Michal Otyepka

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 6

Top Topics

Molecular Dynamics Simulations

Phylogenetic Trees

Complex Structures

Top Venues

J. Chem. Inf. Model.

Nucleic Acids Res.

J. Comput. Chem.

Publications

Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
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. 64 (13) (2024)
Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. J. Chem. Inf. Model. 63 (7) (2023)
Lukás Pravda, David Sehnal, Radka Svobodová Vareková, Veronika Navrátilová, Dominik Tousek, Karel Berka, Michal Otyepka, Jaroslav Koca
ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res. 46 (Database-Issue) (2018)
Lukás Pravda, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Marie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka
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. 57 (2) (2017)
Václav Bazgier, Karel Berka, Michal Otyepka, Pavel Banás
Exponential repulsion improves structural predictability of molecular docking. J. Comput. Chem. 37 (28) (2016)
Veronika Navrátilová, Markéta Paloncýová, Michaela Kajsová, Karel Berka, Michal Otyepka
Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. J. Chem. Inf. Model. 55 (3) (2015)
Lukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka
Anatomy of enzyme channels. BMC Bioinform. 15 (2014)
David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics 5 (2013)
Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Petr Dobes, Jindrich Fanfrlík, Jan Rezác, Michal Otyepka, Pavel Hobza
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J. Comput. Aided Mol. Des. 25 (3) (2011)
Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský
Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J. Comput. Aided Mol. Des. 20 (6) (2006)
Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. 7 (2006)