Protonation states of the key active site residues and structural dynamics of glmS riboswitch as reveled by molecular dynamics

Por Banáš, Pavel, Walter, Nils G., Šponer, Jiří, Otyepka, Michal
Publicado em 2010

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

Por Banáš, Pavel, Jurečka, Petr, Walter, Nils G., Šponer, Jiří, Otyepka, Michal
Publicado em 2009

QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

Por Mlýnský, Vojtěch, Banáš, Pavel, Walter, Nils G., Šponer, Jiří, Otyepka, Michal
Publicado em 2011

Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study

Por Banáš, Pavel, Sklenovský, Petr, Wedekind, Joseph E., Šponer, Jiří, Otyepka, Michal
Publicado em 2012

The Role of an Active Site Mg(2+) in HDV Ribozyme Self-Cleavage: Insights from QM/MM Calculations

Por Mlýnský, Vojtěch, Walter, Nils G., Šponer, Jiří, Otyepka, Michal, Banáš, Pavel
Publicado no Phys Chem Chem Phys (2015)

Chemical Feasibility of the General Acid/Base Mechanism of glmS Ribozyme Self-Cleavage

Por Dubecký, Matúš, Walter, Nils G., Šponer, Jiří, Otyepka, Michal, Banáš, Pavel
Publicado no Biopolymers (2015)

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

Por Koča Jaroslav, Košinová Pavlína, Banáš Pavel, Otyepka Michal, Petřek Martin, Damborský Jiří
Publicado em 2006-06-01

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 em 2006

Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

Por Sripathi, Kamali N., Banáš, Pavel, Reblova, Kamila, Šponer, Jiři, Otyepka, Michal, Walter, Nils G.
Publicado no Phys Chem Chem Phys (2015)

General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

Por Banáš, Pavel, Rulíšek, Lubomír, Hánošová, Veronika, Svozil, Daniel, Walter, Nils G., Šponer, Jiří, Otyepka, Michal
Publicado em 2008

Extensive Molecular Dynamics Simulations Show That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

Por Mlýnský, Vojtěch, Banáš, Pavel, Hollas, Daniel, Réblová, Kamila, Walter, Nils G., Šponer, Jiří, Otyepka, Michal
Publicado em 2010

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 em 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 em 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 no Nucleic Acids Res (2018)

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

Por Kührová, Petra, Best, Robert B., Bottaro, Sandro, Bussi, Giovanni, Šponer, Jiří, Otyepka, Michal, Banáš, Pavel
Publicado no J Chem Theory Comput (2016)

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 no Nucleic Acids Res (2015)

Anatomy of enzyme channels

Por Pravda, Lukáš, Berka, Karel, Svobodová Vařeková, Radka, Sehnal, David, Banáš, Pavel, Laskowski, Roman A, Koča, Jaroslav, Otyepka, Michal
Publicado no BMC Bioinformatics (2014)

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA

Por Krepl, Miroslav, Zgarbová, Marie, Stadlbauer, Petr, Otyepka, Michal, Banáš, Pavel, Koča, Jaroslav, Cheatham, Thomas E., Jurečka, Petr, Šponer, Jiří
Publicado em 2012

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 em 2013

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 em 2012