From Protein—Protein Complexes to Interactomics

  • Vincent Collura
  • Guillaume Boissy
Part of the Subcellular Biochemistry book series (SCBI, volume 43)


  1. Albers, M., Kranz, H., Kober, I., Kaiser, C., Klink, M., Suckow, J., Kern, R. and Koegl, M. (2005) Automated yeast two-hybrid screening for nuclear receptor-interacting proteins. Mol. Cell Proteomics 4, 205–213.PubMedCrossRefGoogle Scholar
  2. Albert, S., Gaudan, S., Knigge, H., Raetsch, A., Delgado, A., Huhse, B., Kirsch, H., Albers, M., Rebholz-Schuhmann, D. and Koegl, M. (2003) Computer-assisted generation of a protein-interaction database for nuclear receptors. Mol. Endocrinol. 17, 1555–1567.PubMedCrossRefGoogle Scholar
  3. Alberts, B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294.PubMedCrossRefGoogle Scholar
  4. Aloy, P., Ceulemans, H., Stark, A. and Russell. R.B. (2003) The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 332, 989–998.PubMedCrossRefGoogle Scholar
  5. Aloy, P. and Russell, R.B. (2006) Structural systems biology: modelling protein interactions. Nat. Rev. Mol. Cell Biol. 7, 188–197.PubMedCrossRefGoogle Scholar
  6. Ambasta, R.K., Kumar, P., Griendling, K.K., Schmidt, H.H., Busse, R. and Brandes, R.P. (2004) Direct interaction of the novel Nox proteins with p22phox is required for the formation of a functionally active NADPH oxidase. J. Biol. Chem. 279, 45935–45941.PubMedCrossRefGoogle Scholar
  7. Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C. and Murzin, A.G. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32, D226-D229.PubMedCrossRefGoogle Scholar
  8. Angers, S., Salahpour, A., Joly, E., Hilairet, S., Chelsky, D., Dennis, M. and Bouvier, M. (2000) Detection of beta 2-adrenergic receptor dimerization in living cells using bioluminescence resonance energy transfer (BRET). Proc. Natl Acad. Sci. U.S.A. 97, 3684–3689.PubMedCrossRefGoogle Scholar
  9. Arkin, M.R. and Wells, J.A. (2004) Small-molecule inhibitors of protein–protein interactions: progressing towards the dream. Nat. Rev. Drug Discov. 3, 301–317.PubMedCrossRefGoogle Scholar
  10. Bader, G.D. and Hogue, C.W. (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 1–27.CrossRefGoogle Scholar
  11. Bahadur, R.P., Chakrabarti, P., Rodier, F. and Janin, J. (2003) Dissecting subunit interfaces in homodimeric proteins. Proteins 53, 708–719.PubMedCrossRefGoogle Scholar
  12. Bahadur, R.P., Chakrabarti, P., Rodier, F. and Janin, J. (2004) A dissection of specific and non-specific protein–protein interfaces. J. Mol. Biol. 336, 943–955.PubMedCrossRefGoogle Scholar
  13. Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113.PubMedCrossRefGoogle Scholar
  14. Bartel, P.L., Roecklein, J.A., SenGupta, D. and Fields, S. (1996) A protein linkage map of Escherichia coli bacteriophage T7. Nat. Genet. 12, 72–77.PubMedCrossRefGoogle Scholar
  15. Batada, N.N. (2004) CNplot: visualizing pre-clustered networks. Bioinformatics 20, 1455–1456.PubMedCrossRefGoogle Scholar
  16. Blaschke, C., Andrade, M.A. Ouzounis, C. and Valencia, A. (1999) Automatic extraction of biological information from scientific text: protein-protein interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol., 60–67.Google Scholar
  17. Bonvin, A.M., Boelens, R. and Kaptein, R. (2005) NMR analysis of protein interactions. Curr. Opin. Chem. Biol. 9, 501–508.PubMedCrossRefGoogle Scholar
  18. Bork, P. and Serrano, L. (2005) Towards cellular systems in 4D. Cell 121, 507–509.PubMedCrossRefGoogle Scholar
  19. Bornberg-Bauer, E., Beaussart, F., Kummerfeld, S.K., Teichmann, S.A. and Weiner, J. 3rd (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol. Life Sci. 62, 435–445.PubMedCrossRefGoogle Scholar
  20. Bouwmeester, T., Bauch, A., Ruffner, H., Angrand, P.O., Bergamini, G., Croughton, K. Cruciat, C., Eberhard, D., Gagneur, J., Ghidelli, S., Hopf, C., Huhse, B., Mangano, R., Michon, A.M., Schirle, M., Schlegl, J., Schwab, M., Stein, M.A., Bauer, A., Casari, G., Drewes, G., Gavin, A.C., Jackson, D.B., Joberty, G., Neubauer, G., Rick, J., Kuster, B. and Superti-Furga, G. (2004) A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat. Cell Biol. 6, 97–105.PubMedCrossRefGoogle Scholar
  21. Breitkreutz, B.J., Stark, C. and Tyers, M. (2003) Osprey: a network visualization system. Genome Biol. 4, R22.PubMedCrossRefGoogle Scholar
  22. Brown, K.R. and Jurisica, I. (2005) Online predicted human interaction database. Bioinformatics 21, 2076–2082.PubMedCrossRefGoogle Scholar
  23. Bürkle, L., Dinkel, M., Auerbach, D. and Stagljar, I. (2005) A GPCR interactome: a comprehensive membrane protein interaction map of Human G-protein coupled receptors using the membrane-based yeast two-hybrid approach. Mol. Cell. Proteomics 4 (Suppl. 1), S45.Google Scholar
  24. Camonis, J.H. and White, M.A. (2005) Ral GTPases: corrupting the exocyst in cancer cells. Trends Cell Biol. 15, 327–332.PubMedCrossRefGoogle Scholar
  25. Chakrabarti, P. and Janin, J. (2002) Dissecting protein-protein recognition sites. Proteins 47, 334–343.PubMedCrossRefGoogle Scholar
  26. Clayton, A.H., Hanley, Q.S., Arndt-Jovin, D.J., Subramaniam, V. and Jovin, T.M. (2002) Dynamic fluorescence anisotropy imaging microscopy in the frequency domain (rFLIM). Biophys. J. 83, 1631–1649.PubMedCrossRefGoogle Scholar
  27. Colland, F., Jacq, X., Trouplin, V., Mougin, C., Groizeleau, C., Hamburger, A., Meil, A., Wojcik, J., Legrain, P. and Gauthier, J.M. (2004) Functional proteomics mapping of a human signaling pathway. Genome Res. 14, 1324–1332.PubMedCrossRefGoogle Scholar
  28. Colland, F., Rain, J.C., Gounon, P., Labigne, A., Legrain, P. and De Reuse, H. (2001) Identification of the Helicobacter pylori anti-sigma28 factor. Mol. Microbiol. 41, 477–487.PubMedCrossRefGoogle Scholar
  29. Dandekar, T., Snel, B., Huynen, M. and Bork, P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324–328.PubMedCrossRefGoogle Scholar
  30. Davis, F.P. and Sali, A. (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21, 1901–1907.PubMedCrossRefGoogle Scholar
  31. Day, R.N. (1998) Visualization of Pit-1 transcription factor interactions in the living cell nucleus by fluorescence resonance energy transfer microscopy. Mol. Endocrinol. 12, 1410–1419.PubMedCrossRefGoogle Scholar
  32. Durand, P., Labarre, L., Meil, A., Divol, J.L., Vandenbrouck, Y., Viari, A. and Wojcik, J. (2006) GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. BMC Bioinformatics 7, 21.PubMedCrossRefGoogle Scholar
  33. Dutta, S. and Berman, H.M. (2005) Large macromolecular complexes in the Protein Data Bank: a status report. Structure 13, 381–388.PubMedCrossRefGoogle Scholar
  34. Dziembowski, A. and Seraphin, B. (2004) Recent developments in the analysis of protein complexes. FEBS Lett. 556, 1–6.PubMedCrossRefGoogle Scholar
  35. Eggers, C.T., Wang, S.X., Fletterick, R.J. and Craik, C.S. (2001) The role of ecotin dimerization in protease inhibition. J. Mol. Biol. 308, 975–991.PubMedCrossRefGoogle Scholar
  36. Emiliani, S., Mousnier, A., Busschots, K., Maroun, M., Van Maele, B., Tempe, D., Vandekerckhove, L., Moisant, F., Ben-Slama, L., Witvrouw, M., Christ, F., Rain, J.C., Dargemont, C., Debyser, Z. and Benarous, R. (2005) Integrase mutants defective for interaction with LEDGF/p75 are impaired in chromosome tethering and HIV-1 replication. J. Biol. Chem. 280, 25517–25523.PubMedCrossRefGoogle Scholar
  37. Erickson, M.G., Alseikhan, B.A., Peterson, B.Z. and Yue, D.T. (2001) Preassociation of calmodulin with voltage-gated Ca(2+) channels revealed by FRET in single living cells. Neuron. 31, 973–985.PubMedCrossRefGoogle Scholar
  38. Fields, S. and Song, O. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245–246.PubMedCrossRefGoogle Scholar
  39. Finley, R.L. Jr. and Brent, R. (1994) Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc. Natl Acad. Sci. U.S.A. 91, 12980–12984.PubMedCrossRefGoogle Scholar
  40. Formstecher, E., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V., Maire, S., Brun, C., Jacq, B., Arpin, M., Bellaiche, Y., Bellusci, S., Benaroch, P., Bornens, M., Chanet, R., Chavrier, P., Delattre, O., Doye, V., Fehon R., Faye, G., Galli, T., Girault, J.A., Goud, B., de Gunzburg, J., Johannes, L., Junier, M.P. Mirouse, V., Mukherjee, A., Papadopoulo, D., Perez, F., Plessis, A., Rosse, C., Saule, S., Stoppa-Lyonnet, D., Vincent, A., White, M., Legrain, P., Wojcik, J., Camonis, J. and Daviet. L. (2005) Protein interaction mapping: a Drosophila case study. Genome Res. 15, 376–384.PubMedCrossRefGoogle Scholar
  41. Fukai, S., Matern, H.T., Jagath, J.R., Scheller, R.H. and Brunger, A.T. (2003) Structural basis of the interaction between RalA and Sec5, a subunit of the sec6/8 complex. EMBO J. 22, 3267–3278.PubMedCrossRefGoogle Scholar
