Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

Abstract

The functions of biomacromolecules usually depend on interactions with other biomacromolecules as well as ions and small molecules, such as water, messenger and endogenous compounds, pollutants and drugs, which can occupy “otherwise empty spaces” in biomacromolecular structures. Thus, information about the nature of empty spaces in a biomacromolecule can provide valuable insights into its functions. Channels and pores are known to play important roles e.g. in enzymatic substrate specificity, or for necessary selectivity of individual transmembrane transport proteins.MOLE is a gold standard in quick geometrical detection of channels and tunnels within biomacromolecular structures. MOLE 2.0 was first tool to come with automatic and user-defined detection of channels and tunnels using Voronoi diagram and Delaunay tesselation representations with analysis of physicochemical properties of amino acids forming the tunnel. New version of MOLE 2.5 in addition enables detection of pores and better selection for starting and end points within protein structures using PatternQuery language together with additional increase of speed. MOLE 2.5 is used in PDBsum database for visualization of pores and channels within the protein structures http://ebi.ac.uk/pdbsum. Stand alone version of MOLE 2.5 for download is available at http://mole.webchemdev.ncbr.muni.cz/MOLE3/ and online version is adapted to be available at http://mole.upol.cz.