Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields
Fadrná, Eva, Špačková, Nad’a, Sarzyñska, Joanna, Koča, Jaroslav, Orozco, Modesto, Cheatham, Thomas E, Kulinski, Tadeusz, Šponer, Jiří
Published in Journal of chemical theory and computation (08.09.2009)
Published in Journal of chemical theory and computation (08.09.2009)
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Journal Article
Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
Réblová, Kamila, Fadrná, Eva, Sarzynska, Joanna, Kulinski, Tadeusz, Kulhánek, Petr, Ennifar, Eric, Koča, Jaroslav, Šponer, Jiří
Published in Biophysical journal (01.12.2007)
Published in Biophysical journal (01.12.2007)
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Journal Article
Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates
Štefl, Richard, Cheatham, Thomas E., Špačková, Nad’a, Fadrná, Eva, Berger, Imre, Koča, Jaroslav, Šponer, Jiří
Published in Biophysical journal (01.09.2003)
Published in Biophysical journal (01.09.2003)
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Journal Article
Molecular Dynamics Simulations of Guanine Quadruplex Loops: Advances and Force Field Limitations
Fadrná, Eva, Špačková, Nad’a, Štefl, Richard, Koča, Jaroslav, Cheatham, Thomas E., Šponer, Jiří
Published in Biophysical journal (01.07.2004)
Published in Biophysical journal (01.07.2004)
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Journal Article
Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study
Fadrná, Eva, Hladečková, Klára, Koča, Jaroslav
Published in Journal of biomolecular structure & dynamics (01.10.2005)
Published in Journal of biomolecular structure & dynamics (01.10.2005)
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Journal Article