Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Jan 1;32(Database issue):D138-41.
doi: 10.1093/nar/gkh121.

The Pfam Protein Families Database

Free PMC article

The Pfam Protein Families Database

Alex Bateman et al. Nucleic Acids Res. .
Free PMC article


Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (, the USA (, France ( and Sweden (


Figure 1
Figure 1
Comparison of Pfam, SCOP and CATH domain definitions for S-adenosylmethionine synthetase. The definitions of SCOP and Pfam are very similar, but rather different from the stricter structural definition of CATH. The definitions can be compared at the level of structure for each database. The two Rasmol windows on the right show the Pfam definition above the CATH definition.
Figure 2
Figure 2
Structure image coloured by Pfam domain, including a coloured domain key below. This structure shows the complex of P27, cyclin and CDK2. Clicking on the image links to the PDBsum resource (10).

Similar articles

  • Pfam: clans, web tools and services.
    Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Finn RD, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51. doi: 10.1093/nar/gkj149. Nucleic Acids Res. 2006. PMID: 16381856 Free PMC article.
  • The Pfam protein families database.
    Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. Bateman A, et al. Nucleic Acids Res. 2002 Jan 1;30(1):276-80. doi: 10.1093/nar/30.1.276. Nucleic Acids Res. 2002. PMID: 11752314 Free PMC article.
  • The Pfam protein families database.
    Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. Finn RD, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8. doi: 10.1093/nar/gkm960. Epub 2007 Nov 26. Nucleic Acids Res. 2008. PMID: 18039703 Free PMC article.
  • Pfam 10 years on: 10,000 families and still growing.
    Sammut SJ, Finn RD, Bateman A. Sammut SJ, et al. Brief Bioinform. 2008 May;9(3):210-9. doi: 10.1093/bib/bbn010. Epub 2008 Mar 15. Brief Bioinform. 2008. PMID: 18344544 Review.
  • The evolution of protein domain families.
    Buljan M, Bateman A. Buljan M, et al. Biochem Soc Trans. 2009 Aug;37(Pt 4):751-5. doi: 10.1042/BST0370751. Biochem Soc Trans. 2009. PMID: 19614588 Review.
See all similar articles

Cited by 1,348 articles

See all "Cited by" articles

Publication types

LinkOut - more resources