Implementation and use of an atom-mapping procedure for similarity searching in databases of 3-D chemical structures

Abstract This paper discusses a procedure for calculating the degree of similarity between an input target molecule and each of the molecules in a database of 3-D chemical structures. A mapping algorithm is used to identify pairs of atoms, one from each of the molecules that are being compared, that lie at the centre of geometrically-related volumes of 3-D space. Techniques are described to increase the run-time efficiency of the basic procedure, so that it can be used for similarity searching in large 3-D databases, and to allow a wide range of types of inter-molecular similarity to be calculated.

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