MOLE 2.0online introduction page

MOLEonline 2.0 web interface provides a direct access to MOLE 2.0 functionality and enables on-line and easy-to-use interactive channel analysis.

MOLE 2.0 is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in (bio)macromolecular structures.

MOLEonline 2.0 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

Example of working environment with gramicidin (1GRM).

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 16MB.
E.g. cleaned PDB with only one chain and without unnecessary HETATMs.


Mac OS Java problems

21. 05. 2014
If you encounter "security" problems with new Java 7 on Mac OS X, go to the Java control panel and lower the security level to medium.

Server failure

09. 04. 2014
Due to severe storms in Moravia area, the webserver went down. All is repaired by now and failed jobs with SOAP warning can be resubmitted.

Web updates

07. 09. 2013

MOLEonline 2.0 new features:

  • Tunnels can be found within biological assemblies
  • Several bugs were removed

MOLE 2.0 published

01. 09. 2013

MOLE 2.0 was published in Journal of Cheminformatics 2013, 5:39. Binaries and PyMOL plugin are here.