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

  • Quickest channel calculation on the market
  • Channel profile - geometry
  • List of residues lining channels (distinguishing sidechain/mainchain contact with the channel)
  • Physico-chemical properties (charge, polarity, hydropathy, hydrophobicity, mutability, etc.) of channel
  • Automatic active site identification for enzymes using CSA
  • Interactive visualization of structure and channels with Jmol
  • Automatic detection of starting points in cavities
  • Interactive selection of starting points
  • Visualization of starting points
  • Cavity and molecular surface visualization
  • Experimental feature - pore identification
  • Download results - as a report, PDB files and script for PyMol®
  • Free of charge

Example of working environment with gramicidin (1GRM).

Quick start

:
PDB ID code as can be found on www.pdb.org, 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.

News

Java problems

21. 11. 2014
If you encounter "security" problems with new Java, go to the Java control panel and lower the security level to medium.

Channels in Enzymes

18. 11. 2014
New paper on analysis of channels in enzymes was published in BMC Bioinformatics 2014, 15:379

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.