appears_in: []
depends_on: []
deprecated: false
description: The Pfam database contains information about protein domains and families.
  For each entry a protein sequence alignment and a Hidden Markov Model is stored.
download_json: https://w3id.org/biopragmatics/resources/pfam/pfam.json
download_obo: https://w3id.org/biopragmatics/resources/pfam/pfam.obo
download_owl: https://w3id.org/biopragmatics/resources/pfam/pfam.owl
example: PF11779
example_extras: []
homepage: https://www.ebi.ac.uk/interpro/
keywords:
- classification
- domain
- family and domain databases
- ontology
- protein
- sequence
license: CC0-1.0
logo: https://upload.wikimedia.org/wikipedia/commons/0/03/Pfam_logo.gif
mappings:
  biocontext: PFAM
  edam: '1138'
  go: Pfam
  integbio: nbdc00163
  miriam: pfam
  n2t: pfam
  ncbi: PFAM
  prefixcommons: pfam
  re3data: r3d100012850
  togoid: Pfam
  uniprot: DB-0073
  wikidata: P3519
name: Pfam protein family
namespace_in_lui: false
owners:
- name: European Bioinformatics Institute
  ror: 02catss52
pattern: ^PF\d{5}$
preferred_prefix: pfam
prefix: pfam
providers:
- code: bio2rdf
  description: Bio2RDF is an open-source project that uses Semantic Web technologies
    to build and provide the largest network of Linked Data for the Life Sciences.
    Bio2RDF defines a set of simple conventions to create RDF(S) compatible Linked
    Data from a diverse set of heterogeneously formatted sources obtained from multiple
    data providers.
  homepage: https://bio2rdf.org
  name: Bio2RDF
  uri_format: http://bio2rdf.org/pfam:$1
- code: sanger
  description: The Pfam database contains information about protein domains and families.
    For each entry a protein sequence alignment and a Hidden Markov Model is stored.
  homepage: http://pfam.sanger.ac.uk/
  name: Sanger Pfam Mirror
  uri_format: http://pfam.sanger.ac.uk/family?entry=$1
- code: xfam
  description: Pfam's familes in their old home in the xfam.org
  homepage: https://pfam.xfam.org
  name: Xfam
  uri_format: https://pfam.xfam.org/family?acc=$1
publications:
- doi: 10.1093/nar/27.1.260
  pmc: PMC148151
  pubmed: '9847196'
  title: 'Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of
    proteins'
  year: 1999
- doi: 10.1093/nar/26.1.320
  pmc: PMC147209
  pubmed: '9399864'
  title: 'Pfam: multiple sequence alignments and HMM-profiles of protein domains'
  year: 1998
- doi: 10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l
  pubmed: '9223186'
  title: 'Pfam: a comprehensive database of protein domain families based on seed
    alignments'
  year: 1997
- doi: 10.1093/nar/gkae997
  pubmed: '39540428'
  title: 'The Pfam protein families database: embracing AI/ML'
  year: 2024
- doi: 10.1093/nar/gkaa913
  pmc: PMC7779014
  pubmed: '33125078'
  title: 'Pfam: The protein families database in 2021'
  year: 2021
- doi: 10.1093/nar/gky995
  pmc: PMC6324024
  pubmed: '30357350'
  title: The Pfam protein families database in 2019
  year: 2019
- doi: 10.1093/nar/gkv1344
  pmc: PMC4702930
  pubmed: '26673716'
  title: 'The Pfam protein families database: towards a more sustainable future'
  year: 2015
- doi: 10.1093/nar/gkt1223
  pmc: PMC3965110
  pubmed: '24288371'
  title: 'Pfam: the protein families database'
  year: 2013
- doi: 10.1093/nar/gkr1065
  pmc: PMC3245129
  pubmed: '22127870'
  title: The Pfam protein families database
  year: 2011
- doi: 10.1093/nar/gkp985
  pmc: PMC2808889
  pubmed: '19920124'
  title: The Pfam protein families database
  year: 2009
- doi: 10.1093/nar/gkm960
  pmc: PMC2238907
  pubmed: '18039703'
  title: The Pfam protein families database
  year: 2007
- doi: 10.1093/nar/gkj149
  pmc: PMC1347511
  pubmed: '16381856'
  title: 'Pfam: clans, web tools and services'
  year: 2006
- doi: 10.1093/nar/gkh121
  pmc: PMC308855
  pubmed: '14681378'
  title: The Pfam protein families database
  year: 2004
- doi: 10.1093/nar/30.1.276
  pmc: PMC99071
  pubmed: '11752314'
  title: The Pfam protein families database
  year: 2002
- doi: 10.1093/nar/28.1.263
  pmc: PMC102420
  pubmed: '10592242'
  title: The Pfam protein families database
  year: 2000
references:
- https://twitter.com/PfamDB/status/1555149527228813314
synonyms:
- PF
uri_format: https://www.ebi.ac.uk/interpro/entry/pfam/$1
