12. Bhattacharyya M, Vishveshwara S (2011) Probing the allosteric mechanism in pyrrolysyltRNA synthetase using energy-weighted network formalism. Biochemistry 50:6225–6236
13. Vijayabaskar MS, Vishveshwara S (2010) Interaction energy based protein structure
networks. Biophys J J99:3704–3715
14. Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S (2004)
Network analysis of protein structures identifies functional residues. J Mol Biol 344:1135–
1146
15. Brinda KV, Vishveshwara S (2005) A network representation of protein structures:
implications for protein stability. Biophys J J89:4159–4170
16. Brinda KV, Vishveshwara S (2005) Oligomeric protein structure networks: insights into
protein-protein interactions. BMC Bioinform 6:296
17. Atilgan AR, Akan P, Baysal C (2004) Small-world communication of residues and
significance for protein dynamics. Biophys J J86:85–91
18. Bagler G, Sinha S (2007) Assortative mixing in protein contact networks and protein folding
kinetics. Bioinformatics 23:1760–1767
19. Zhou J, Yan W, Hu G, Shen B (2014) Amino acid network for the discrimination of native
protein structures from decoys. Curr Protein Pept Sci 15:522–528
20. Hu G, Zhou J, Yan W, Chen J, Shen B (2013) The topology and dynamics of protein
complexes: insights from intra–molecular network theory. Curr Protein Pept Sci 14:121–132
21. Martin AJ, Vidotto M, Boscariol F, Di Domenico T, Walsh I, Tosatto SC (2011) RING:
networking interacting residues, evolutionary information and energetics in protein structures.
Bioinformatics 27:2003–2005
22. Rao F, Caflisch A (2004) The protein folding network. J Mol Biol 342:299–306
23. Grewal RK, Roy S (2015) Modeling proteins as residue interaction networks. Protein Pept
Lett 22:923–933
24. Zhou J, Yan W, Hu G, Shen B (2016) Amino acid network for prediction of catalytic residues
in enzymes: a comparison survey. Curr Protein Pept Sci 17:41–51
25. Pons C, Glaser F, Fernandez-Recio J (2011) Prediction of protein-binding areas by
small-world residue networks and application to docking. BMC Bioinform 12:378
26. Schueler-Furman O, Wodak SJ (2016) Computational approaches to investigating allostery.
Curr Opin Struct Biol 41:159–171
27. Cheng TMK, Lu Y-E, Vendruscolo M, Lio P, Blundell TL (2008) Prediction by graph
theoretic measures of structural effects in proteins arising from non-synonymous single
nucleotide polymorphisms. PLoS Comput Biol 4:e1000135
28. Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A (2013) Protein contact networks: an
emerging paradigm in chemistry. Chem Rev 113:1598–1613
29. Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R (2013) Structure and dynamics
of molecular networks: a novel paradigm of drug discovery: a comprehensive review.
