Mole

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New MOLE software 2.0 and higher

The latest MOLE version is available at http://mole.chemi.muni.cz

Lagacy MOLE software 1.4 and older

Program MOLE is an universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is a powerful software (overcomming some limitations of CAVER tool) for exploring large molecular channels, complex networks of channels and molecular dynamics trajectories (AMBER ascii traj and parm7 are supported) in which analysis of a large number of snapshots is required.

Program is available as standalone application for Linux(Unix), MacOS and Windows. Plugin for pyMol enables calling the MOLE program via an user friendly interface and allows results visualization. The on-line interface provides another interactive and easy-to-use interface to analyze molecular channels.

Program was developed in NCBR in cooperation with FCH UPOL.

Using of Mole

Figures show channels found by MOLE software and visualized in VMD and PyMol tools.

Channel to the active site of restriction endonuclease HincII (PDB code 1TW8) is colored by an electrostatic potential (calculated by DELPHI) along the channel. The small arrows show gradient of the electrostatic field on the channel surface directing toward the active site. Figure was prepared by VMD.

MOLE found six channels in the open KscA K+ channel structure (PDB: 1k4c). From top one can distinguish the selectivity filter (with botlleneck radius 0.82 Å), cavity and channel gating (with bottleneck radius of 1.36 Å). Four perpendicular channels (leading to the membrane) have bottleneck radii equal to 1.28 Å but their biological role is unknown if any. Figure was prepared by pyMol.