Publications by authors named "Nada Spackova"

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Role of Inosine⁻Uracil Base Pairs in the Canonical RNA Duplexes.
Naďa Špačková, Kamila Réblová

Genes (Basel)· June 2018

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Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants.
Nad'a Špačková, Zuzana Trošanová, Filip Šebesta, Séverine Jansen, Jaroslav V Burda

Phys Chem Chem Phys· May 2018

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DNA mutation motifs in the genes associated with inherited diseases.
Michal Růžička, Petr Kulhánek, Lenka Radová, Andrea Čechová, Naďa Špačková

PLoS One· September 2017

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Mechanical Model of DNA Allostery.
Tomáš Dršata, Marie Zgarbová, Naďa Špačková, Petr Jurečka, Jiří Šponer

J Phys Chem Lett· November 2014

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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
Marco Pasi, John H Maddocks, David Beveridge, Thomas C Bishop, David A Case, Nada Spackova

Nucleic Acids Res· October 2014

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Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.
Tomáš Dršata, Nada Špačková, Petr Jurečka, Marie Zgarbová, Jiří Šponer

Nucleic Acids Res· June 2014

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Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.
Jiří Šponer, Arnošt Mládek, Naďa Špačková, Xiaohui Cang, Thomas E Cheatham

J Am Chem Soc· July 2013

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A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.
Kamila Réblová, Judit E Šponer, Naďa Špačková, Ivana Beššeová, Jiří Šponer

J Phys Chem B· December 2011

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NMR cross-correlated relaxation rates reveal ion coordination sites in DNA.
Radovan Fiala, Nada Spacková, Silvie Foldynová-Trantírková, Jirí Sponer, Vladimír Sklenár

J Am Chem Soc· September 2011

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Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.
Nad'a Spacková, Kamila Réblová, Jirí Sponer

J Phys Chem B· August 2010

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A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.
Richard Lavery, Krystyna Zakrzewska, David Beveridge, Thomas C Bishop, David A Case, Nada Spackova

Nucleic Acids Res· January 2010

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Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion.
Vladimir Sychrovsky, Silvie Foldynova-Trantirkova, Nada Spackova, Koen Robeyns, Luc Van Meervelt

Nucleic Acids Res· November 2009

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Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields.
Eva Fadrná, Nad'a Špačková, Joanna Sarzyñska, Jaroslav Koča, Modesto Orozco

J Chem Theory Comput· September 2009

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Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.
Ilyas Yildirim, Harry A Stern, Jiri Sponer, Nada Spackova, Douglas H Turner

J Chem Theory Comput· August 2009

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Molecular dynamics simulations and their application to four-stranded DNA.
Jirí Sponer, Nad'a Spacková

Methods· December 2007

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Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.
Jana Sefcikova, Maryna V Krasovska, Nad'a Spacková, Jirí Sponer, Nils G Walter

Biopolymers· July 2007

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Molecular dynamics simulations of RNA: an in silico single molecule approach.
S Elizabeth McDowell, Nad'a Spacková, Jirí Sponer, Nils G Walter

Biopolymers· February 2007

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Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids.
Vladimír Sychrovský, Zuzana Vokácová, Jirí Sponer, Nad'a Spacková, Bohdan Schneider

J Phys Chem B· November 2006

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Molecular dynamics simulations of sarcin-ricin rRNA motif.
Nad'a Spacková, Jirí Sponer

Nucleic Acids Res· February 2006

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Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence.
Flavia Barone, Filip Lankas, Nada Spackova, Jiri Sponer, Peter Karran

Biophys Chem· October 2005

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Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations.
Maryna V Krasovska, Jana Sefcikova, Nad'a Spacková, Jirí Sponer, Nils G Walter

J Mol Biol· August 2005

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Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs.
Judit E Sponer, Nad'a Spackova, Jerzy Leszczynski, Jirí Sponer

J Phys Chem B· June 2005

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Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.
Judit E Sponer, Nad'a Spacková, Petr Kulhanek, Jerzy Leszczynski, Jirí Sponer

J Phys Chem A· March 2005

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Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
Kamila Réblová, Nad'a Spacková, Jaroslav Koca, Neocles B Leontis, Jirí Sponer

Biophys J· November 2004

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Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes.
Nad'a Spacková, Elena Cubero, Jirí Sponer, Modesto Orozco

J Am Chem Soc· November 2004

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