We present a method for identifying and representing indentations, cavities and holes in a known protein structure. The identification procedure is performed initially. Once a pocket in the protein has been found, we use a boundary representation technique to represent it. Both the identification and the representation procedures rely upon modifications to the Marching Cubes algorithm of Lorensen and Cline (1987), which can be used to give a piecewise planar representation of a three-dimensional object. The identification of a pocket essentially involves finding a point, (x/sub 0/, y/sub 0/, z/sub 0/) say. The point should be such that a sphere of radius r can he centred there, without touching the centre of any atom in the protein, but there exists R>r such that a sphere of radius R centred at (x/sub 0/, y/sub 0/, z/sub 0/) does touch the centre of an atom. If such a point is found, then it is deemed to be in a pocket. The boundary representation technique involves storing information about a boundary in the structure of a graph. The graph structure of a pocket, potential docking site, can then be compared to the graph structure of a candidate binding substrate using standard graph comparison algorithms. The required input for the algorithm is in the form of a Protein Data Bank (PDB) file.

UNLABELLED: TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for: detection of breaks in alpha helical structure of transmembrane regions; examination of differences in coverage between PDB and SWISS-PROT files; examination of annotation differences between PDB files and associated SWISS-PROT files; examination and comparison of assigned PDB alpha helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format; examination of these differences in 3D using the CHIME plugin, allowing; analysis of the alpha and non-alpha content of transmembrane regions. AVAILABILITY: TMCompare is available for use through selection of a query protein via the internet (http://www.membraneproteins.org/TMCompare) CONTACT: [email protected]