Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Jan 1;26(1):323–326. doi: 10.1093/nar/26.1.323

The ProDom database of protein domain families.

F Corpet 1, J Gouzy 1, D Kahn 1
PMCID: PMC147246  PMID: 9399865

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 (289.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Appel R. D., Bairoch A., Hochstrasser D. F. 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. doi: 10.1016/0968-0004(94)90153-8. [DOI] [PubMed] [Google Scholar]
  4. Attwood T. K., Beck M. E., Bleasby A. J., Degtyarenko K., Michie A. D., Parry-Smith D. J. Novel developments with the PRINTS protein fingerprint database. Nucleic Acids Res. 1997 Jan 1;25(1):212–217. doi: 10.1093/nar/25.1.212. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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. doi: 10.1093/nar/26.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bairoch A., Bucher P., Hofmann K. The PROSITE database, its status in 1997. Nucleic Acids Res. 1997 Jan 1;25(1):217–221. doi: 10.1093/nar/25.1.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988 Nov 25;16(22):10881–10890. doi: 10.1093/nar/16.22.10881. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Glémet E., Codani J. J. LASSAP, a LArge Scale Sequence compArison Package. Comput Appl Biosci. 1997 Apr;13(2):137–143. doi: 10.1093/bioinformatics/13.2.137. [DOI] [PubMed] [Google Scholar]
  9. Henikoff S., Pietrokovski S., Henikoff J. G. Superior performance in protein homology detection with the Blocks Database servers. Nucleic Acids Res. 1998 Jan 1;26(1):309–312. doi: 10.1093/nar/26.1.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hubbard T. J., Murzin A. G., Brenner S. E., Chothia C. SCOP: a structural classification of proteins database. Nucleic Acids Res. 1997 Jan 1;25(1):236–239. doi: 10.1093/nar/25.1.236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Peitsch M. C. ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. Biochem Soc Trans. 1996 Feb;24(1):274–279. doi: 10.1042/bst0240274. [DOI] [PubMed] [Google Scholar]
  12. Sayle R. A., Milner-White E. J. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 Sep;20(9):374–374. doi: 10.1016/s0968-0004(00)89080-5. [DOI] [PubMed] [Google Scholar]
  13. Schuler G. D., Epstein J. A., Ohkawa H., Kans J. A. Entrez: molecular biology database and retrieval system. Methods Enzymol. 1996;266:141–162. doi: 10.1016/s0076-6879(96)66012-1. [DOI] [PubMed] [Google Scholar]
  14. Sonnhammer E. L., Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 1994 Mar;3(3):482–492. doi: 10.1002/pro.5560030314. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES