Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides

por Mlýnský, Vojtěch, Bussi, Giovanni
Publicado 2017

Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility

por Mlýnský, Vojtěch, Bussi, Giovanni
Publicado 2017

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

por Stadlbauer, Petr, Mlýnský, Vojtěch, Krepl, Miroslav, Šponer, Jiří
Publicado 2023

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes

por Kührová, Petra, Mlýnský, Vojtěch, Otyepka, Michal, Šponer, Jiří, Banáš, Pavel
Publicado 2023

Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field

por Krepl, Miroslav, Pokorná, Pavlína, Mlýnský, Vojtěch, Stadlbauer, Petr, Šponer, Jiří
Publicado 2022

Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations

por Mlýnský, Vojtěch, Kührová, Petra, Stadlbauer, Petr, Krepl, Miroslav, Otyepka, Michal, Banáš, Pavel, Šponer, Jiří
Publicado 2023

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

por Fröhlking, Thorben, Mlýnský, Vojtěch, Janeček, Michal, Kührová, Petra, Krepl, Miroslav, Banáš, Pavel, Šponer, Jiří, Bussi, Giovanni
Publicado 2022

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

por Zhang, Zhengyue, Šponer, Jiří, Bussi, Giovanni, Mlýnský, Vojtěch, Šulc, Petr, Simmons, Chad R., Stephanopoulos, Nicholas, Krepl, Miroslav
Publicado 2023