MOLEonline documentation

Method section describes the channel detection algorithm used in MOLE

Examples section shows possible uses of MOLEonline application

Tour section guide through MOLEonline application

FAQ Frequently Asked Questions

Updates - list of new features implemented in individual MOLEonline versions


Channels (tunnels and pores) are highly important structural pathways within proteins and other biomacromolecules. Tunnels connect internal spaces of biomacromolecules with exterior enabling, e.g., substrate/product transport towards enzymes’ active sites, nascent synthesized proteins to leave ribosomal proteosynthetic center via ribosomal exit tunnel, etc. Pores are channels passing through the whole biomacromolecular structure, typically facilitating transport of ions or molecules through cellular biomembranes. (Figure 1)

Description of GUI
Figure 1 – UX design of MOLEonline result webpage for human aquaporin (PDB ID: 4CSK).

MOLEonline Features

The calculation setup is realized via an interactive interface consisting of a few components (Figure 1). Structure visualization is achieved by LiteMol Viewer JavaScript application which is capable to visualize the uploaded structure and the computed channels.


Mode selection and Channel calculation parameters

Results visualization and analysis

Calculated channels are sorted according to their type to

Channels are further sorted according to their cavities by their lengths.

Interactive channels visualization runs in LiteMol Viewer.

Channel profile can be seen in the bottom left corner of the webpage. Two profiles can be visualized simultaneously showing physicochemical properties along channel length (on x-axis):

Overall results for all considered channels are also summarized in Channels properties.


Export of results

Results can be downloaded in various formats: