Michal Otyepka

16 papers Journal 16
YearRankTypeTitle / Venue / Authors
2026 J jnl
Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge.
J. Chem. Inf. Model.
Andrea Nedelníková, Petr Stadlbauer, Pavel Banás, Jirí Sponer, Michal Otyepka, Petra Kührová, Markéta Paloncýová
2025 J jnl
Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome.
J. Comput. Chem.
Andrea Nedelníková, Petr Stadlbauer, Michal Otyepka, Petra Kührová, Markéta Paloncýová
2025 J jnl
Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.
J. Comput. Chem.
Michal Janecek, Petra Kührová, Vojtech Mlýnský, Petr Stadlbauer, Michal Otyepka, Giovanni Bussi, Jirí Sponer, Pavel Banás
2024 J jnl
Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes".
J. Chem. Inf. Model.
Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
2023 J jnl
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.
J. Chem. Inf. Model.
Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
2018 J jnl
ChannelsDB: database of biomacromolecular tunnels and pores.
Nucleic Acids Res.
Lukás Pravda, David Sehnal, Radka Svobodová Vareková, Veronika Navrátilová, Dominik Tousek, Karel Berka, Michal Otyepka, Jaroslav Koca
2018 J jnl
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).
Nucleic Acids Res.
Lukás Pravda, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2017 J jnl
Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.
J. Chem. Inf. Model.
Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka
2016 J jnl
Exponential repulsion improves structural predictability of molecular docking.
J. Comput. Chem.
Václav Bazgier, Karel Berka, Michal Otyepka, Pavel Banás
2015 J jnl
Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4.
J. Chem. Inf. Model.
Veronika Navrátilová, Markéta Paloncýová, Michaela Kajsová, Karel Berka, Michal Otyepka
2014 J jnl
Anatomy of enzyme channels.
BMC Bioinform.
Lukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka
2013 J jnl
MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
J. Cheminformatics
David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca
2012 J jnl
MOLE
Nucleic Acids Res.
Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2011 J jnl
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.
J. Comput. Aided Mol. Des.
Petr Dobes, Jindrich Fanfrlík, Jan Rezác, Michal Otyepka, Pavel Hobza
2006 J jnl
CAVER: a new tool to explore routes from protein clefts, pockets and cavities.
BMC Bioinform.
Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský
2006 J jnl
Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.
J. Comput. Aided Mol. Des.
Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský