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Literature DB >> 11752314

The Pfam protein families database.

Alex Bateman¹, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R Eddy, Sam Griffiths-Jones, Kevin L Howe, Mhairi Marshall, Erik L L Sonnhammer.

Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.

Entities: Chemical

Mesh：

Substances：

Year: 2002 PMID： 11752314 PMCID： PMC99071 DOI： 10.1093/nar/30.1.276

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

16 in total

1. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

Authors: F Corpet; F Servant; J Gouzy; D Kahn
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

Authors: A Krogh; B Larsson; G von Heijne; E L Sonnhammer
Journal: J Mol Biol Date: 2001-01-19 Impact factor: 5.469

3. InterPro--an integrated documentation resource for protein families, domains and functional sites.

Authors: R Apweiler; T K Attwood; A Bairoch; A Bateman; E Birney; M Biswas; P Bucher; L Cerutti; F Corpet; M D Croning; R Durbin; L Falquet; W Fleischmann; J Gouzy; H Hermjakob; N Hulo; I Jonassen; D Kahn; A Kanapin; Y Karavidopoulou; R Lopez; B Marx; N J Mulder; T M Oinn; M Pagni; F Servant; C J Sigrist; E M Zdobnov
Journal: Bioinformatics Date: 2000-12 Impact factor: 6.937

4. TIGRFAMs: a protein family resource for the functional identification of proteins.

Authors: D H Haft; B J Loftus; D L Richardson; F Yang; J A Eisen; I T Paulsen; O White
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

5. PDBsum: summaries and analyses of PDB structures.

Authors: R A Laskowski
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

6. NIFAS: visual analysis of domain evolution in proteins.

Authors: C E Storm; E L Sonnhammer
Journal: Bioinformatics Date: 2001-04 Impact factor: 6.937

7. Initial sequencing and analysis of the human genome.

Authors: E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

Review 8. Machine learning approaches for the prediction of signal peptides and other protein sorting signals.

Authors: H Nielsen; S Brunak; G von Heijne
Journal: Protein Eng Date: 1999-01

9. Predicting coiled coils from protein sequences.

Authors: A Lupas; M Van Dyke; J Stock
Journal: Science Date: 1991-05-24 Impact factor: 47.728

10. The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors: F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal: J Mol Biol Date: 1977-05-25 Impact factor: 5.469

857 in total

1. SCOP database in 2002: refinements accommodate structural genomics.

Authors: Loredana Lo Conte; Steven E Brenner; Tim J P Hubbard; Cyrus Chothia; Alexey G Murzin
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

2. Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.

Authors: Gregory L Moore; Costas D Maranas
Journal: Proc Natl Acad Sci U S A Date: 2003-04-16 Impact factor: 11.205

3. Structure of the GAT domain of human GGA1: a syntaxin amino-terminal domain fold in an endosomal trafficking adaptor.

Authors: Silke Suer; Saurav Misra; Layla F Saidi; James H Hurley
Journal: Proc Natl Acad Sci U S A Date: 2003-03-31 Impact factor: 11.205

4. Enhanced protein domain discovery by using language modeling techniques from speech recognition.

Authors: Lachlan Coin; Alex Bateman; Richard Durbin
Journal: Proc Natl Acad Sci U S A Date: 2003-03-31 Impact factor: 11.205

5. Retrieval-independent localization of lysyl hydroxylase in the endoplasmic reticulum via a peptide fold in its iron-binding domain.

Authors: Marko Suokas; Outi Lampela; André H Juffer; Raili Myllylä; Sakari Kellokumpu
Journal: Biochem J Date: 2003-03-15 Impact factor: 3.857

6. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.

Authors: Klaas Vandepoele; Yvan Saeys; Cedric Simillion; Jeroen Raes; Yves Van De Peer
Journal: Genome Res Date: 2002-11 Impact factor: 9.043

7. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea.

Authors: Igor B Zhulin; Anastasia N Nikolskaya; Michael Y Galperin
Journal: J Bacteriol Date: 2003-01 Impact factor: 3.490