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

CAVER: a new tool to explore routes from protein clefts, pockets and cavities

por Petřek, Martin, Otyepka, Michal, Banáš, Pavel, Košinová, Pavlína, Koča, Jaroslav, Damborský, Jiří
Publicado 2006

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

Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

por Stadlbauer, Petr, Kührová, Petra, Vicherek, Lukáš, Banáš, Pavel, Otyepka, Michal, Trantírek, Lukáš, Šponer, Jiří
Publicado 2019

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

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

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

por Sripathi, Kamali N., Tay, Wendy W., Banáš, Pavel, Otyepka, Michal, Šponer, Jiří, Walter, Nils G.
Publicado 2014

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

por Havrila, Marek, Stadlbauer, Petr, Kührová, Petra, Banáš, Pavel, Mergny, Jean-Louis, Otyepka, Michal, Šponer, Jiří
Publicado 2018

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

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

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

Anatomy of enzyme channels

por Pravda, Lukáš, Berka, Karel, Svobodová Vařeková, Radka, Sehnal, David, Banáš, Pavel, Laskowski, Roman A, Koča, Jaroslav, Otyepka, Michal
Publicado 2014

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

por Sehnal, David, Svobodová Vařeková, Radka, Berka, Karel, Pravda, Lukáš, Navrátilová, Veronika, Banáš, Pavel, Ionescu, Crina-Maria, Otyepka, Michal, Koča, Jaroslav
Publicado 2013

Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch

por Suddala, Krishna C., Price, Ian R., Dandpat, Shiba S., Janeček, Michal, Kührová, Petra, Šponer, Jiří, Banáš, Pavel, Ke, Ailong, Walter, Nils G.
Publicado 2019

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

por Berka, Karel, Hanák, Ondřej, Sehnal, David, Banáš, Pavel, Navrátilová, Veronika, Jaiswal, Deepti, Ionescu, Crina-Maria, Svobodová Vařeková, Radka, Koča, Jaroslav, Otyepka, Michal
Publicado 2012

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

por Islam, Barira, Stadlbauer, Petr, Gil-Ley, Alejandro, Pérez-Hernández, Guillermo, Haider, Shozeb, Neidle, Stephen, Bussi, Giovanni, Banas, Pavel, Otyepka, Michal, Sponer, Jiri
Publicado 2017

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

por Šponer, Jiří, Bussi, Giovanni, Krepl, Miroslav, Banáš, Pavel, Bottaro, Sandro, Cunha, Richard A., Gil-Ley, Alejandro, Pinamonti, Giovanni, Poblete, Simón, Jurečka, Petr, Walter, Nils G., Otyepka, Michal
Publicado 2018