MOLE 2.0: advanced approach for analysis of biomacromolecular channels

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Example of channel system of 1JJ2
MOLE 2 is a successor of a popular software tool Mole for detection and characterization of channels in biomacromolecules (proteins, nucleic acids and glycans). This completely redesigned version allows user rapid and accurate analysis of channels and transmembrane pores even in large structures (hundreds of thousands of atoms). As a new feature, MOLE 2 estimates not only physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability, but also physicochemical properties of the cavities. For thorough description of the functionality and instructions on working with MOLE 2 please consult the paper or our manual.

MOLE 2.5 Update

Update of MOLE 2 with novel functionality and bug fixes has been released. The binaries and plugins are available for download from the | main page.

  • Easily remove parts of the PDB entry with PatternQuery.
  • New PDB standard mmCIF is supported and recommended for all calculations.
  • New weight functions for tunnel/pore calculation.

Availability and Requirements

MOLE 2.5 is available as a GUI application with in-built molecular browser enabling user interactive work; command-line application and PyMOL & Chimera plugin. Some functionality is also available via online web service.

  • GUI application is available for Windows with .NET 4.0 framework or newer installed.
  • Command-line application and PyMOL&Chimera plugin are available for Windows, Linux (Unix) and MacOS. For Linux (Unix) and MacOS systems Mono framework 2.10 or newer is required.

MOLE 2.5 PyMOL plugin


  1. Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C-M, Otyepka M, Koča J: MOLE 2.0: advanced approach for analysis of biomacromolecular channels. Journal of Cheminformatics 2013, 5:39.
  2. Pravda,L., Berka,K., Svobodová Vařeková,R., Sehnal,D., Banáš,P., Laskowski,R.A., Koča,J. and Otyepka,M. (2014) Anatomy of enzyme channels. BMC Bioinformatics, 15, 379.
  3. Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu C-M, Svobodová Vařeková R, Koča J, Otyepka M: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic acids research 2012, 40:W222–7.