Pharmacol Ther 138:333–408
30. Yan W, Zhou J, Sun M, Chen J, Hu G, Shen B (2014) The construction of an amino acid
network for understanding protein structure and function. Amino Acids 46:1419–1439
31. Bhattacharyya M, Ghosh S, Vishveshwara S (2016) Protein structure and function: looking
through the network of side-chain interactions. Curr Protein Pept Sci 17:4–25
32. Grewal RK, Mitra D, Roy S (2015) Mapping networks of light-dark transition in LOV
photoreceptors. Bioinformatics 31:3608–3616
33. Doncheva NT, Assenov Y, Domingues FS, Albrecht M (2012) Topological analysis and
interactive visualization of biological networks and protein structures. Nat Protoc 7:670–685
34. del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residues crucial for maintaining short
paths in network communication mediate signaling in proteins. Mol Syst Biol 2:0019
35. Ghosh A, Sakaguchi R, Liu C, Vishveshwara S, Hou YM (2011) Allosteric communication in
cysteinyl tRNA synthetase: a network of direct and indirect readout. J Biol Chem 286:37721–
37731
36. Estrada E (2010) Universality in protein residue networks. Biophys J 98:890–900
66
D. Shcherbinin and A. Veselovsky
13. Vijayabaskar MS, Vishveshwara S (2010) Interaction energy based protein structure
networks. Biophys J J99:3704–3715
14. Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S (2004)
Network analysis of protein structures identifies functional residues. J Mol Biol 344:1135–
1146
15. Brinda KV, Vishveshwara S (2005) A network representation of protein structures:
implications for protein stability. Biophys J J89:4159–4170
16. Brinda KV, Vishveshwara S (2005) Oligomeric protein structure networks: insights into
protein-protein interactions. BMC Bioinform 6:296
17. Atilgan AR, Akan P, Baysal C (2004) Small-world communication of residues and
significance for protein dynamics. Biophys J J86:85–91
18. Bagler G, Sinha S (2007) Assortative mixing in protein contact networks and protein folding
kinetics. Bioinformatics 23:1760–1767
19. Zhou J, Yan W, Hu G, Shen B (2014) Amino acid network for the discrimination of native
protein structures from decoys. Curr Protein Pept Sci 15:522–528
20. Hu G, Zhou J, Yan W, Chen J, Shen B (2013) The topology and dynamics of protein
complexes: insights from intra–molecular network theory. Curr Protein Pept Sci 14:121–132
21. Martin AJ, Vidotto M, Boscariol F, Di Domenico T, Walsh I, Tosatto SC (2011) RING:
networking interacting residues, evolutionary information and energetics in protein structures.
Bioinformatics 27:2003–2005
22. Rao F, Caflisch A (2004) The protein folding network. J Mol Biol 342:299–306
23. Grewal RK, Roy S (2015) Modeling proteins as residue interaction networks. Protein Pept
Lett 22:923–933
24. Zhou J, Yan W, Hu G, Shen B (2016) Amino acid network for prediction of catalytic residues
in enzymes: a comparison survey. Curr Protein Pept Sci 17:41–51
25. Pons C, Glaser F, Fernandez-Recio J (2011) Prediction of protein-binding areas by
small-world residue networks and application to docking. BMC Bioinform 12:378
26. Schueler-Furman O, Wodak SJ (2016) Computational approaches to investigating allostery.
Curr Opin Struct Biol 41:159–171
27. Cheng TMK, Lu Y-E, Vendruscolo M, Lio P, Blundell TL (2008) Prediction by graph
theoretic measures of structural effects in proteins arising from non-synonymous single
nucleotide polymorphisms. PLoS Comput Biol 4:e1000135
28. Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A (2013) Protein contact networks: an
emerging paradigm in chemistry. Chem Rev 113:1598–1613
29. Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R (2013) Structure and dynamics
of molecular networks: a novel paradigm of drug discovery: a comprehensive review.
Pharmacol Ther 138:333–408
30. Yan W, Zhou J, Sun M, Chen J, Hu G, Shen B (2014) The construction of an amino acid
network for understanding protein structure and function. Amino Acids 46:1419–1439
31. Bhattacharyya M, Ghosh S, Vishveshwara S (2016) Protein structure and function: looking
through the network of side-chain interactions. Curr Protein Pept Sci 17:4–25
32. Grewal RK, Mitra D, Roy S (2015) Mapping networks of light-dark transition in LOV
photoreceptors. Bioinformatics 31:3608–3616
33. Doncheva NT, Assenov Y, Domingues FS, Albrecht M (2012) Topological analysis and
interactive visualization of biological networks and protein structures. Nat Protoc 7:670–685
34. del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residues crucial for maintaining short
paths in network communication mediate signaling in proteins. Mol Syst Biol 2:0019
35. Ghosh A, Sakaguchi R, Liu C, Vishveshwara S, Hou YM (2011) Allosteric communication in
cysteinyl tRNA synthetase: a network of direct and indirect readout. J Biol Chem 286:37721–
37731
36. Estrada E (2010) Universality in protein residue networks. Biophys J 98:890–900
66
D. Shcherbinin and A. Veselovsky