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Comparative study of elastic network model
and protein contact network for protein complexes: the hemoglobin case. Biomed Res Int
2017:2483264
15. Santoni D, Paci P, Paola LD, Giuliani A (2016)
Are proteins just coiled cords? Local and global
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Pept Sci 17:26–29
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graph. Psychometrika 31:581–603. https://
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18. Amitai G, Shemesh A, Sitbon E et al (2004)
Network analysis of protein structures identifies functional residues. J Mol Biol
344:1135–1146. https://doi.org/10.1016/j.
jmb.2004.10.055
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graph theory: introduction and fundamentals.
Gordon & Breach Science Publishers, London
20. Cimini S, Di Paola L, Giuliani A et al (2016)
GH32 family activity: a topological approach
through protein contact networks. Plant Mol
Biol:1–10
21. Di Paola L, Mei G, Di Venere A, Giuliani A
(2016) Exploring the stability of dimers
through protein structure topology. Curr Protein Pept Sci 17:30–36. https://doi.org/10.
2174/1389203716666150923104054
22. del Sol A, Arau ´ zo-Bravo MJ, Amoros D, Nussinov R (2007) Modular architecture of protein
structures and allosteric communications:
potential implications for signaling proteins
and regulatory linkages. Genome Biol 8:R92
23. Tasdighian S, Di Paola L, De Ruvo M et al
(2013) Modules identification in protein
structures: the topological and geometrical
solutions. J Chem Inf Model 54:159–168
24. Cumbo F, Paci P, Santoni D et al (2014)
GIANT: a cytoscape plugin for modular networks. PLoS One 9:e105001. https://doi.
org/10.1371/journal.pone.0105001
25. Tasdighian S, Di Paola L, De Ruvo M et al
(2014) Modules identification in protein structures: the topological and geometrical solutions. J Chem Inf Model 54:159–168.
https://doi.org/10.1021/ci400218v
26. Tsai CJ, del Sol A, Nussinov R (2008) Allostery: absence of a change in shape does not
imply that allostery is not at play. J Mol Biol
378:1–11
27. Nussinov R, Tsai C-J (2012) The different
ways through which specificity works in orthosteric and allosteric drugs. Curr Pharm Des
18:1311–1316.
https://doi.org/10.2174/
138920012799362855
28. Csermely P, Nussinov R, Szila ´gyi A (2013)
From allosteric drugs to allo-network drugs:
state of the art and trends of design, synthesis
and computational methods. Curr Top Med
Chem 13:2–4. https://doi.org/10.2174/
1568026611313010002
29. Di Paola L, Platania CBM, Oliva G et al (2015)
Characterization of protein–protein interfaces
through a protein contact network approach.
Front Bioeng Biotechnol 3:170. https://doi.
org/10.3389/fbioe.2015.00170
30. Di Paola L, De Ruvo M, Paci P et al (2012)
Protein contact networks: an emerging paradigm in chemistry. Chem Rev 113:1598–1613
31. Viloria JS, Allega MF, Lambrughi M, Papaleo
E (2017) An optimal distance cutoff for
contact-based Protein Structure Networks
using side chain center of masses. Sci Rep
7:2838. https://doi.org/10.1038/s41598017-01498-6
32. Brandes U (2001) A faster algorithm for
betweenness centrality. J Math Sociol
25:163–177.
https://doi.org/10.1080/
0022250X.2001.9990249
20
Luisa Di Paola et al.
shortest paths in sparse networks. J ACM
24:1–13. https://doi.org/10.1145/321992.
321993
14. Hu G, Di Paola L, Liang Z, Giuliani A (2017)
Comparative study of elastic network model
and protein contact network for protein complexes: the hemoglobin case. Biomed Res Int
2017:2483264
15. Santoni D, Paci P, Paola LD, Giuliani A (2016)
Are proteins just coiled cords? Local and global
analysis of contact maps reveals the backbonedependent nature of proteins. Curr Protein
Pept Sci 17:26–29
16. Borgatti SP, Everett MG (2006) A graphtheoretic perspective on centrality. Soc Networks
28:466–484.
https://doi.org/10.
1016/j.socnet.2005.11.005
17. Sabidussi G (1966) The centrality index of a
graph. Psychometrika 31:581–603. https://
doi.org/10.1007/BF02289527
18. Amitai G, Shemesh A, Sitbon E et al (2004)
Network analysis of protein structures identifies functional residues. J Mol Biol
344:1135–1146. https://doi.org/10.1016/j.
jmb.2004.10.055
19. Bonchev DD, Rouvray DH (1990) Chemical
graph theory: introduction and fundamentals.
Gordon & Breach Science Publishers, London
20. Cimini S, Di Paola L, Giuliani A et al (2016)
GH32 family activity: a topological approach
through protein contact networks. Plant Mol
Biol:1–10
21. Di Paola L, Mei G, Di Venere A, Giuliani A
(2016) Exploring the stability of dimers
through protein structure topology. Curr Protein Pept Sci 17:30–36. https://doi.org/10.
2174/1389203716666150923104054
22. del Sol A, Arau ´ zo-Bravo MJ, Amoros D, Nussinov R (2007) Modular architecture of protein
structures and allosteric communications:
potential implications for signaling proteins
and regulatory linkages. Genome Biol 8:R92
23. Tasdighian S, Di Paola L, De Ruvo M et al
(2013) Modules identification in protein
structures: the topological and geometrical
solutions. J Chem Inf Model 54:159–168
24. Cumbo F, Paci P, Santoni D et al (2014)
GIANT: a cytoscape plugin for modular networks. PLoS One 9:e105001. https://doi.
org/10.1371/journal.pone.0105001
25. Tasdighian S, Di Paola L, De Ruvo M et al
(2014) Modules identification in protein structures: the topological and geometrical solutions. J Chem Inf Model 54:159–168.
https://doi.org/10.1021/ci400218v
26. Tsai CJ, del Sol A, Nussinov R (2008) Allostery: absence of a change in shape does not
imply that allostery is not at play. J Mol Biol
378:1–11
27. Nussinov R, Tsai C-J (2012) The different
ways through which specificity works in orthosteric and allosteric drugs. Curr Pharm Des
18:1311–1316.
https://doi.org/10.2174/
138920012799362855
28. Csermely P, Nussinov R, Szila ´gyi A (2013)
From allosteric drugs to allo-network drugs:
state of the art and trends of design, synthesis
and computational methods. Curr Top Med
Chem 13:2–4. https://doi.org/10.2174/
1568026611313010002
29. Di Paola L, Platania CBM, Oliva G et al (2015)
Characterization of protein–protein interfaces
through a protein contact network approach.
Front Bioeng Biotechnol 3:170. https://doi.
org/10.3389/fbioe.2015.00170
30. Di Paola L, De Ruvo M, Paci P et al (2012)
Protein contact networks: an emerging paradigm in chemistry. Chem Rev 113:1598–1613
31. Viloria JS, Allega MF, Lambrughi M, Papaleo
E (2017) An optimal distance cutoff for
contact-based Protein Structure Networks
using side chain center of masses. Sci Rep
7:2838. https://doi.org/10.1038/s41598017-01498-6
32. Brandes U (2001) A faster algorithm for
betweenness centrality. J Math Sociol
25:163–177.
https://doi.org/10.1080/
0022250X.2001.9990249
20
Luisa Di Paola et al.