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. 2008 Jun 13;24(15):1743–1744. doi: 10.1093/bioinformatics/btn285

MPIDB: the microbial protein interaction database

Johannes Goll 1,*, Seesandra V Rajagopala 1, Shen C Shiau 1, Hank Wu 1, Brian T Lamb 1, Peter Uetz 1
PMCID: PMC2638870  PMID: 18556668

Abstract

Summary: The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 22 530 experimentally determined interactions among proteins of 191 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 24 060 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 8150 additional evidences based on interaction conservation, co-purification and 3D domain contacts (iPfam, 3did).

Availability: http://www.jcvi.org/mpidb/

Contact: jgoll@jcvi.org

Supplementary Material

[Supplementary Data]
btn285_index.html (595B, html)

REFERENCES

  1. Alfarano, et al. The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 2005;33(Database issue):D418–D424. doi: 10.1093/nar/gki051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Finn RD, et al. iPfam: visualization of protein–protein interactions in PDB at domain and amino acid resolutions. Bioinformatics. 2005;21:410–412. doi: 10.1093/bioinformatics/bti011. [DOI] [PubMed] [Google Scholar]
  3. Jeong H, et al. Lethality and centrality in protein networks. Nature. 2001;411:41–42. doi: 10.1038/35075138. [DOI] [PubMed] [Google Scholar]
  4. Kerrien S, et al. Broadening the horizon–level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007a;5:44. doi: 10.1186/1741-7007-5-44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kerrien S, et al. IntAct–open source resource for molecular interaction data. Nucleic Acids Res. 2007b;35(Database issue):D561–D565. doi: 10.1093/nar/gkl958. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Salwinski L, et al. The database of interacting proteins: 2004 update. Nucleic Acids Res. 2004;32(Database issue):D449–D451. doi: 10.1093/nar/gkh086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Stein A, et al. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 2005;33(Database issue):D413–D417. doi: 10.1093/nar/gki037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Titz B, et al. The binary protein interactome of Treponema pallidum–the syphilis spirochete. PLoS ONE. 2008;3:e2292. doi: 10.1371/journal.pone.0002292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. UniProt Consortium. The universal protein resource (UniProt) Nucleic Acids Res. 2008;36(Database issue):D190–D195. doi: 10.1093/nar/gkm895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. von Mering C, et al. STRING 7–recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007;35(Database issue):D358–D362. doi: 10.1093/nar/gkl825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Zanzoni A, et al. MINT: the molecular INTeraction database. FEBS Lett. 2002;513:135–140. doi: 10.1016/s0014-5793(01)03293-8. [DOI] [PubMed] [Google Scholar]

Associated Data

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Supplementary Materials

[Supplementary Data]
btn285_index.html (595B, html)
btn285_1.pdf (176.2KB, pdf)

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