SIMILARITY SEARCHING IN FILES OF 3-DIMENSIONAL CHEMICAL STRUCTURES - REPRESENTATION AND SEARCHING OF MOLECULAR ELECTROSTATIC POTENTIALS USING FIELD-GRAPHS

This paper reports a method for the identification of those molecules in a database of rigid 3D structures with molecular electrostatic pote ntial (MEP) grids that are most similar to that of a user-defined targ et molecule. The most important features of an MEP grid are encoded in field-graphs, and a target molecule is matched against a database mole cule by a comparison of the corresponding field-graphs. The matching i s effected using a maximal common subgraph isomorphism algorithm, whic h provides an alignment of the target molecule's field-graph with thos e of each of the database molecules in turn. These alignments are used in the second stage of the search algorithm to calculate the intermol ecular MEP similarities. Several different ways of generating field-gr aphs are evaluated, in terms of the effectiveness of the resulting sim ilarity measures and of the associated computational costs. The most a ppropriate procedure has been implemented in an operational system tha t searches a corporate database, containing ca. 173 000 3D structures.