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Literature DB >> 10592242

The Pfam protein families database.

A Bateman¹, E Birney, R Durbin, S R Eddy, K L Howe, E L Sonnhammer.

Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the WWW in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgr.ki.se/Pfam/ and in the US at http://pfam.wustl.edu/. The latest version (4.3) of Pfam contains 1815 families. These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9. For complete genomes Pfam currently matches up to half of the proteins. Genomic DNA can be directly searched against the Pfam library using the Wise2 package.

Mesh：

Substances：
Proteins

Year: 2000 PMID： 10592242 PMCID： PMC102420 DOI： 10.1093/nar/28.1.263

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

12 in total

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Journal: In Silico Biol Date: 1998

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Authors: S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal: J Mol Biol Date: 1990-10-05 Impact factor: 5.469

3. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

Authors: A Bateman; E Birney; R Durbin; S R Eddy; R D Finn; E L Sonnhammer
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

4. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.

Authors: E Birney; R Durbin
Journal: Proc Int Conf Intell Syst Mol Biol Date: 1997

5. Pfam: a comprehensive database of protein domain families based on seed alignments.

Authors: E L Sonnhammer; S R Eddy; R Durbin
Journal: Proteins Date: 1997-07

6. 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

7. RASMOL: biomolecular graphics for all.

Authors: R A Sayle; E J Milner-White
Journal: Trends Biochem Sci Date: 1995-09 Impact factor: 13.807

8. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors: W Kabsch; C Sander
Journal: Biopolymers Date: 1983-12 Impact factor: 2.505

9. Modular arrangement of proteins as inferred from analysis of homology.

Authors: E L Sonnhammer; D Kahn
Journal: Protein Sci Date: 1994-03 Impact factor: 6.725

Review 10. Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors:
Journal: Science Date: 1998-12-11 Impact factor: 47.728

492 in total

1. SMART: a web-based tool for the study of genetically mobile domains.

Authors: J Schultz; R R Copley; T Doerks; C P Ponting; P Bork
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. The InterPro database, 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: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

3. The MetaFam Server: a comprehensive protein family resource.

Authors: K A Silverstein; E Shoop; J E Johnson; A Kilian; J L Freeman; T M Kunau; I A Awad; M Mayer; E F Retzel
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

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. trEST, trGEN and Hits: access to databases of predicted protein sequences.

Authors: M Pagni; C Iseli; T Junier; L Falquet; V Jongeneel; P Bucher
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

6. The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments.

Authors: J Murvai; K Vlahovicek; E Barta; S Pongor
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

7. Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names.

Authors: D Lonsdale; M Crowe; B Arnold; B C Arnold
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

8. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.

Authors: R Apweiler; M Biswas; W Fleischmann; A Kanapin; Y Karavidopoulou; P Kersey; E V Kriventseva; V Mittard; N Mulder; I Phan; E Zdobnov
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

9. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.

Authors: A Bahr; J D Thompson; J C Thierry; O Poch
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

10. Protein Information Resource: a community resource for expert annotation of protein data.

Authors: W C Barker; J S Garavelli; Z Hou; H Huang; R S Ledley; P B McGarvey; H W Mewes; B C Orcutt; F Pfeiffer; A Tsugita; C R Vinayaka; C Xiao; L S Yeh; C Wu
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971