Substructure search

Substructure search (SSS) is a method to retrieve from a database only those chemicals matching a pattern of atoms and bonds which a user specifies. It is an application of graph theory, specifically subgraph matching in which the query is a hydrogen-depleted molecular graph. The mathematical foundations for the method were laid in the 1870s, when it was suggested that chemical structure drawings were equivalent to graphs with atoms as vertices and bonds as edges. SSS is now a standard part of cheminformatics and is widely used by pharmaceutical chemists in drug discovery.

There are many commercial systems that provide SSS, typically having a graphical user interface and chemical drawing software. Large publicly-available databases like PubChem and ChemSpider can be searched this way, as can Wikipedia's articles describing individual chemicals.

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