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Clustering chemical structures alleviates the tedious task of browsing a large set of compounds by grouping individual structures into generic categories. ChemAxon's JKlustor product offers clustering solutions ranging from similarity based non-hierarchical method to a pure graph based technique. This latter exhibits some clear advantages over the more conventional approaches: clusters are more likely to meet human expectations and tangible explanation why certain compounds are grouped together is also produced. And even it is faster. If you 'farm your classes' then it's time to 'MCS your library'!
Latest developments are here: http://www.chemaxon.com/product/jklustor.html