Development of an atom mapping procedure for similarity searching in databases of three‐dimensional chemical structures

Abstract

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 3D chemical structures. A mapping procedure is used to identify pairs of atoms, one from each of the molecules that are being compared, that lie at the centre of topographically similar volumes of 3D space. Experiments are reported to validate the significance of the similarities that result from the use of the procedure and to determine the effect on the calculated similarities of the structural representation that is used to characterise the molecules in a database.