Skip to main content
SpringerLink
Log in

Computational Methods For Predicting Protein–Protein Interactions

  • Chapter
  • First Online:
Protein – Protein Interaction

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 110))

Abstract

Protein–protein interactions (PPIs) play a critical role in many cellular functions. A numberof experimental techniques have been applied to discover PPIs; however, these techniques are expensive interms of time, money, and expertise. There are also large discrepancies between the PPI data collectedby the same or different techniques in the same organism. We therefore turn to computational techniquesfor the prediction of PPIs. Computational techniques have been applied to the collection, indexing, validation,analysis, and extrapolation of PPI data. This chapter will focus on computational prediction of PPI, reviewinga number of techniques including PIPE, developed in our own laboratory. For comparison, the conventionallarge-scale approaches to predict PPIs are also briefly discussed. The chapter concludes with a discussionof the limitations of both experimental and computational methods of determining PPIs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alm E, Arkin AP (2003) Curr Opin Struct Biol 13:193

    Article  CAS  Google Scholar 

  2. Claverie JM (2001) Science 291:1255

    Article  CAS  Google Scholar 

  3. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M et al. (2001) Nature 409:860

    Article  CAS  Google Scholar 

  4. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C et al. (2001) Science 291:1304

    Article  CAS  Google Scholar 

  5. Price ND, Papin JA, Schilling CH, Palsson BO (2003) Trends Biotechnol 21:162

    Article  CAS  Google Scholar 

  6. Franzot G, Carugo O (2003) J Struct Funct Genomics 4:245

    Article  CAS  Google Scholar 

  7. Salwinski L, Eisenberg D (2003) Curr Opin Struct Biol 13:377

    Article  CAS  Google Scholar 

  8. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Science 274:546

    Article  CAS  Google Scholar 

  9. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, 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, Rothberg JM (2000) Nature 403:623

    Article  CAS  Google Scholar 

  10. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) Proc Natl Acad Sci USA 98:4569

    Article  CAS  Google Scholar 

  11. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, 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 AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M (2002) Nature 415:180

    Article  CAS  Google Scholar 

  12. Mann M, Pandey A (2001) Trends Biochem Sci 26:54

    Article  CAS  Google Scholar 

  13. 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 RA, Gerstein M, Snyder M (2001) Science 293:2101

    Article  CAS  Google Scholar 

  14. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G (2002) Science 295:321

    Article  CAS  Google Scholar 

  15. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C (2001) Science 294:2364

    Article  CAS  Google Scholar 

  16. Ge H, Liu Z, Church GM, Vidal M (2001) Nat Genet 29:482

    Article  CAS  Google Scholar 

  17. Aloy P, Russell RB (2002) Trends Biochem Sci 27:633

    Article  CAS  Google Scholar 

  18. Fields S, Song O (1989) Nature 340:245

    Article  CAS  Google Scholar 

  19. Stephens DJ, Banting G (2000) Traffic 1:763

    Article  CAS  Google Scholar 

  20. Semple JI, Sanderson CM, Campbell RD (2002) Brief Funct Genomic Proteomic 1:40

    Article  CAS  Google Scholar 

  21. James P, Halladay J, Craig EA (1996) Genetics 144:1425

    CAS  Google Scholar 

  22. Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999) Nat Biotechnol 17:1030

    Article  CAS  Google Scholar 

  23. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, 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 MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Nature 415:141

    Article  CAS  Google Scholar 

  24. Rohila JS, Chen M, Cerny R, Fromm ME (2004) Plant J 38:172

    Article  CAS  Google Scholar 

  25. Rubio V, Shen Y, Saijo Y, Liu Y, Gusmaroli G, Dinesh-Kumar SP, Deng XW (2005) Plant J 41:767

    Article  CAS  Google Scholar 

  26. Werler PJ, Hartsuiker E, Carr AM (2003) Gene 304:133

    Article  CAS  Google Scholar 

  27. Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW (2001) Nucleic Acids Res 29:242

    Article  CAS  Google Scholar 

  28. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, Eisenberg D (2002) Nucleic Acids Res 30:303

    Article  CAS  Google Scholar 

  29. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) Nucleic Acids Res 34:D535

    Article  CAS  Google Scholar 

  30. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B (2002) Nucleic Acids Res 30:31

    Article  CAS  Google Scholar 

  31. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G (2007) Nucleic Acids Res 35:D572

    Article  CAS  Google Scholar 

  32. Dandekar T, Snel B, Huynen M, Bork P (1998) Trends Biochem Sci 23:324

    Article  CAS  Google Scholar 

  33. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D (1999) Science 285:751

    Article  CAS  Google Scholar 

  34. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Nature 402:86

    Article  CAS  Google Scholar 

  35. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Proc Natl Acad Sci USA 96:4285

    Article  CAS  Google Scholar 

  36. Vert JP (2002) Bioinformatics 18(1):S276

    Article  Google Scholar 

  37. Pazos F, Valencia A (2001) Protein Eng 14:609

    Article  CAS  Google Scholar 

  38. Ma B, Elkayam T, Wolfson H, Nussinov R (2003) Proc Natl Acad Sci USA 100:5772

    Article  CAS  Google Scholar 

  39. Aloy P, Russell RB (2003) Bioinformatics 19:161

    Article  CAS  Google Scholar 

  40. Lu L, Lu H, Skolnick J (2002) Proteins 49:350

    Article  CAS  Google Scholar 

  41. Wodak SJ, Mendez R (2004) Curr Opin Struct Biol 14:242

    Article  CAS  Google Scholar 

  42. Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A (2005) Nucleic Acids Res 33:W331