  42. Gales, C., Rebois, R.V., Hogue, M., Trieu, P., Breit, A., Hebert, T.E. and Bouvier, M. (2005) Real-time monitoring of receptor and G-protein interactions in living cells. Nat. Methods 2, 177–184.PubMedCrossRefGoogle Scholar
  43. Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B., Edelmann, A., Heurtier, M.A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A.M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J.M., Kuster, B., Bork, P., Russell, R.B. and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636.PubMedCrossRefGoogle Scholar
  44. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. and Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.PubMedCrossRefGoogle Scholar
  45. Germain-Desprez, D., Bazinet, M., Bouvier, M. and Aubry, M. (2003) Oligomerization of transcriptional intermediary factor 1 regulators and interaction with ZNF74 nuclear matrix protein revealed by bioluminescence resonance energy transfer in living cells. J. Biol. Chem. 278, 22367–22373.PubMedCrossRefGoogle Scholar
  46. Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M. Voss, E. Furtak, K. Renzulli, R. Aanensen, N. Carrolla, S. Bickelhaupt, E. Lazovatsky, Y. DaSilva, A. Zhong, J. Stanyon, C.A. Finley, R.L. Jr., White, K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J. and Rothberg, J.M. (2003) Aprotein interaction map of Drosophila melanogaster. Science 302, 1727–1736.PubMedCrossRefGoogle Scholar
  47. Goh, C.S., Milburn, D. and Gerstein, M. (2004) Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14, 104–109.PubMedCrossRefGoogle Scholar
  48. Gong, S., Yoon, G., Jang, I., Bolser, D., Dafas, P., Schroeder, M., Choi, H., Cho, Y., Han, K., Lee, S., Choi, H., Lappe, M., Holm, L., Kim, S., Oh, D. and Bhak, J. (2005) PSIbase: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics 21, 2541–2543.PubMedCrossRefGoogle Scholar
  49. Guo, Z., Zhou, D. and Schultz, P.G. (2000) Designing small-molecule switches for protein–protein interactions. Science 288, 2042–2045.PubMedCrossRefGoogle Scholar
  50. Hammond, P.W., Alpin, J. Rise, C.E., Wright, M. and Kreider, B.L. (2001) In vitro selection and characterization of Bcl-X(L)-binding proteins from a mix of tissue-specific mRNA display libraries. J. Biol. Chem. 276, 20898–20906.PubMedCrossRefGoogle Scholar
  51. Han, J.D., Bertin, N., Hao, T., Goldberg, D.S., Berriz, G.F., Zhang, L.V., Dupuy, D., Walhout, A.J., Cusick, M.E., Roth, F.P. and Vidal, M. (2004b) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88–93.PubMedCrossRefGoogle Scholar
  52. Han, J.D., Dupuy, D., Bertin, N., Cusick, M.E. and Vidal, M. (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat. Biotechnol. 23, 839–844.PubMedCrossRefGoogle Scholar
  53. Han, K., Park, B., Kim, H., Hong, J. and Park, J. (2004a) HPID: the human protein interaction database. Bioinformatics 20, 2466–2470.PubMedCrossRefGoogle Scholar
  54. Henrick, K. and Thornton, J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23, 358–361.PubMedCrossRefGoogle Scholar
  55. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S.G., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C. and Apweiler, R. (2004) The HUPO PSI’s molecular interaction format – a community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177–183.PubMedCrossRefGoogle Scholar
  56. Heyduk, E. and Heyduk, T. (1994) Mapping protein domains involved in macromolecular interactions: a novel protein footprinting approach. Biochemistry 33, 9643–9650.PubMedCrossRefGoogle Scholar
  57. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W., Figeys, D. and Tyers, M. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183.PubMedCrossRefGoogle Scholar
  58. Hoffmann, R. and Valencia, A. (2004) A gene network for navigating the literature. Nat. Genet. 36, 664.PubMedCrossRefGoogle Scholar
  59. Hooper, S.D. and Bork, P. (2005) Medusa: a simple tool for interaction graph analysis. Bioinformatics 21, 4432–4433.PubMedCrossRefGoogle Scholar
  60. Houtman, J.C., Barda-Saad, M. and Samelson, L.E. (2005) Examining multiprotein signaling complexes from all angles. FEBS J. 272, 5426–5435.PubMedCrossRefGoogle Scholar
  61. Hsu, S.C., TerBush, D., Abraham, M. and Guo, W. (2004) The exocyst complex in polarized exocytosis. Int. Rev. Cytol. 233, 243–265.PubMedCrossRefGoogle Scholar
