About this archive

MOLEonline has moved to new servers. This site is the read-only archive of its previous version: it keeps the computations made until November 2026, so that their links keep working. You can view them, explore their channels and download their results and PDF reports, but you cannot start, repeat or delete computations here.

For new computations, go to moleonline.cz. To repeat an archived computation there, open it here, click Export at its submission (the Submissions tab) to download its parameters as JSON, and load them into the new MOLEonline.

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://old.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 (2025 update)
  Raček T, Veľký D, Bučeková G, Schindler O, Hutařová Vařeková I, Špačková A, Bazgier V, Berka K, Svobodová R: MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update). Bioinformatics, 41, 2025. (DOI)

Web:

• MOLEonline (2018 update)
  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)
• 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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