    Article  CAS  Google Scholar 

  43. Espadaler J, Romero-Isart O, Jackson RM, Oliva B (2005) Bioinformatics 21:3360

    Article  CAS  Google Scholar 

  44. Deng M, Mehta S, Sun F, Chen T (2002) Genome Res 12:1540

    Article  CAS  Google Scholar 

  45. Han DS, Kim HS, Jang WH, Lee SD, Suh JK (2004) Nucleic Acids Res 32:6312

    Article  CAS  Google Scholar 

  46. Han DS, Kim HS, Jang WH, Lee SD, Suh JK (2004) Genome Inform 15:171

    CAS  Google Scholar 

  47. Kim WK, Park J, Suh JK (2002) Genome Inform 13:42

    CAS  Google Scholar 

  48. Sprinzak E, Margalit H (2001) J Mol Biol 311:681

    Article  CAS  Google Scholar 

  49. Bock JR, Gough DA (2001) Bioinformatics 17:455

    Article  CAS  Google Scholar 

  50. Martin S, Roe D, Faulon JL (2005) Bioinformatics 21:218

    Article  CAS  Google Scholar 

  51. Ben-Hur A, Noble WS (2005) Bioinformatics 21(1):i38

    Article  CAS  Google Scholar 

  52. Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A (2006) BMC Bioinformatics 7:365

    Article  Google Scholar 

  53. Marcotte EM (2000) Curr Opin Struct Biol 10:359

    Article  CAS  Google Scholar 

  54. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Proc Natl Acad Sci USA 95:14863

    Article  CAS  Google Scholar 

  55. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D (1999) Nature 402:83

    Article  CAS  Google Scholar 

  56. Aloy P, Russell RB (2002) Proc Natl Acad Sci USA 99:5896

    Article  CAS  Google Scholar 

  57. Berman H, Henrick K, Nakamura H, Markley JL (2007) Nucleic Acids Res 35:301–303

    Article  Google Scholar 

  58. Sonnhammer EL, Eddy SR, Durbin R (1997) Proteins 28:405

    Article  CAS  Google Scholar 

  59. Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H (2007) Proc Natl Acad Sci USA 104:4337

    Article  CAS  Google Scholar 

  60. Edwards AM, Kus B, Jansen R, Greenbaum D, Greenblatt J, Gerstein M (2002) Trends Genet 18:529

    Article  CAS  Google Scholar 

  61. Regelmann J, Schule T, Josupeit FS, Horak J, Rose M, Entian KD, Thumm M, Wolf DH (2003) Mol Biol Cell 14:1652

    Article  CAS  Google Scholar 

  62. Saito R, Suzuki H, Hayashizaki Y (2002) Nucleic Acids Res 30:1163

    Article  CAS  Google Scholar 

  63. Deane CM, Salwinski L, Xenarios I, Eisenberg D (2002) Mol Cell Proteomics 1:349

    Article  CAS  Google Scholar 

  64. Grigoriev A (2003) Nucleic Acids Res 31:4157

    Article  CAS  Google Scholar 

  65. Bader GD, Hogue CW (2002) Nat Biotechnol 20:991

    Article  CAS  Google Scholar 

  66. Legrain P, Wojcik J, Gauthier JM (2001) Trends Genet 17:346

    Article  CAS  Google Scholar 

  67. Tucker CL, Gera JF, Uetz P (2001) Trends Cell Biol 11:102

    Article  CAS  Google Scholar 

  68. Sprinzak E, Sattath S, Margalit H (2003) J Mol Biol 327:919

    Article  CAS  Google Scholar 

  69. Walhout AJ, Boulton SJ, Vidal M (2000) Yeast 17:88

    Article  CAS  Google Scholar 

  70. Hazbun TR, Fields S (2001) Proc Natl Acad Sci USA 98:4277

    Article  CAS  Google Scholar 

  71. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF (2006) Nature 440:637

    Article  CAS  Google Scholar 

  72. Wang H, Segal E, Ben-Hur A, Li Q, Vidal M, Koller D (2007) Genome Biol 8:R192

    Article  Google Scholar 

  73. van Berlo RJP, Wessels LFA, de Ridder D, Reinders MJT (2007) J Bioinform Comput Biol 5:839

    Article  Google Scholar 

  74. Mahdavi MA, Lin YH (2007) BMC Bioinformatics 8:262

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Computer Science, Carleton University, 5304 Herzberg Building, 1125 Colonel By Drive, K1S 5B6, Ottawa, Ontario, Canada

    Sylvain Pitre, Michel Dumontier & Frank Dehne

  2. Department of Biology and Ottawa Institute of Systems Biology, Carleton University, 209 Nesbitt Building, 1125 Colonel By Drive, K1S 5B6, Ottawa, Ontario, Canada

    Md Alamgir, Michel Dumontier & Ashkan Golshani

  3. Department of Systems and Computer Engineering, Carleton University, 4456 Mackenzie Building, 1125 Colonel By Drive, K1S 5B6, Ottawa, Ontario, Canada

    James R. Green

Authors
  1. Sylvain Pitre
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Md Alamgir
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James R. Green
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michel Dumontier
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Frank Dehne
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ashkan Golshani
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ashkan Golshani .

Editor information

Meike Werther Harald Seitz

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Pitre, S., Alamgir, M., Green, J.R., Dumontier, M., Dehne, F., Golshani, A. (2008). Computational Methods For Predicting Protein–Protein Interactions. In: Werther, M., Seitz, H. (eds) Protein – Protein Interaction. Advances in Biochemical Engineering/Biotechnology, vol 110. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10_2007_089

Download citation

Publish with us

Policies and ethics

Search

Navigation