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.

Downloads and Links

MOLE 2.0

Current version: 2.13.9.6 (September 6th 2013, news). For installation instructions, please consult the manual.


MOLEonline 2.0 link

An online service for channel computation.

Additional Tools & Products

PyMOL plugin [11 MB] MOLE 1.4 link

Licence

Licence conditions in accordance with § 11 of Act No. 130/2002 Coll. The owner of the software is Masaryk University, a public university, ID: 00216224. Masaryk University allows other companies and individuals to use this software free of charge and without territorial restrictions in usual way, that does not depreciate its value. This permission is granted for the duration of property rights. This software is not subject to special information treatment according to Act No. 412/2005 Coll., as amended. In case that a person who will use the software under this licence offer violates the licence terms, the permission to use the software terminates.

Documentation

The documentation can be downloaded here and is also included with the application downloads.

References

  • 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. Journal of Cheminformatics 2013, 5:39. doi:10.1186/1758-2946-5-39
  • 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

Authors and Contacts

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 (technical questions here)
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  • UPOL: Karel Berka, Ondřej Hanák, Veronika Navrátilová, Pavel Banáš, and Michal Otyepka
  • E-mail: michal.otyepkaupol.cz