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

Additional features of MOLE 2.0 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 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

Web updates

04. 09. 2012

MOLEonline 2.0 new features:

  • Filtering of tunnels based on its bottleneck radius
  • Filtering of tunnels based on their similarities
  • Tunnel profile shows local physicochemical properties
  • Tunnel profile shows both local and global radii minima

MOLEonline 2.0 citation update

01. 07. 2012

Open access paper about MOLEonline 2.0 was published within WebServer issue in Nucleic Acid Research:

Berka et al. Nucl. Acids Res. 2012, 40(W1): W222-W227 doi:10.1093/nar/gks363

Web updates

21. 05. 2012

MOLEonline 2.0 new features:

  • Ignore HETATM coordinates in input
  • Automatic detection of pores

Web updates

28. 03. 2012

MOLEonline 2.0 new features:

  • Cavity and molecular surface visualization
  • Automatic detection of starting points in cavities
  • Visualization of starting points
  • Default values for Interior threshold and Origin Radius were set to 1.25 Å and 5 Å, respectively