The SUPERFAMILY database has numerous research applications and has been used by many research groups for various studies. It can serve either as a database for proteins that the user wishes to examine with other methods, or to assign a function and structure to a novel or uncharacterized protein. One study found SUPERFAMILY to be very adept at correctly assigning an appropriate function and structure to a large number of domains of unknown function by comparing them to the databases hidden Markov models. Another study used SUPERFAMILY to generate a data set of 1,733 Fold superfamily domains (FSF) in use of  a comparison of proteomes and functionomes for to identify the origin of cellular diversification.