  62. Hu, Z., Mellor, J., Wu, J. and DeLisi, C. (2004) VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics 5, 17.PubMedCrossRefGoogle Scholar
  63. Huynen, M., Snel, B., Lathe, W. 3rd and Bork, P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res. 10, 1204–1210.PubMedCrossRefGoogle Scholar
  64. Huynen, M.A., Snel, B., von Mering, C. and Bork, P. (2003) Function prediction and protein networks. Curr. Opin. Cell. Biol. 15, 191–198.PubMedCrossRefGoogle Scholar
  65. Iragne, F., Nikolski, M., Mathieu, B., Auber, D. and Sherman, D. (2005) ProViz: protein interaction visualization and exploration. Bioinformatics 21, 272–274.PubMedCrossRefGoogle Scholar
  66. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M. and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. U.S.A. 98, 4569–4574.PubMedCrossRefGoogle Scholar
  67. Johnsson, N. and Varshavsky, A. (1994) Split ubiquitin as a sensor of protein interactions in vivo. Proc. Natl Acad. Sci. U.S.A. 91, 10340–10344.CrossRefGoogle Scholar
  68. Jones, R.B., Gordus, A., Krall, J.A. and MacBeath, G. (2006) A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439, 168–174.PubMedCrossRefGoogle Scholar
  69. Joyce, A.R. and Palsson, B.O. (2006) The model organism as a system: integrating ‘omics’ data sets. Nat. Rev. Mol. Cell Biol. 7, 198–210.PubMedCrossRefGoogle Scholar
  70. Karlsson, R. (2004) SPR for molecular interaction analysis: a review of emerging application areas. J. Mol. Recognit. 17, 151–161.PubMedCrossRefGoogle Scholar
  71. Kelley, B.P., Sharan, R., Karp, R.M., Sittler, T., Root, D.E., Stockwell, B.R. and Ideker, T. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl Acad. Sci. U.S.A. 100, 11394–11399.PubMedCrossRefGoogle Scholar
  72. Kenworthy, A.K. (2001) Imaging protein-protein interactions using fluorescence resonance energy transfer microscopy. Methods 24, 289–296.PubMedCrossRefGoogle Scholar
  73. Kerppola, T.K. (2006) Visualization of molecular interactions by fluorescence complementation. Nat. Rev. Mol. Cell Biol. 7, 449–456.PubMedCrossRefGoogle Scholar
  74. Kim, W.K. and Ison, J.C. (2005) Survey of the geometric association of domain-domain interfaces. Proteins 61, 1075–1088.PubMedCrossRefGoogle Scholar
  75. Lakey, J.H. and Raggett, E.M. (1998) Measuring protein-protein interactions. Curr. Opin. Struct. Biol. 8, 119–123.PubMedCrossRefGoogle Scholar
  76. Lebreton, A., Saveanu, C., Decourty, L., Rain, J.C., Jacquier, A. and Fromont-Racine, M. (2006) A functional network involved in the recycling of nucleocytoplasmic pre-60S factors. J. Cell Biol. 173, 349–360.PubMedCrossRefGoogle Scholar
  77. Legrain, P. and Selig, L. (2000) Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 480, 32–36.PubMedCrossRefGoogle Scholar
  78. Legrain, P. and Strosberg, D. (2002) Protein interaction domain mapping for the selection of validated targets and lead compounds in the anti-infectious area. Curr. Pharm. Des. 8, 1189–1198.PubMedCrossRefGoogle Scholar
  79. Legrain, P., Wojcik, J. and Gauthier, J.M. (2001) Protein–protein interaction maps: a lead towards cellular functions. Trends Genet. 17, 346–352.PubMedCrossRefGoogle Scholar
  80. Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E. and Vidal, M. (2004) A map of the interactome network of the metazoan C.Elegans. Science 303, 540–543.PubMedCrossRefGoogle Scholar
  81. Lipovsek, D. and Pluckthun, A. (2004) In-vitro protein evolution by ribosome display and mRNA display. J. Immunol. Methods 290, 51–67.CrossRefGoogle Scholar
  82. Luban, J., Bossolt, K.L., Franke, E.K., Kalpana, G.V. and Goff, S.P. (1993) Human immunodeficiency virus type 1 Gag protein binds to cyclophilins A and B. Cell 73, 1067–1078.PubMedCrossRefGoogle Scholar
  83. MacBeath, G. and Schreiber, S.L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763.PubMedGoogle Scholar
  84. Mahajan, N.P., Linder, K., Berry, G., Gordon, G.W., Heim, R. and Herman, B. (1998) Bcl-2 and Bax interactions in mitochondria probed with green fluorescent protein and fluorescence resonance energy transfer. Nat. Biotechnol. 16, 547–552.PubMedCrossRefGoogle Scholar
  85. Mann, M., Hendrickson, R.C. and Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70, 437–473.PubMedCrossRefGoogle Scholar
  86. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O. and Eisenberg, D. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751–753.PubMedCrossRefGoogle Scholar
