title: MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
abstract: BACKGROUND
  Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.
  
  
  RESULTS
  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, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily.
  
  
  CONCLUSIONS
  Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz.
authors: National Centre for Biomolecular Research, Faculty of Science and CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic. michal.otyepka@upol.cz.
authors: David
authors: D
authors: Sehnal
authors: Radka
authors: R
authors: Svobodová Vařeková
authors: Karel
authors: K
authors: Berka
authors: Lukáš
authors: L
authors: Pravda
authors: Veronika
authors: V
authors: Navrátilová
authors: Pavel
authors: P
authors: Banáš
authors: Crina-Maria
authors: CM
authors: Ionescu
authors: Michal
authors: M
authors: Otyepka
authors: Jaroslav
authors: J
authors: Koča
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