Sensitivity-dependent model of protein-protein interaction networks

Physical Biology

Volumn 5, Issue 3, 2008, Pages

  Zhang, Jingshan ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; METABOLISM; PROTEIN BINDING; THERMODYNAMICS;

ALGORITHMS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 58149163463     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/5/3/036011     Document Type: Article

References (30)

1. Albert R and Barabsi A-L 2002 Statistical mechanics of complex networks Rev. Mod. Phys. 74 47
2. Xenarios I, Rice D W, Salwinski L, Baron M K, Marcotte E M and Eisenberg D 2000 DIP: the database of interacting proteins Nucl. Acids Res. 28 289
3. Mewes H W, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S and Weil B 2002 MIPS: a database for genomes and protein sequences Nucl. Acids Res. 30 31
4. Uetz P et al 2000 A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 403 623
5. Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S and Sakaki Y 2000 Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins Proc. Natl Acad. Sci. USA 97 1143
6. 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. USA 98 4569
7. Rual J F et al 2005 Towards a proteome-scale map of the human protein-protein interaction network Nature 437 1173
8. Lim J et al 2006 A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration Cell 125 801
9. Deeds E J, Ashenberg O and Shakhnovich E I 2006 A simple physical model for scaling in protein-protein interaction networks Proc. Natl Acad. Sci. USA 103 311
10. Shi Y, Miller G, Qian H and Bomsztyk K 2006 Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences Proc. Natl Acad. Sci. USA 103 11527
11. Jeong H, Mason S, Barabsi A-L and Oltvai Z N 2001 Lethality and centrality in protein networks Nature 411 41
12. Wagner A 2001 The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes Mol. Biol. Evol. 18 1283
13. Yook S Y, Oltvai Z N and Barabsi A-L 2004 Functional and topological characterization of protein interaction networks Proteomics 4 928
14. Rzhetsky A and Gomez S M 2001 Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome Bioinfomatics 17 988
15. Qian J, Luscombe N M and Gerstein M 2001 Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model J. Mol. Biol. 313 673
16. Bhan A, Galas D J and Dewey T G 2002 A duplication growth model of gene expression networks Bioinfomatics 18 1486
17. Sole R V, Pastor-Satorras R, Smith E and Kepler T B 2002 A model of large-scale proteome evolution Adv. Complex Syst. 5 43
18. Vazquez A, Flammini A, Maritan A and Vespignani A 2003 Modeling of protein interaction networks ComPlexUs 1 38
19. Kim J, Krapivsky P L, Kahng B and Redner S 2002 Infinite-order percolation and giant fluctuations in a protein interaction network Phys. Rev. E 66 055101
20. Pastor-Satorras R, Smith E and Sole R V 2003 Evolving protein interaction networks through gene duplication J. Theor. Biol. 222 199
21. Ispolatov I, Krapivsky P L and Yuryev A 2005 Duplication-divergence model of protein interaction network Phys. Rev. E 71 061911
22. Barabsi A-L and Oltvai Z N 2004 Network biology : understanding the cell functional organization Nature Rev. Genetics 5 101
23. Janin J 1995 Protein-protein recognition Prog. Biophys. Mol. Biol. 64 145
24. Tamura A and Privalov P L 1997 The entropy cost of protein association J. Mol. Biol. 273 1048
25. Estojak J, Brent R and Golemis E A 1995 Correlation of 2-hybrid affinity data with in-vitro measurements Mol. Cell. Biol. 15 5820
26. Masuda N, Miwa H and Konno N 2004 Analysis of scale-free networks based on a threshold graph with intrinsic vertex weights Phys. Rev. E 70 036124
27. Boguna M and Pastor-Satorras R 2003 Class of correlated random networks with hidden variables Phys. Rev. E 68 036112
28. Deane C M, Salwinski L, Xenarios I and Eisenberg D 2002 Protein interactions-two methods for assessment of the reliability of high throughput observations Mol. Cell. Proteomics 1 349
29. Caldarelli G, Capocci A, De Los Rios P and Muoz M A 2002 Scale-free networks from varying vertex intrinsic fitness Phys. Rev. Lett. 89 258702
30. Balcan D and Erzan A 2004 Random model for RNA interference yields scale free network Euro. Phys. J. B 38 253