CAVER: a new tool to explore routes from protein clefts, pockets and cavities. - Martin Petrek; Michal Otyepka; Pavel Banás; Pavlína Kosinová; Jaroslav Koca; Jirí Damborský (BMC Bioinform., 2006)

Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. - Pavel Banás; Michal Otyepka; Petr Jerábek; Martin Petrek; Jirí Damborský (J. Comput. Aided Mol. Des., 2006)

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. - Petr Dobes; Jindrich Fanfrlík; Jan Rezác; Michal Otyepka; Pavel Hobza (J. Comput. Aided Mol. Des., 2011)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. - Karel Berka; Ondrej Hanák; David Sehnal; Pavel Banás; Veronika Navrátilová; Deepti Jaiswal Kundu; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2012)

MOLE 2.0: advanced approach for analysis of biomacromolecular channels. - David Sehnal; Radka Svobodová Vareková; Karel Berka; Lukás Pravda; Veronika Navrátilová; Pavel Banás; Crina-Maria Ionescu; Michal Otyepka; Jaroslav Koca (J. Cheminformatics, 2013)

Anatomy of enzyme channels. - Lukás Pravda; Karel Berka; Radka Svobodová Vareková; David Sehnal; Pavel Banás; Roman A. Laskowski; Jaroslav Koca; Michal Otyepka (BMC Bioinform., 2014)

Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4. - Veronika Navrátilová; Markéta Paloncýová; Michaela Kajsová; Karel Berka; Michal Otyepka (J. Chem. Inf. Model., 2015)

Exponential repulsion improves structural predictability of molecular docking. - Václav Bazgier; Karel Berka; Michal Otyepka; Pavel Banás (J. Comput. Chem., 2016)

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. - Marie Zgarbová; Petr Jurecka; Filip Lankas; Thomas E. Cheatham III; Jirí Sponer; Michal Otyepka (J. Chem. Inf. Model., 2017)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). - Lukás Pravda; David Sehnal; Dominik Tousek; Veronika Navrátilová; Václav Bazgier; Karel Berka; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2018)

ChannelsDB: database of biomacromolecular tunnels and pores. - Lukás Pravda; David Sehnal; Radka Svobodová Vareková; Veronika Navrátilová; Dominik Tousek; Karel Berka; Michal Otyepka; Jaroslav Koca (Nucleic Acids Res., 2018)

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. - Petra Kührová; Vojtech Mlýnský; Michal Otyepka; Jirí Sponer; Pavel Banás (J. Chem. Inf. Model., 2023)

Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes". - Petra Kührová; Vojtech Mlýnský; Michal Otyepka; Jirí Sponer; Pavel Banás (J. Chem. Inf. Model., 2024)

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space. - Michal Janecek; Petra Kührová; Vojtech Mlýnský; Petr Stadlbauer; Michal Otyepka; Giovanni Bussi; Jirí Sponer; Pavel Banás (J. Comput. Chem., 2025)

Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome. - Andrea Nedelníková; Petr Stadlbauer; Michal Otyepka; Petra Kührová; Markéta Paloncýová (J. Comput. Chem., 2025)