONER. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. JOURNAL OF PHYSICAL CHEMISTRY A. 2005, roč. 109, č. 10, s. 2292-2301. ISSN 1089-5639.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn motif - a flexible molecular hinge. In Materials Structure in chemistry, biology, physics and technology. prve. Praha: Krystalograficka spolecnost, 2005, s. 38-38. ISBN 1221-5894.

RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Jaroslav KOČA, Neocles LEONTIS a Jiri SPONER. Long-residency hydration, cation binding and dynamics of Loop E/Helix IV rRNA - L25 protein complex. Biophysical Journal. New York, USA: Rockefeller University, 2004, roč. 87, č. 5, s. 3397-3412. ISSN 0006-3465.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jaroslav KOČA, Thomas E. CHEATHAM a Jiří ŠPONER. Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations. Biophysical Journal. Bethesda, USA: Biophysical Society, 2004, roč. 87, č. 1, s. 227-242. ISSN 0006-3495.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn motif - a flexible molecular hinge. In Conference on Current Trends in Computational Chemistry. prve. Jackson, MS, USA: Jackson, Miss, USA, 2004, s. 87-87.

RÁZGA, Filip, Naďa ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS a Jiří ŠPONER. Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2004, roč. 22, č. 2, s. 183-193. ISSN 0739-1102.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Conformational Flexibility of DNA sequences studied by Advanced Molecular Mechanics and Dynamics Tools. In Book of Abstracts. 2003. vyd. Praha: Workshop on Modeling Interactions in Biomolecules, 2003, s. 20.

ŠTEFL, Richard, Thomas E. CHEATHAM, Naděžda ŠPAČKOVÁ, Eva FADRNÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamics Analysis of the Substates. Biophysical Journal. Bethesda, USA: Biophysical Society, 2003, roč. 85, č. 3, s. 1787-1804. ISSN 0006-3495.

ŠPAČKOVÁ, Naděžda, Richard ŠTEFL, Imre BERGER, Eva FADRNÁ, Jaroslav KOČA, T.E. CHEATHAM III a Jiří ŠPONER. Molecular Dynamics of Guanine Quadruplex Molecules. In Book of Abstracts. Albany, NY, USA: 13th Conversatin in the Discipline Biomolecular Structure and Dynamics, 2003, s. 001-1.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Judit ŠPONER, Jaroslav KOČA a Jiři ŠPONER. Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research. Oxford University Press, 2003, roč. 31, č. 23, s. 6942-6952. ISSN 0006-3465.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Jaroslav KOČA, Neocles LEONTIS a Jiří ŠPONER. Non-Watson-Crick Base Pairing and Hydration in RNA motifs: Molecular Dynamics of 5S rRNA Loop E. In Journal of Biomolecular Structure and Dynamics. Schenectady, New York 12304 USA: Adenine Press, 2003, s. 896-896.

RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Richard STEFL, Kristina CSASZAR, Jaroslav KOCA, Neocles LEONTIS a Jiri SPONER. Non-Watson-Crick Basepairing and Hydration in RNA Motifs:. Biophysical Journal. New York, USA: Rockefeller University, 2003, roč. 84, č. 6, s. 3564-3582, 18 s. ISSN 0006-3465.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER a Neocles, B. LEONTIS. Structure and Dynamics of RNA K-turn Motifs. In RNA klub. vyd. Praha: Praha, 2003, s. 21-21.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Computer modelling of DNA quadruplex conformational behavior. In Chemické Listy. 2002. vyd. Praha: 54. Sjezd chemických společností, 2002, s. 425-426.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. DNA quadruplexes with lateral loops - molecular modelling study of conformational behavior. In Chemometrics VI. 2002. vyd. Brno: Chemometrics VI, 2002, s. O17, 1 s. ISBN 80-210-2918-8.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Kristina CSASZAR, Jaroslav KOČA, Neocles LEONTIS a Jiří ŠPONER. Molecular dynamics of the 5S rRNA loop E. In Chemometrics. Brno: Chemometrics VI., 2002, s. 18-18.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Jiří ŠPONER a Jaroslav KOČA. Molecular modelling of DNA fragment conformational behavior. In WATOC 02. 2002. vyd. Lugano, Švýcarsko: WATOC'02, 2002, s. PC438, 1 s.

ŠTEFL, Richard, Naděžda ŠPAČKOVÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophysical Journal. Bethesda, USA: Biophysical Society, 2001, roč. 80, č. 1, s. 455-468. ISSN 0006-3495.

CSASZAR, Kristina, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jiří ŠPONER a Neocles B. LEONTIS. 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. Journal of Molecular Biology. London: Academic Press, 2001, roč. 313, č. 5, s. 1073-1091. ISSN 0022-2836.

DORNBERGER, Utz, Naděžda ŠPAČKOVÁ, Axel WALTER, Friedrich A. GOLLMICK, Jiří ŠPONER a hartmut FRITZSCHE. Solution structure of the dodecamer d-(CATGGGCC-CATG)(2) is B-DNA. Experimental and molecular dynamics study. Journal of Biomolecular Structure and Dynamics. GUILDERLAND: Adenine Press, 2001, roč. 19, č. 1, s. 159-174. ISSN 0739-1102.

ŠPAČKOVÁ, Naděžda, Imre BERGER a Jiří ŠPONER. Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2001, roč. 123, č. 14, s. 3295-3307. ISSN 0002-7863.

ŠPAČKOVÁ, Naděžda, Imre BERGER a Jiří ŠPONER. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1999, roč. 121, č. 23, s. 5519-5534. ISSN 0002-7863.

ŠPAČKOVÁ, Naděžda, Imre BERGER, Martin EGLI a Jiří ŠPONER. Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: stable trajectories on a nanosecond scale. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1998, roč. 120, č. 24, s. 6147-6151. ISSN 0002-7863.