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)

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)

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

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)