MOLE 2.0
A universal toolkit for rapid location and characterization of channels and pores in biomacromolecules.

Biomacromolecular channels and pores play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels.

Current version: 2.13.1.8. For installation instructions, please consult the manual.

An online service for channel computation.

• MOLE 2.0: Sehnal D., Svobodova Varekova R., Berka K., Pravda L., Navratilova V., Banas P., Ionescu C.-M., Geidl S., Otyepka M., Koca J.: MOLE 2.0: Advanced Approach for Analysis of Biomacromolecular Channels, submitted.
• MOLEonline 2.0: Berka, K; Hanak, O; Sehnal, D; Banas, P; Navratilova, V; Jaiswal, D; Ionescu, C-M; Svobodova Varekova, R; Koča, J; Otyepka, M: MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nucleic Acid Research 2012, 40(W1): W222-W227. doi:10.1093/nar/GKS363
• MOLE 1.0: Petrek M., Kosinova P., Koca J., Otyepka M.: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure 2007, 15, 1357-1363. doi:10.1016/j.str.2007.10.007

MOLE 2.0 was developed in collaboration of the teams at National Centre for Biomolecular Research at the Masaryk University Brno/CEITEC, and Department of Physical Chemistry/RCPTM at the Palacky University Olomouc.

• NCBR: David Sehnal, Radka Svobodová Vařeková, Crina M. Ionescu, Lukáš Pravda, and Jaroslav Koča
• E-mail: jaroslav.kocaceitec.muni.cz, david.sehnalmail.muni.cz
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• UPOL: Karel Berka, Ondřej Hanák, Veronika Navrátilová, Pavel Banáš, and Michal Otyepka
• E-mail: michal.otyepkaupol.cz