  87. Marcotte, E.M., Xenarios, I. and Eisenberg, D. (2001) Mining literature for protein-protein interactions. Bioinformatics 17, 359–363.PubMedCrossRefGoogle Scholar
  88. Marianayagam, N.J., Sunde, M. and Matthews, J.M. (2004) The power of two: protein dimerization in biology. Trends Biochem. Sci. 29, 618–625.PubMedCrossRefGoogle Scholar
  89. Matthews, L.R., Vaglio, P., Reboul, J., Ge, H., Davis, B.P., Garrels, J., Vincent, S. and Vidal, M. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or “interologs.” Genome Res. 11, 2120–2126.PubMedCrossRefGoogle Scholar
  90. Mayer, M.L. and Hieter, P. (2000) Protein networks-built by association. Nat. Biotechnol. 18, 1242–1243.PubMedCrossRefGoogle Scholar
  91. Meil, A., Durand, P. and Wojcik, J. (2005) PIMWalker: visualising protein interaction networks using the HUPO PSI molecular interaction format. Appl. Bioinformatics 4, 137–139.PubMedCrossRefGoogle Scholar
  92. Michnick, S.W. (2001) Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments. Curr. Opin. Struct. Biol. 11, 472–477.PubMedCrossRefGoogle Scholar
  93. Miller, J.P., Lo, R.S., Ben-Hur, A., Desmarais, C., Stagljar, I., Noble, W.S. and Fields, S. (2005) Large-scale identification of yeast integral membrane protein interactions. Proc. Natl Acad. Sci. U.S.A. 102, 12123–12128.PubMedCrossRefGoogle Scholar
  94. Milligan, G. (2004) G protein-coupled receptor dimerization: function and ligand pharmacology. Mol. Pharmacol. 66, 1–7.PubMedCrossRefGoogle Scholar
  95. Milligan, G., Wilson, S. and Lopez-Gimenez, J.F. (2005) The specificity and molecular basis of alphal-adrenoceptor and CXCR chemokine receptor dimerization. J. Mol. Neurosci. 26, 161–168.PubMedCrossRefGoogle Scholar
  96. Nakai, K. and Horton, P. (1999) PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24, 34–36.PubMedCrossRefGoogle Scholar
  97. Neduva, V., Linding, R., Su-Angrand, I., Stark, A., de Masi, F., Gibson, T.J., Lewis, J., Serrano, L. and Russell, R.B. (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol. 3, e405.PubMedCrossRefGoogle Scholar
  98. Nickell, S., Kofler, C., Leis, A.P. and Baumeister, W. (2006) A visual approach to proteomics. Nat. Rev. Mol. Cell Biol. 7, 225–230.PubMedCrossRefGoogle Scholar
  99. Nilsson, P., Paavilainen, L., Larsson, K., Odling, J., Sundberg, M., Andersson, A.C., Kampf, C., Persson, A., Al-Khalili Szigyarto, C., Ottosson, J., Bjorling, E., Hober, S., Wernerus, H., Wester, K., Ponten, F. and Uhlen, M. (2005) Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling. Proteomics 5, 4327–4337.PubMedCrossRefGoogle Scholar
  100. Nooren, I.M. and Thornton, J.M. (2003a) Diversity of protein-protein interactions. EMBO J. 22, 3486–3492.PubMedCrossRefGoogle Scholar
  101. Nooren, I.M. and Thornton. J.M. (2003b) Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325, 991–1018.PubMedCrossRefGoogle Scholar
  102. Oka, T. and Krieger, M. (2005) Multi-component protein complexes and Golgi membrane trafficking. J. Biochem. (Tokyo) 137, 109–114.Google Scholar
  103. Oltersdorf, T., Elmore, S.W., Shoemaker, A.R., Armstrong, R.C., Augeri, D.J., Belli, B.A., Bruncko, M., Deckwerth, T.L., Dinges, J., Hajduk, P.J., Joseph, M.K., Kitada, S., Korsmeyer, S.J., Kunzer, A.R., Letai, A., Li, C., Mitten, M.J., Nettesheim, D.G., Ng, S., Nimmer, P.M., O’Connor, J.M., Oleksijew, A., Petros, A.M., Reed, J.C., Shen, W., Tahir, S.K., Thompson, C.B., Tomaselli, K.J., Wang, B., Wendt, M.D., Zhang, H., Fesik, S.W. and Rosenberg, S.H. (2005) An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature 435, 677–681.PubMedCrossRefGoogle Scholar
  104. Ono, T., Hishigaki, H., Tanigami, A. and Takagi, T. (2001) Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17, 155–161.PubMedCrossRefGoogle Scholar
  105. Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frishman, G., Montrone, C., Mark, P., Stumpflen, V., Mewes, H.W., Ruepp, A. and Frishman, D. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21, 832–834.PubMedCrossRefGoogle Scholar
  106. Pazos, F., Ranea, J.A., Juan, D. and Sternberg, M.J. (2005) Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J. Mol. Biol. 352, 1002–1015.PubMedCrossRefGoogle Scholar
  107. Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14, 609–614.PubMedCrossRefGoogle Scholar
  108. Pazos, F. and Valencia, A. (2002) In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47, 219–227.PubMedCrossRefGoogle Scholar
