Universality in protein residue networks

Biophysical Journal

Volumn 98, Issue 5, 2010, Pages 890-900

  Estrada, Ernesto ^a  

^a UNIVERSITY OF STRATHCLYDE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77749318502     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.11.017     Document Type: Article

References (40)

1. Strogatz, S. H. 2001. Exploring complex networks. Nature. 410: 268-276.
2. Newman, M. E. J. 2003. The structure and function of complex networks. SIAM Rev. 45:167-256.
3. Boccaletti, S., V. Latora, ., D.-U. Hwang. 2006. Complex networks: structure and dynamics. Phys. Rep. 424:175-308.
4. Watts, D. J., and S. H. Strogatz. 1998. Collective dynamics of 'small-orld' networks. Nature. 393:440-442.
5. Barabási, A.-L., and R. Albert. 1999. Emergence of scaling in random networks. Science. 286:509-512.
6. Song, C., S. Havlin, and H. A. Makse. 2005. Self-similarity of complex networks. Nature. 433:392-395.
7. Milo, R., S. Shen-Orr, ..., U. Alon. 2002. Network motifs: simple building blocks of complex networks. Science. 298:824-827.
8. Newman, M. J. E. 2003. Mixing patterns in networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 67:026166.
9. Böde, C., I. A. Kovács, ., P. Csermely. 2007. Network analysis of protein dynamics. FEBS Lett. 581:2776-2782.
10. Vendruscolo, M., N. V. Dokholyan, ..., M. Karplus. 2002. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65:061910.
11. Atilgan, A. R., P. Akan, and C. Baysal. 2004. Small-world communication of residues and significance for protein dynamics. Biophys. J. 86:85-91.
12. Bagler, G., and S. Sinha. 2005. Network properties of protein structures. Physica A. 346:27-33.
13. Brinda, K. V., and S. Vishveshwara. 2005. A network representation of protein structures: implications for protein stability. Biophys. J. 89:4159-4170.
14. Greene, L. H., and V. A. Higman. 2003. Uncovering network systems within protein structures. J. Mol. Biol. 334:781-791.
15. da Silveira, C. H., D. E. V. Pires, ..., M. M. Santoro. 2008. Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. Proteins. 74:727-743.
16. Bartoli, L., P. Fariselli, and R. Casadio. 2007. The effect of backbone on the small-world properties of protein contact maps. Phys. Biol. 4:L1-L5.
17. Berman, H. M., J. Westbrook, ..., P. E. Bourne. 2000. The protein data bank. Nucleic Acids Res. 28:235-242.
18. Fariselli, P., and R. Casadio. 1999. A neural network based predictor of residue contacts in proteins. Protein Eng. 12:15-21.
19. Biggs, N. 1993. Algebraic Graph Theory. Cambridge University Press, Cambridge, UK.
20. Hoory, S., N. Lineal, and A. Wigderson. 2006. Expander graphs and their applications. Bull. Am. Math. Soc. 43:439-561.
21. Estrada, E. 2006. Spectral scaling and good expansion properties in complex networks. Europhys. Lett. 73:649-655.
22. Estrada, E. 2006. Network robustness. The interplay of expansibility and degree distribution. Eur. Phys. J. B. 52:563-574.
23. Estrada, E., and J. A. Rodríguez-Velázquez. 2005. Subgraph centrality in complex networks. Phys. Rev.EStat.Nonlin. SoftMatterPhys. 71:056103.
24. Estrada, E. 2007. Topological structural classes of complex networks. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 75:016103.
25. González-Díaz, H., Y. González-Díaz, ..., E. Uriarte. 2008. Proteomics, networks and connectivity indices. Proteomics. 8:750-778.
26. Privalov, P. L. 1989. Thermodynamic problems of protein structure. Annu. Rev. Biophys. Biophys. Chem. 18:47-69.
27. Dengler, U., A. S. Siddiqui, and G. J. Barton. 2001. Protein structural domains: analysis of the 3Dee domains database. Proteins. 42:332-344.
28. Estrada, E. 2004. A protein folding degree measure and its dependence on crystal packing, protein size, secondary structure, and domain structural class. J. Chem. Inf. Comput. Sci. 44:1238-1250.
29. Chandrasekharan, N., V. S. Lakshmanan, and M. Medidi. 1993. Efficient parallel algorithms for finding chordless cycles in graphs. Parallel Process. Lett. 3:165-170.
30. Lubiw, A. 1988/89. A note on odd/even cycles. Discrete Appl. Math. 22:87-92.
31. Hayward, R. 1987. Two classes of perfect graphs. PhD thesis. School of Computer Science, McGill University, Montreal, Quebec, Canada.
32. Spinard, J. P. 1991. Finding large holes. Inf. Process. Lett. 39:227-229.
33. Laskowski, R. A. 2001. PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res. 29:221-222.
34. Liang, J., H. Edelsbrunner, and C. Woodward. 1998. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7:1884-1897.
35. Weisel, M., E. Proschak, ..., G. Schneider. 2009. Form follows function: shape analysis of protein cavities for receptor-based drug design. Proteomics. 9:451-459.
36. Bohne-Lang, A., G. Wolf-Dieter, and R. Ranzinger. 2005. AISMIG: an interactive server-side molecule image generator. Nucleic Acids Res. 33:705-709.
37. Ravasz, E., A. L. Somera, ..., A. L. Barabási. 2002. Hierarchical organization ofmodularity inmetabolic networks. Science. 297:1551-1555.
38. Erdös, P., and A. Rényi. 1959. On random graphs. I. Publ. Math. (Debrecen). 6:290-297.
39. Friedman, J. 1991. On the second eigenvalue and random walks in random d-regular graphs. Combinatorica. 11:331-362.
40. Gkantsidis, C., A. Saberi, and M. Mihail. 2003. Conductance and congestion in power law graphs. Proc. A.C.M. Sigmetrics. San Diego, CA.