• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Jan 1, 1998; 26(1): 323–326.
PMCID: PMC147246

The ProDom database of protein domain families.

Abstract

The ProDom database contains protein domain families generated from the SWISS-PROT database by automated sequence comparisons. It can be searched on the World Wide Web (http://protein.toulouse.inra. fr/prodom.html ) or by E-mail (prodom@toulouse.inra.fr) to study domain arrangements within known families or new proteins. Strong emphasis has been put on the graphical user interface which allows for interactive analysis of protein homology relationships. Recent improvements to the server include: ProDom search by keyword; links to PROSITE and PDB entries; more sensitive ProDom similarity search with BLAST or WU-BLAST; alignments of query sequences with homologous ProDom domain families; and links to the SWISS-MODEL server (http: //www.expasy.ch/swissmod/SWISS-MODEL.html ) for homology based 3-D domain modelling where possible.

Full Text

The Full Text of this article is available as a PDF (290K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998 Jan 1;26(1):38–42. [PMC free article] [PubMed]
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Sonnhammer EL, Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 1994 Mar;3(3):482–492. [PMC free article] [PubMed]
  • Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988 Nov 25;16(22):10881–10890. [PMC free article] [PubMed]
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. [PMC free article] [PubMed]
  • Henikoff S, Pietrokovski S, Henikoff JG. Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Res. 1998 Jan 1;26(1):309–312. [PMC free article] [PubMed]
  • Attwood TK, Beck ME, Bleasby AJ, Degtyarenko K, Michie AD, Parry-Smith DJ. Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res. 1997 Jan 1;25(1):212–217. [PMC free article] [PubMed]
  • Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1997. Nucleic Acids Res. 1997 Jan 1;25(1):217–221. [PMC free article] [PubMed]
  • Glémet E, Codani JJ. LASSAP, a LArge Scale Sequence compArison Package. Comput Appl Biosci. 1997 Apr;13(2):137–143. [PubMed]
  • Schuler GD, Epstein JA, Ohkawa H, Kans JA. Entrez: molecular biology database and retrieval system. Methods Enzymol. 1996;266:141–162. [PubMed]
  • Hubbard TJ, Murzin AG, Brenner SE, Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res. 1997 Jan 1;25(1):236–239. [PMC free article] [PubMed]
  • Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 Sep;20(9):374–374. [PubMed]
  • Peitsch MC. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem Soc Trans. 1996 Feb;24(1):274–279. [PubMed]
  • Appel RD, Bairoch A, Hochstrasser DF. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem Sci. 1994 Jun;19(6):258–260. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...