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 2.5, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.5 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.5 estimates physicochemical properties of the identified channels.

Downloads and Links

MOLE 2.5

Current version: (June 8 2024, news). For installation instructions, please consult the manual.

MOLEonline link

An online service for channel computation.

Additional Tools & Products

PyMOL and Chimera plug-in 2.5 [4.6 MB]

For more information about plug-in usage, please refer to the wiki.


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.


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


Authors and Contacts

MOLE 2 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:
  • UPOL: Karel Berka, Ondřej Hanák, Veronika Navrátilová, Pavel Banáš, and Michal Otyepka
  • E-mail:

MOLE 2 is a part of services provided by ELIXIR – European research infrastructure for biological information. For other services provided by ELIXIR's Czech Republic Node visit