Pfam

The Pfam database contains information about protein domains and families. Pfam-A is the manually curated portion of the database that contains over 9,000 entries. For each entry a protein sequence alignment and a hidden Markov model is stored. These hidden Markov models can be used to search sequence databases with the HMMer package written by Sean Eddy. Because the entries in Pfam-A do not cover all known proteins an automatically generated supplement is provided called Pfam-B. Pfam-B is derived from the PRODOM database.

The database iPfam builds on the domain description of Pfam. It investigates if different proteins described together in the protein structure database PDB are close enough to potentially interact.