About MOLEonline

MOLE 2.5 is a universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures.

MOLEonline web interface enables on-line and easy-to-use interactive analysis of (bio)macromolecular channels.

Old version of MOLEonline (2018) is available at https://mole.upol.cz/.

Desktop and command-line versions of MOLE and MOLE plugins are available at https://webchem.ncbr.muni.cz/Platform/App/Mole.

Pre-calculated channels, tunnels and pores can be found at ChannelsDB 2.0 database available at https://channelsdb2.biodata.ceitec.cz/.

Contact

Email: mole@upol.cz

How to cite

Current version:

• MOLEonline update 2018
  Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vařeková R, Koča J, Otyepka M: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res, 46(W1), 2018. (DOI)

Web:

• MOLEonline 2.0:
  

  Berka K, Hanák O, Sehnal D, Banáš P, Navrátilová V, Jaiswal D, Ionescu CM, Svobodová Vařekova R, Koča J, Otyepka M: MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res., 40(W1), W222-W227, 2012. (DOI)

Desktop:

• MOLE 2.0:
  

  Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu C, Otyepka M, Koča J: MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminf., 5(1), 1-39, 2013. (DOI)

• MOLE:
  

  Petřek M, Košinová P, Koča J, Otyepka M: MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels. Structure, 15(11), 1357-1363, 2007. (DOI)

Book tutorials

• MOLEonline and ChannelsDB 2.0
  

  Špačková A, Bazgier V, Raček T, Sehnal D, Svobodová R, Berka K: (2024) Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In: Lisacek, F. (eds) Protein Bioinformatics. Methods in Molecular Biology, vol 2836. Humana, New York, NY. (DOI)

• Structural Bioinformatics Tools for Drug Design
  

  Koča J, Svobodová Vařeková R, Pravda L, Berka K, Geidl S, Sehnal D, Otyepka M: (2016) Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases. SpringerBriefs in Biochemistry and Molecular Biology, Springer Cham. (DOI)

Examples of usage:

• ChannelsDB 2.0:
  

  Špačková A, Vávra O, Raček T, Bazgier V, Sehnal D, Damborský J, Svobodová R, Bednář D, Berka K: ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Res, 51(D1), 2024. (DOI)

• ChannelsDB:
  

  Pravda L, Sehnal D, Svobodová Vařeková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koča J: ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res, 46(D1), 2018. (DOI)

• MOLE + BE-META for ligand egress in molecular dynamics:
  

  Paloncýová M, Navrátilová V, Berka K, Laio A, Otyepka M: Role of Enzyme Flexibility in Ligand Access and Egress to Active Site – Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4 J. Chem. Theory Comput., 12(4), 2101–2109, 2016. (DOI)

• Enzyme channels:
  

  Pravda L, Berka K, Svobodová Vařeková R, Sehnal D, Banáš P, Laskowski RA, Koča J, Otyepka M: Anatomy of enzyme channels. BMC Bioinf., 15(1), 379, 2014. (DOI)

• PDBsum:
  

  de Beer TAP, Berka K, Thornton JM, Laskowski RA: PDBsum additions. Nucleic Acids Res., 42(D1), 292-296, 2014. (DOI)

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