Molecular dynamics simulations of sarcin–ricin rRNA motif

by Špačková, Nad'a, Šponer, Jiří
Published 2006

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

by Cang, Xiaohui, Šponer, Jiří, Cheatham, Thomas E.
Published 2011

Structure and mechanical properties of the ribosomal L1 stalk three-way junction

by Réblová, Kamila, Šponer, Jiří, Lankaš, Filip
Published 2012

Structural and evolutionary classification of G/U wobble basepairs in the ribosome

by Mokdad, Ali, Krasovska, Maryna V., Sponer, Jiri, Leontis, Neocles B.
Published 2006

The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

by Sefcikova, Jana, Krasovska, Maryna V., Šponer, Jiří, Walter, Nils G.
Published 2007

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

by Rázga, Filip, Koča, Jaroslav, Mokdad, Ali, Šponer, Jiří
Published 2007

Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis

by Cang, Xiaohui, Šponer, Jiří, Cheatham, III, Thomas E.
Published 2011

Classification and energetics of the base-phosphate interactions in RNA

by Zirbel, Craig L., Šponer, Judit E., Šponer, Jiri, Stombaugh, Jesse, Leontis, Neocles B.
Published 2009

Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

by Réblová, Kamila, Fadrná, Eva, Sarzynska, Joanna, Kulinski, Tadeusz, Kulhánek, Petr, Ennifar, Eric, Koča, Jaroslav, Šponer, Jiří
Published 2007

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

by Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E., Jurečka, Petr
Published 2011

How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex

by Ovaere, Margriet, Sponer, Jiri, Sponer, Judit E., Herdewijn, Piet, Van Meervelt, Luc
Published 2012

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

by Stadlbauer, Petr, Krepl, Miroslav, Cheatham, Thomas E., Koča, Jaroslav, Šponer, Jiří
Published 2013

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

by Islam, Barira, Sgobba, Miriam, Laughton, Charlie, Orozco, Modesto, Sponer, Jiri, Neidle, Stephen, Haider, Shozeb
Published 2013

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

by Dršata, Tomáš, Špačková, Naďa, Jurečka, Petr, Zgarbová, Marie, Šponer, Jiří, Lankaš, Filip
Published 2014

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2′-deoxycytidine† †Electronic supplementary information (ESI) available: Including relevant preliminary re...

by Szabla, Rafał, Campos, Jesús, Šponer, Judit E., Šponer, Jiří, Góra, Robert W., Sutherland, John D.
Published 2015

Extended molecular dynamics of a c-kit promoter quadruplex

by Islam, Barira, Stadlbauer, Petr, Krepl, Miroslav, Koca, Jaroslav, Neidle, Stephen, Haider, Shozeb, Sponer, Jiri
Published 2015

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

by Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Koča, Jaroslav, Bussi, Giovanni, Trantírek, Lukáš, Otyepka, Michal, Šponer, Jiří
Published 2015

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

by Reshetnikov, Roman V., Sponer, Jiri, Rassokhina, Olga I., Kopylov, Alexei M., Tsvetkov, Philipp O., Makarov, Alexander A., Golovin, Andrey V.
Published 2011

Assessing the Current State of Amber Force Field Modifications for DNA

by Galindo-Murillo, Rodrigo, Robertson, James C., Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E.
Published 2016

Corrigendum: TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth

by Civiš, Svatopluk, Szabla, Rafał, Szyja, Bartłomiej M., Smykowski, Daniel, Ivanek, Ondřej, Knížek, Antonín, Kubelík, Petr, Šponer, Jiří, Ferus, Martin, Šponer, Judit E.
Published 2016