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. 2001 Oct;2(5):338–343. doi: 10.1002/cfg.111

Website Review: Protein-Protein Interactions on the Web

Jo Wixon 1
PMCID: PMC2448406  PMID: 18629244

Abstract

We present a brief guide to resources on the Internet relating to Protein-Protein Interactions. These include databases containing experimentally verified and computationally inferred physical and functional interactions. There are also tools for predicting interactions and for extracting information on interactions from the literature, and organism specific databases.

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Selected References

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

  1. Bader G. D., Donaldson I., Wolting C., Ouellette B. F., Pawson T., Hogue C. W. BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res. 2001 Jan 1;29(1):242–245. doi: 10.1093/nar/29.1.242. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bader G. D., Hogue C. W. BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics. 2000 May;16(5):465–477. doi: 10.1093/bioinformatics/16.5.465. [DOI] [PubMed] [Google Scholar]
  3. Bartel P. L., Roecklein J. A., SenGupta D., Fields S. A protein linkage map of Escherichia coli bacteriophage T7. Nat Genet. 1996 Jan;12(1):72–77. doi: 10.1038/ng0196-72. [DOI] [PubMed] [Google Scholar]
  4. Blaschke C., Valencia A. Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study. Comp Funct Genomics. 2001;2(4):196–206. doi: 10.1002/cfg.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Enright A. J., Iliopoulos I., Kyrpides N. C., Ouzounis C. A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999 Nov 4;402(6757):86–90. doi: 10.1038/47056. [DOI] [PubMed] [Google Scholar]
  6. Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature. 1989 Jul 20;340(6230):245–246. doi: 10.1038/340245a0. [DOI] [PubMed] [Google Scholar]
  7. Hanes J., Plückthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A. 1997 May 13;94(10):4937–4942. doi: 10.1073/pnas.94.10.4937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hazbun T. R., Fields S. Networking proteins in yeast. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4277–4278. doi: 10.1073/pnas.091096398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Jeong H., Mason S. P., Barabási A. L., Oltvai Z. N. Lethality and centrality in protein networks. Nature. 2001 May 3;411(6833):41–42. doi: 10.1038/35075138. [DOI] [PubMed] [Google Scholar]
  10. Marcotte E. M., Pellegrini M., Thompson M. J., Yeates T. O., Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 1999 Nov 4;402(6757):83–86. doi: 10.1038/47048. [DOI] [PubMed] [Google Scholar]
  11. Marcotte E. M., Xenarios I., Eisenberg D. Mining literature for protein-protein interactions. Bioinformatics. 2001 Apr;17(4):359–363. doi: 10.1093/bioinformatics/17.4.359. [DOI] [PubMed] [Google Scholar]
  12. Rain J. C., Selig L., De Reuse H., Battaglia V., Reverdy C., Simon S., Lenzen G., Petel F., Wojcik J., Schächter V. The protein-protein interaction map of Helicobacter pylori. Nature. 2001 Jan 11;409(6817):211–215. doi: 10.1038/35051615. [DOI] [PubMed] [Google Scholar]
  13. Rodi D. J., Makowski L. Phage-display technology--finding a needle in a vast molecular haystack. Curr Opin Biotechnol. 1999 Feb;10(1):87–93. doi: 10.1016/s0958-1669(99)80016-0. [DOI] [PubMed] [Google Scholar]
  14. Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol. 2000 Dec;18(12):1257–1261. doi: 10.1038/82360. [DOI] [PubMed] [Google Scholar]
  15. Uetz P., Giot L., Cagney G., Mansfield T. A., Judson R. S., Knight J. R., Lockshon D., Narayan V., Srinivasan M., Pochart P. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000 Feb 10;403(6770):623–627. doi: 10.1038/35001009. [DOI] [PubMed] [Google Scholar]
  16. Xenarios I., Rice D. W., Salwinski L., Baron M. K., Marcotte E. M., Eisenberg D. DIP: the database of interacting proteins. Nucleic Acids Res. 2000 Jan 1;28(1):289–291. doi: 10.1093/nar/28.1.289. [DOI] [PMC free article] [PubMed] [Google Scholar]

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