We thank SERC and MBU of the Indian Institute of Science for
computational facilities.
References
1. Jones S, Thornton JM (1996) Principles of
protein-protein interactions. Proc Natl Acad
Sci U S A 93(1):13–20
2. Szklarczyk D et al (2015) STRING v10:
protein-protein
interaction
networks,
integrated over the tree of life. Nucleic Acids
Res 43(Database issue):D447–D452
3. Suel GM et al (2003) Evolutionarily conserved
networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10
(1):59–69
4. Tsai CJ, Ma B, Nussinov R (2009) Proteinprotein interaction networks: how can a hub
protein bind so many different partners?
Trends Biochem Sci 34(12):594–600
5. Kuriyan J, Eisenberg D (2007) The origin of
protein interactions and allostery in colocalization. Nature 450(7172):983–990
6. Motlagh HN et al (2014) The ensemble nature
of allostery. Nature 508(7496):331–339
7. Bagler G, Sinha S (2007) Assortative mixing in
Protein Contact Networks and protein folding
kinetics. Bioinformatics 23(14):1760–1767
8. Piovesan D, Minervini G, Tosatto SC (2016)
The RING 2.0 web server for high quality
residue interaction networks. Nucleic Acids
Res 44(W1):W367–W374
9. Di Paola L et al (2013) Protein contact networks: an emerging paradigm in chemistry.
Chem Rev 113(3):1598–1613
10. Bhattacharyya M, Ghosh S, Vishveshwara S
(2016) Protein structure and function: looking
through the network of side-chain Interactions. Curr Protein Pept Sci 17(1):4–25
11. Vishveshwara S, Ghosh A, Hansia P (2009)
Intra and inter-molecular communications
through protein structure network. Curr Protein Pept Sci 10(2):146–160
12. Vishveshwara S, Brinda KV, Kannan N (2002)
Protein structure: insights from graph theory. J
Theor Comput Chem 01(01):187–211
13. Gadiyaram V, Ghosh S, Vishveshwara S (2017)
A graph spectral-based scoring scheme for network comparison. J Complex Networks 5
(2):219–244
14. Ghosh S, Gadiyaram V, Vishveshwara S (2017)
Validation of protein structure models using
network similarity score. Proteins 85
(9):1759–1776
15. Gadiyaram V, Dighe A, Vishveshwara S (2019)
Identification of crucial elements for network
integrity: a perturbation approach through
graph spectral method. Int J Adv Eng Sci
Appl Math 11:91–104
16. Vijayabaskar MS, Vidya N, Saraswathi V
(2011) GraProStr—graphs of protein structures: a tool for constructing graphs and generating graph parameters for protein structures
17. Adamcsek B et al (2006) CFinder: locating
cliques and overlapping modules in biological
networks. Bioinformatics 22(8):1021–1023
18. Dijkstra EW (1959) A note on two problems in
connexion with graphs. Numer Math 1
(1):269–271
19. Bhattacharyya M, Bhat CR, Vishveshwara S
(2013) An automated approach to network
features of protein structure ensembles. Protein Sci 22(10):1399–1416
20. Patra SM, Vishveshwara S (2000) Backbone
cluster identification in proteins by a graph
theoretical method. Biophys Chem 84
(1):13–25
21. Vendruscolo M et al (2002) Small-world view
of the amino acids that play a key role in protein
folding. Phys Rev E Stat Nonlinear Soft Matter
Phys 65(6 Pt 1):061910
22. Brinda KV, Kannan N, Vishveshwara S (2002)
Analysis of homodimeric protein interfaces by
graph-spectral methods. Protein Eng 15
(4):265–277
23. Miyazawa S, Jernigan RL (1985) Estimation of
effective interresidue contact energies from
protein crystal structures: quasi-chemical
approximation.
Macromolecules
18
(3):534–552
24. Miyazawa S, Jernigan RL (1996) Residueresidue potentials with a favorable contact pair
term and an unfavorable high packing density
term, for simulation and threading. J Mol Biol
256(3):623–644
25. Kannan N, Vishveshwara S (1999) Identification of side-chain clusters in protein structures
by a graph spectral method. J Mol Biol 292
(2):441–464
26. Bhattacharya S, Vaidehi N (2014) Differences
in allosteric communication pipelines in the
inactive and active states of a GPCR. Biophys
J 107(2):422–434
27. Ghosh A, Vishveshwara S (2008) Variations in
clique and community patterns in protein
Network Re-Wiring During Allostery and PPI
111
computational facilities.
