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.
- TrEMBL Database performing an automated protein sequence annotation
- InterPro Integration of protein domain and protein family databases
- Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). "Pfam: clans, web tools and services". Nucleic Acids Res. 34: D247–D251. PMID 16381856.
- Finn RD, Marshall M, Bateman A (2005). "iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions". Bioinformatics. 21: 410–412. PMID 15353450.
- Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004). "The Pfam protein families database". Nucleic Acids Res. 32(Database issue): D138–D141. PMID 14681378.
- Pfam - Protein family database at Sanger Institute UK
- Pfam - Protein family database at Janelia Farm Research Campus USA
- Pfam - Protein family database at Center for Genomics and Bioinformatics Sweden
- iPfam - Interactions of Pfam domains in PDB