PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families.

While other protein domain databases such as Pfam (5) aim to be comprehensive and to a maximum sequence coverage, PROSITE concentrates on precise functional characterization, which can be used for protein database annotation.

PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns. Profiles and patterns have complementary qualities.

PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.