References
1. Jones S, Thornton JM (1996) Principles of
protein-protein interactions. Proc Natl Acad
Sci U S A 93(1):13–20
2. Szklarczyk D et al (2015) STRING v10:
protein-protein
interaction
networks,
integrated over the tree of life. Nucleic Acids
Res 43(Database issue):D447–D452
3. Suel GM et al (2003) Evolutionarily conserved
networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10
(1):59–69
4. Tsai CJ, Ma B, Nussinov R (2009) Proteinprotein interaction networks: how can a hub
protein bind so many different partners?
Trends Biochem Sci 34(12):594–600
5. Kuriyan J, Eisenberg D (2007) The origin of
protein interactions and allostery in colocalization. Nature 450(7172):983–990
6. Motlagh HN et al (2014) The ensemble nature
of allostery. Nature 508(7496):331–339
7. Bagler G, Sinha S (2007) Assortative mixing in
Protein Contact Networks and protein folding
kinetics. Bioinformatics 23(14):1760–1767
8. Piovesan D, Minervini G, Tosatto SC (2016)
The RING 2.0 web server for high quality
residue interaction networks. Nucleic Acids
Res 44(W1):W367–W374
9. Di Paola L et al (2013) Protein contact networks: an emerging paradigm in chemistry.
Chem Rev 113(3):1598–1613
10. Bhattacharyya M, Ghosh S, Vishveshwara S
(2016) Protein structure and function: looking
through the network of side-chain Interactions. Curr Protein Pept Sci 17(1):4–25
11. Vishveshwara S, Ghosh A, Hansia P (2009)
Intra and inter-molecular communications
through protein structure network. Curr Protein Pept Sci 10(2):146–160
12. Vishveshwara S, Brinda KV, Kannan N (2002)
Protein structure: insights from graph theory. J
Theor Comput Chem 01(01):187–211
13. Gadiyaram V, Ghosh S, Vishveshwara S (2017)
A graph spectral-based scoring scheme for network comparison. J Complex Networks 5
(2):219–244
14. Ghosh S, Gadiyaram V, Vishveshwara S (2017)
Validation of protein structure models using
network similarity score. Proteins 85
(9):1759–1776
15. Gadiyaram V, Dighe A, Vishveshwara S (2019)
Identification of crucial elements for network
integrity: a perturbation approach through
graph spectral method. Int J Adv Eng Sci
Appl Math 11:91–104
16. Vijayabaskar MS, Vidya N, Saraswathi V
(2011) GraProStr—graphs of protein structures: a tool for constructing graphs and generating graph parameters for protein structures
17. Adamcsek B et al (2006) CFinder: locating
cliques and overlapping modules in biological
networks. Bioinformatics 22(8):1021–1023
18. Dijkstra EW (1959) A note on two problems in
connexion with graphs. Numer Math 1
(1):269–271
19. Bhattacharyya M, Bhat CR, Vishveshwara S
(2013) An automated approach to network
features of protein structure ensembles. Protein Sci 22(10):1399–1416
20. Patra SM, Vishveshwara S (2000) Backbone
cluster identification in proteins by a graph
theoretical method. Biophys Chem 84
(1):13–25
21. Vendruscolo M et al (2002) Small-world view
of the amino acids that play a key role in protein
folding. Phys Rev E Stat Nonlinear Soft Matter
Phys 65(6 Pt 1):061910
22. Brinda KV, Kannan N, Vishveshwara S (2002)
Analysis of homodimeric protein interfaces by
graph-spectral methods. Protein Eng 15
(4):265–277
23. Miyazawa S, Jernigan RL (1985) Estimation of
effective interresidue contact energies from
protein crystal structures: quasi-chemical
approximation.
Macromolecules
18
(3):534–552
24. Miyazawa S, Jernigan RL (1996) Residueresidue potentials with a favorable contact pair
term and an unfavorable high packing density
term, for simulation and threading. J Mol Biol
256(3):623–644
25. Kannan N, Vishveshwara S (1999) Identification of side-chain clusters in protein structures
by a graph spectral method. J Mol Biol 292
(2):441–464
26. Bhattacharya S, Vaidehi N (2014) Differences
in allosteric communication pipelines in the
inactive and active states of a GPCR. Biophys
J 107(2):422–434
27. Ghosh A, Vishveshwara S (2008) Variations in
clique and community patterns in protein
Network Re-Wiring During Allostery and PPI
111