Superfamily database

SUPERFAMILY
Content
DescriptionThe SUPERFAMILY database provides structural and functional annotation for all proteins and genomes.
Data types
captured		Protein families, genome annotation, alignments, Hidden Markov models (HMMs)
Organismsall
Contact
Research centerUniversity of Bristol
Laboratory
Primary citationPMID 19036790
Access
Data formatFASTA format
Websitesupfam.org
Download URLsupfam.org/SUPERFAMILY/downloads.html
Miscellaneous
LicenseGNU General Public License
Version1.75

SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes.[1][2][3][4][5][6][7] It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies.[8][9] Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP.[8][10] Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.[11]

  1. ^ Wilson, D; Pethica, R; Zhou, Y; Talbot, C; Vogel, C; Madera, M; Chothia, C; Gough, J (January 2009). "SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny". Nucleic Acids Research. 37 (Database issue): D380-6. doi:10.1093/NAR/GKN762. ISSN 0305-1048. PMC 2686452. PMID 19036790. Wikidata Q26781958.
  2. ^ Madera, Martin; Vogel, Christine; Kummerfeld, Sarah K.; Chothia, Cyrus; Gough, Julian (2004-01-01). "The SUPERFAMILY database in 2004: additions and improvements". Nucleic Acids Research. 32 (suppl 1): D235–D239. doi:10.1093/nar/gkh117. ISSN 0305-1048. PMC 308851. PMID 14681402.
  3. ^ Wilson, D.; Madera, M.; Vogel, C.; Chothia, C.; Gough, J. (2007). "The SUPERFAMILY database in 2007: Families and functions". Nucleic Acids Research. 35 (Database issue): D308–D313. doi:10.1093/nar/gkl910. PMC 1669749. PMID 17098927.
  4. ^ Gough, J. (2002). "The SUPERFAMILY database in structural genomics". Acta Crystallographica Section D. 58 (Pt 11): 1897–1900. doi:10.1107/s0907444902015160. PMID 12393919.
  5. ^ Gough, J.; Chothia, C. (2002). "SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments". Nucleic Acids Research. 30 (1): 268–272. doi:10.1093/nar/30.1.268. PMC 99153. PMID 11752312.
  6. ^ De Lima Morais, D. A.; Fang, H.; Rackham, O. J. L.; Wilson, D.; Pethica, R.; Chothia, C.; Gough, J. (2010). "SUPERFAMILY 1.75 including a domain-centric gene ontology method". Nucleic Acids Research. 39 (Database issue): D427–D434. doi:10.1093/nar/gkq1130. PMC 3013712. PMID 21062816.
  7. ^ Oates, M. E.; Stahlhacke, J; Vavoulis, D. V.; Smithers, B; Rackham, O. J.; Sardar, A. J.; Zaucha, J; Thurlby, N; Fang, H; Gough, J (2015). "The SUPERFAMILY 1.75 database in 2014: A doubling of data". Nucleic Acids Research. 43 (Database issue): D227–33. doi:10.1093/nar/gku1041. PMC 4383889. PMID 25414345.
  8. ^ a b Hubbard, T. J.; Ailey, B.; Brenner, S. E.; Murzin, A. G.; Chothia, C. (1999). "SCOP: A Structural Classification of Proteins database". Nucleic Acids Research. 27 (1): 254–256. doi:10.1093/nar/27.1.254. PMC 148149. PMID 9847194.
  9. ^ Lo Conte, L.; Ailey, B.; Hubbard, T. J.; Brenner, S. E.; Murzin, A. G.; Chothia, C. (2000). "SCOP: A Structural Classification of Proteins database". Nucleic Acids Research. 28 (1): 257–259. doi:10.1093/nar/28.1.257. PMC 102479. PMID 10592240.
  10. ^ Cite error: The named reference :1 was invoked but never defined (see the help page).
  11. ^ Dayhoff, M. O.; McLaughlin, P. J.; Barker, W. C.; Hunt, L. T. (1975-04-01). "Evolution of sequences within protein superfamilies". Naturwissenschaften. 62 (4): 154–161. Bibcode:1975NW.....62..154D. doi:10.1007/BF00608697. ISSN 0028-1042. S2CID 40304076.