  109. Pellegrini, M., Haynor, D. and Johnson, J.M. (2004) Protein interaction networks. Expert Rev Proteomics 1, 239–249.PubMedCrossRefGoogle Scholar
  110. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. and Yeates, T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. U.S.A. 96, 4285–4288.PubMedCrossRefGoogle Scholar
  111. Pereira-Leal, J.B., Levy, E.D. and Teichmann, S.A. (2006) The origins and evolution of functional modules: lessons from protein complexes. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 361, 507–517.PubMedCrossRefGoogle Scholar
  112. Peri, S., Navarro, J.D., Amanchy, R., Kristiansen, T.Z., Jonnalagadda, C.K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T.K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H.N., Rashmi, B.P., Ramya, M.A., Zhao, Z., Chandrika, K.N., Padma, N., Harsha, H.C., Yatish, A.J., Kavitha, M.P., Menezes, M., Choudhury, D.R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S.K., Madavan, V., Joseph, A., Wong, G.W., Schiemann, W.P., Constantinescu, S.N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G.C., Dang, C.V., Garcia, J.G., Pevsner, J., Jensen, O.N., Roepstorff, P., Deshpande, K.S., Chinnaiyan, A.M., Hamosh, A., Chakravarti, A. and Pandey, A. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome. Res. 13, 2363–2371.PubMedCrossRefGoogle Scholar
  113. Peter, M., Ameer-Beg, S.M., Hughes, M.K., Keppler, M.D., Prag, S., Marsh, M., Vojnovic, B. and Ng, T. (2005) Multiphoton-FLIM quantification of the EGFP-mRFPl FRET pair for localization of membrane receptor-kinase interactions. Biophys. J. 88, 1224–1237.PubMedCrossRefGoogle Scholar
  114. Piehler, J. (2005) New methodologies for measuring protein interactions in vivo and in vitro. Curr. Opin. Struct. Biol. 15, 4–14.CrossRefGoogle Scholar
  115. Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M. and Seraphin, B. (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218–229.PubMedCrossRefGoogle Scholar
  116. Qoronfleh, M.W., Ren, L., Emery, D., Perr, M. and Kaboord, B. (2003) Use of immunomatrix Methods to improve protein-protein interaction detection. J. Biomed. Biotechnol. 2003, 291–298.PubMedCrossRefGoogle Scholar
  117. Rain, J.C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schachter, V., Chemama, Y., Labigne, A. and Legrain, P. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409, 211–215.PubMedCrossRefGoogle Scholar
  118. Ramani, A.K., Bunescu, R.C., Mooney, R.J. and Marcotte, E.M. (2005) Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol. 6, R40.PubMedCrossRefGoogle Scholar
  119. Ramani, A.K. and Marcotte, E.M. (2003) Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327, 273–284.PubMedCrossRefGoogle Scholar
  120. Reichmann, D., Rahat, O., Albeck, S., Meged, R., Dym, O. and Schreiber, G. (2005) The modular architecture of protein-protein binding interfaces. Proc. Natl Acad. Sci. U.S.A. 102, 57–62.PubMedCrossRefGoogle Scholar
  121. Remy, I. and Michnick, S.W. (2001) Visualization of biochemical networks in living cells. Proc. Natl Acad. Sci. U.S.A. 98, 7678–7683.PubMedCrossRefGoogle Scholar
  122. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M. and Seraphin, B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030–1032.PubMedCrossRefGoogle Scholar
  123. Rodier, F., Bahadur, R.P., Chakrabarti, P. and Janin, J. (2005) Hydration of protein-protein interfaces. Proteins 60, 36–45.PubMedCrossRefGoogle Scholar
  124. Rossmann, M.G., Morais, M.C., Leiman, P.G. and Zhang, W. (2005) Combining X-ray crystallography and electron microscopy. Structure 13, 355–362.PubMedCrossRefGoogle Scholar
  125. Royer, W.E. Jr, Zhu, H., Gorr, T.A., Flores, J.F. and Knapp, J.E. (2005) Allosteric hemoglobin assembly: diversity and similarity. J. Biol. Chem. 280, 27477–27480.PubMedCrossRefGoogle Scholar
  126. Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D.S., Zhang, L.V., Wong, S.L., Franklin, G., Li, S., Albala, J.S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R.S., Vandenhaute, J., Zoghbi, H.Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M.E., Hill, D.E., Roth, F.P. and Vidal, M. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173–1178.PubMedCrossRefGoogle Scholar
