MOLE 2.5online introduction page

MOLEonline 2.5 web interface provides a direct access to MOLE 2.5 functionality and enables on-line and easy-to-use interactive channel analysis.

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

MOLEonline 2.5 features

  • Channel calculation three times quicker than previous version of MOLE
  • Automatic active site identification for enzymes using CSA
  • Interactive visualization of structure and channels with Jmol
  • Interactive selection of starting points from the sequence or set of residues
  • Automatic detection of starting points in cavities
  • Visualization of starting points
  • Cavity and molecular surface visualization
  • Tunnel size profile
  • Analysis of residues lining channels along with sidechain/mainchain resolution with physicochemical properties (charge, polarity, hydropathy, hydrophobicity, mutability, etc.)
  • Results download in form of report, channel export in format of PDB and pymol python script
  • Free of charge

Additional features of MOLE 2.5 standalone application

  • Additional powerful selection options for structure preparation prior channel calculation
  • Comparison of channels in several different structures
  • Selection of channels to a specific exit
  • Vizualization of cavities and unconnected voids
  • Powerful visualization engine with 3D option

Windows desktop version and Windows, Linux and Mac OS command line version can be downloaded on webchem site.

Quick start

PDB ID code as can be found on, for example 1z10.
no value - assymetric unit (default)
1 - biological unit 1,
(2 - biological unit 2, etc. )
no value - all chains (default)
AB1 - only chains A, B and 1
Plain text PDB files (UTF-8 encoding), ZIP and GZIP archives are supported, maximal file size is 50MB.
E.g. cleaned PDB with only one chain and without unnecessary HETATMs.



01. 01. 2018
New MOLE webserver started You can access it at


01. 04. 2017
MOLEonline 2.5 with integrated Litemol vizualization overcomes previous problems of tunnel visualization in Jmol and brings some new functionality. Try it e.g. better patway detection with selection of would-be starts and ends.

ELIXIR CZ support

01. 04. 2017
MOLEonline is supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).