A system for encoding and searching Markush structures.

The encoding and searching of generic chemical structures, so-called Markush structures, have received little attention in the literature of late. The ability to encode and search these complex entities is of use in various branches of chemoinformatics. We describe a general language for encoding Markush structures and algorithms for searching them and give three examples of the utility of such a system: development of general Free-Wilson analyses of chemical series, detection of controlled substances within a large database of molecular structures, and searching of large databases of virtual compounds.