  127. Russell, R.B., Alber, F., Aloy, P., Davis, F.P., Korkin, D., Pichaud, M., Topf, M. and Sali, A. (2004) A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14, 313–324.PubMedCrossRefGoogle Scholar
  128. Sali, A., Glaeser, R., Earnest, T. and Baumeisterm, W. (2003) From words to literature in structural proteomics. Nature 422, 216–225.PubMedCrossRefGoogle Scholar
  129. Salwinski, L., Miller, C.S., Smith, A.J., Pettit, F.K., Bowie, J.U. and Eisenberg, D. (2004) The Database of interacting proteins: 2004 update. Nucleic Acids Res. 32, D449-D451.PubMedCrossRefGoogle Scholar
  130. Sato, T., Yamanishi, Y., Kanehisa, M. and Toh, H. (2005) The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21, 3482–3489.PubMedCrossRefGoogle Scholar
  131. Schimmele, B. and Pluckthun, A. (2005) Identification of a functional epitope of the Nogo receptor by a combinatorial approach using ribosome display. J. Mol. Biol. 352, 229–241.PubMedCrossRefGoogle Scholar
  132. Schreiber, G. (2002) Kinetic studies of protein-protein interactions. Curr. Opin. Struct. Biol. 12, 41–47.PubMedCrossRefGoogle Scholar
  133. Séraphin, B. (2002) Identification of transiently interacting proteins and of stable protein complexes. In: Advances in Protein Chemistry. J. Janin and S.J. Wodak, eds. (U.S.A.: Elsevier Science), vol. 61, pp. 99–117.Google Scholar
  134. Serebriiskii, I.G., Mitina, O., Pugacheva, E.N., Benevolenskaya, E., Kotova, E., Toby, G.G., Khazak, V., Kaelin, W.G., Chernoff, J. and Golemis, E.A. (2002) Detection of peptides, proteins, and drugs that selectively interact with protein targets. Genome Res. 12, 1785–1791.PubMedCrossRefGoogle Scholar
  135. Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504.PubMedCrossRefGoogle Scholar
  136. Sharan, R., Suthram, S., Kelley, R.M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R.M. and Ideker. T. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. U.S.A. 102, 1974–1979.PubMedCrossRefGoogle Scholar
  137. Sprinzak, E., Sattath, S. and Margalit, H. (2003) How reliable are experimental protein-protein interaction data? J. Mol. Biol. 327, 919–923.PubMedCrossRefGoogle Scholar
  138. Stagljar, I. and Fields, S. (2002) Analysis of membrane protein interactions using yeast-based technologies. Trends. Biochem. Sci. 27, 559–563.PubMedCrossRefGoogle Scholar
  139. Stagljar, I., Korostensky, C., Johnsson, N. and te Heesen, S. (1998) A genetic system based on splitubiquitin for the analysis of interactions between membrane proteins in vivo. Proc. Natl Acad. Sci. U.S.A. 95, 5187–5192.CrossRefGoogle Scholar
  140. Stanyon, C.A., Liu, G., Mangiola, B.A., Patel, N., Giot, L., Kuang, B., Zhang, H., Zhong, J. and Finley, Jr. R.L. (2004) A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol. 5, R96.PubMedCrossRefGoogle Scholar
  141. Stark, C., Breitkreutz, B.J., Reguly, T., Boucher, L., Breitkreutz, A. and Tyers, M. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 34, D535-D539.PubMedCrossRefGoogle Scholar
  142. Stein, A., Russell, R.B. and Aloy, P. (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 33, D413-D417.PubMedCrossRefGoogle Scholar
  143. Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F.H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksoz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H. and Wanker, E.E. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957–968.PubMedCrossRefGoogle Scholar
  144. Stiffler, M.A., Grantcharova, V.P., Sevecka, M. and Macbeath, G. (2006) Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays. J. Am. Chem. Soc. 128, 5913–5922.PubMedCrossRefGoogle Scholar
  145. Suzuki, H., Saito, R., Kanamori, M., Kai, C., Schonbach, C., Nagashima, T., Hosaka, J. and Hayashizaki, Y. (2003) The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer. Genome Res. 13, 1534–1541.PubMedCrossRefGoogle Scholar
  146. Templin, M.F., Stoll, D., Schwenk, J.M., Potz, O., Kramer, S. and Joos, T.O. (2003) Protein microarrays: promising tools for proteomic research. Proteomics 3, 2155–2166.PubMedCrossRefGoogle Scholar
  147. Tewari, M., Hu, P.J., Ahn, J.S., Ayivi-Guedehoussou, N., Vidalain, P.O., Li, S., Milstein, S., Armstrong, C.M., Boxem, M., Butler, M.D., Busiguina, S., Rual, J.F., Ibarrola, N., Chaklos, S.T., Bertin, N., Vaglio, P., Edgley, M.L., King, K.V., Albert, P.S., Vandenhaute, J., Pandey, A., Riddle, D.L., Ruvkun, G. and Vidal, M. (2004) Systematic interactome mapping and genetic perturbation analysis of a C.Elegans TGF-beta signaling network. Mol. Cell 13, 469–482.PubMedCrossRefGoogle Scholar
