Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of smoothed bounded distances for incompletely specified query patterns

Abstract

This paper describes a technique for increasing the screen out of pharmacophoric pattern searches in the databases of three-dimensional chemical structures when only some of the interatomic distances in the query pattern are specified. The technique involves the application of a distance bounds smoothing procedure to the query distances; this smoothing allows the calculation of upper and lower bounds for the unspecified distances. The bounded distances can then be used to set screens additional to those that are set to describe the distances that have been specified by the searcher. Evidence is presented to suggest that use of the technique can lead to increases in the efficiency of substructure searches for partially specified query patterns.