  148. Thaminy, S., Auerbach, D., Arnoldo, A. and Stagljar, I. (2003) Identification of novel ErbB3-interacting factors using the split-ubiquitin membrane yeast two-hybrid system. Genome Res. 13, 1744–1753.PubMedCrossRefGoogle Scholar
  149. Tirode, F., Malaguti, C., Romero, F., Attar, R., Camonis, J. and Egly, J.M. (1997) A conditionally expressed third partner stabilizes or prevents the formation of a transcriptional activator in a three-hybrid system. J. Biol. Chem. 272, 22995–22999.PubMedCrossRefGoogle Scholar
  150. Tong, A.H., Drees, B., Nardelli, G., Bader, G.D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., Quondam, M., Zucconi, A., Hogue C.W., Fields, S., Boone, C. and Cesareni, G. (2002) A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295, 321–324.PubMedCrossRefGoogle Scholar
  151. Toogood, P.L. (2002) Inhibition of protein-protein association by small molecules: approaches and progress. J. Med. Chem. 45, 1543–1558.PubMedCrossRefGoogle Scholar
  152. Trakselis, M.A., Alley, S.C. and Ishmael, F.T. (2005) Identification and mapping of protein-protein interactions by a combination of cross-linking, cleavage, and proteomics. Bioconjug. Chem. 16, 741–750.PubMedCrossRefGoogle Scholar
  153. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S. and Rothberg, J.M. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627.PubMedCrossRefGoogle Scholar
  154. Uetz, P., Ideker, T. and Schwikowski, B. (2002) Visualization an integration of protein-protein interactions. In: Protein-protein interactions. E. Golemis, ed. (New York: CSHL Press), pp. 623–646.Google Scholar
  155. Veenhoff, L.M., Heuberger, E.H. and Poolman, B. (2002) Quaternary structure and function of transport proteins. Trends Biochem. Sci. 27, 242–249.PubMedCrossRefGoogle Scholar
  156. Vidal, M. (2005) Interactome modeling. FEBS Lett. 579, 1834–1838.PubMedCrossRefGoogle Scholar
  157. Vidal, M. (2006) Time for a human interactome project? The Scientist 20, 46–51.Google Scholar
  158. Vidal, M. and Endoh, H. (1999) Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol. 17, 374–381.PubMedCrossRefGoogle Scholar
  159. Vidal, M. and Legrain, P. (1999) Yeast forward and reverse ‘n’-hybrid systems. Nucleic Acids Res. 27, 919–929.PubMedCrossRefGoogle Scholar
  160. von Mering, C., Jensen, L.J., Snel, B., Hooper, S.D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M.A. and Bork, P. (2005) STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33, D433-D437.PubMedCrossRefGoogle Scholar
  161. von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403.PubMedCrossRefGoogle Scholar
  162. Vondriska, T.M., Pass, J.M. and Ping, P. (2004) Scaffold proteins and assembly of multiprotein signaling complexes. J. Mol. Cell Cardiol. 37, 391–397.PubMedCrossRefGoogle Scholar
  163. Walhout, A.J., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N. and Vidal, M. (2000) Protein interaction mapping in C.Elegans using proteins involved in vulval development. Science 287, 116–122.PubMedCrossRefGoogle Scholar
  164. Wilkinson, K.D. (2004) Quantitative analysis of protein-protein interactions. Methods Mol. Biol. 261, 15–32.PubMedGoogle Scholar
  165. Winter, C., Henschel, A., Kim, W.K. and Schroeder, M. (2006) SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res. 34, D310-D314.PubMedCrossRefGoogle Scholar
  166. Wojcik, J., Boneca, I.G. and Legrain, P. (2002) Prediction, assessment and validation of protein interaction maps in bacteria. J. Mol. Biol. 323, 763–770.PubMedCrossRefGoogle Scholar
  167. Wojcik, J. and Hamburger, A. (2003) Proteomic Informatics. In: Bioinformatics for Geneticists. M.R. Barnes and I.C. Gray, eds. (Paris, France: John Wiley & Sons, Ltd), pp. 345–371.CrossRefGoogle Scholar
  168. Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M. and Cesareni, G. (2002) MINT: a Molecular INTeraction database. FEBS Lett. 513, 135–140.PubMedCrossRefGoogle Scholar
  169. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., Mitchell, T., Miller, P., Dean, R.A., Gerstein, M. and Snyder, M. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101–2105.PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Vincent Collura
    • 1
  • Guillaume Boissy
    • 1
  1. 1.Hybrigenics S.A.France

Personalised recommendations