37. Ghosh A, Vishveshwara S (2008) Variations in clique and community patterns in protein
structures during allosteric communication: investigation of dynamically equilibrated
structures of methionyl tRNA synthetase complexes. Biochemistry 47:11398–11407
38. Pasi M, Tiberti M, Arrigoni A, Papaleo E (2012) xPyder: a PyMOL plugin to analyze coupled
residues and their networks in protein structures. J Chem Inf Model 52:1865–1874
39. Eargle J, Luthey-Schulten Z (2012) NetworkView: 3D display and analysis of proteinÁ RNA
interaction networks. Bioinformatics 28:3000–3001
40. 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
41. Doncheva NT, Klein K, Domingues FS, Albrecht M (2011) Analyzing and visualizing residue
networks of protein structures. Trends Biochem Sci 36:179–182
42. Morris JH, Huang CC, Babbitt PC, Ferrin TE (2007) structureViz: linking Cytoscape and
UCSF Chimera. Bioinformatics 23:2345–2347
43. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B,
Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular
interaction networks. Genome Res 13:2498–2504
44. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
(2004) UCSF Chimera—a visualization system for exploratory research and analysis.
J Comput Chem 25:1605–1612
45. Yan Y, Zhang SG, Wu FX (2011) Applications of graph theory in protein structure
identification. Proteome Sci 9(Suppl 1):S17
46. Thibert B, Bredesen DE, del Rio G (2005) Improved prediction of critical residues for protein
function based on network and phylogenetic analyses. BMC Bioinform 6:213
47. Emerson IA, Gothandam KM (2012) Residue centrality in alpha helical polytopic
transmembrane protein structures. J Theor Biol 309:78–87
48. Tse A, Verkhivker GM (2015) Molecular dynamics simulations and structural network
analysis of c-Abl and c-Src kinase core proteins: capturing allosteric mechanisms and
communication pathways from residue centrality. J Chem Inf Model 55:1645–1662
49. Chea E, Livesay DR (2007) How accurate and statistically robust are catalytic site predictions
based on closeness centrality? BMC Bioinform 8:153
50. Tang YR, Sheng ZY, Chen YZ, Zhang Z (2008) An improved prediction of catalytic residues
in enzyme structures. Protein Eng Des Sel 21:295–302
51. Sheftel S, Muratore K, Black M, Costanzi S (2013) Graph analysis of b2 adrenergic receptor
structures: a “social network” of GPCR residues. Silico Pharmacol 1:16
52. Slama P, Filippis I, Lappe M (2008) Detection of protein catalytic residues at high precision
using local network properties. BMC Bioinform 9:517
53. Veselovsky AV, Archakov AI (2007) Inhibitors of protein-protein interactions as potential
drugs. Curr Comput-Aided Drug Des 3:51–58
54. Marino Buslje C, Teppa E, Di Domenico T, Delfino JM, Nielsen M (2010) Networks of high
mutual information define the structural proximity of catalytic sites: implications for catalytic
residue identification. PLoS Comput Biol 6:e1000978
55. Aguilar D, Oliva B, Buslje CM (2012) Mapping the mutual information network of enzymatic
families in the protein structure to unveil functional features. PLoS ONE 7:e41430
56. Poirrette AR, Artymiuk PJ, Grindley HM, Rice DW, Willett P (1994) Structural similarity
between binding sites in influenza sialidase and isocitrate dehydrogenase: implications for an
alternative approach to rational drug design. Protein Sci 3:1128–1130
57. Liu ZP, Wu LY, Wang Y, Zhang XS, Chen L (2008) Analysis of protein surface patterns by
pocket similarity network. Prot Pept Lett 15:448–455
58. Yan W, Hu G, Liang Z, Zhou J, Yang Y, Chen J, Shen B (2018) Node-weighted amino acid
network strategy for characterization and identification of protein functional residues. J Chem
Inf Model. (in press). https://doi.org/10.1021/acs.jcim.8b00146
59. Brinda KV, Kannan N, Vishveshwara S (2002) Analysis of homodimeric protein interfaces by
graph-spectral methods. Protein Eng 15:265–277
Analysis of Protein Structures Using Residue Interaction …
67
structures during allosteric communication: investigation of dynamically equilibrated
structures of methionyl tRNA synthetase complexes. Biochemistry 47:11398–11407
38. Pasi M, Tiberti M, Arrigoni A, Papaleo E (2012) xPyder: a PyMOL plugin to analyze coupled
residues and their networks in protein structures. J Chem Inf Model 52:1865–1874
39. Eargle J, Luthey-Schulten Z (2012) NetworkView: 3D display and analysis of proteinÁ RNA
interaction networks. Bioinformatics 28:3000–3001
40. 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
41. Doncheva NT, Klein K, Domingues FS, Albrecht M (2011) Analyzing and visualizing residue
networks of protein structures. Trends Biochem Sci 36:179–182
42. Morris JH, Huang CC, Babbitt PC, Ferrin TE (2007) structureViz: linking Cytoscape and
UCSF Chimera. Bioinformatics 23:2345–2347
43. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B,
Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular
interaction networks. Genome Res 13:2498–2504
44. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
(2004) UCSF Chimera—a visualization system for exploratory research and analysis.
J Comput Chem 25:1605–1612
45. Yan Y, Zhang SG, Wu FX (2011) Applications of graph theory in protein structure
identification. Proteome Sci 9(Suppl 1):S17
46. Thibert B, Bredesen DE, del Rio G (2005) Improved prediction of critical residues for protein
function based on network and phylogenetic analyses. BMC Bioinform 6:213
47. Emerson IA, Gothandam KM (2012) Residue centrality in alpha helical polytopic
transmembrane protein structures. J Theor Biol 309:78–87
48. Tse A, Verkhivker GM (2015) Molecular dynamics simulations and structural network
analysis of c-Abl and c-Src kinase core proteins: capturing allosteric mechanisms and
communication pathways from residue centrality. J Chem Inf Model 55:1645–1662
49. Chea E, Livesay DR (2007) How accurate and statistically robust are catalytic site predictions
based on closeness centrality? BMC Bioinform 8:153
50. Tang YR, Sheng ZY, Chen YZ, Zhang Z (2008) An improved prediction of catalytic residues
in enzyme structures. Protein Eng Des Sel 21:295–302
51. Sheftel S, Muratore K, Black M, Costanzi S (2013) Graph analysis of b2 adrenergic receptor
structures: a “social network” of GPCR residues. Silico Pharmacol 1:16
52. Slama P, Filippis I, Lappe M (2008) Detection of protein catalytic residues at high precision
using local network properties. BMC Bioinform 9:517
53. Veselovsky AV, Archakov AI (2007) Inhibitors of protein-protein interactions as potential
drugs. Curr Comput-Aided Drug Des 3:51–58
54. Marino Buslje C, Teppa E, Di Domenico T, Delfino JM, Nielsen M (2010) Networks of high
mutual information define the structural proximity of catalytic sites: implications for catalytic
residue identification. PLoS Comput Biol 6:e1000978
55. Aguilar D, Oliva B, Buslje CM (2012) Mapping the mutual information network of enzymatic
families in the protein structure to unveil functional features. PLoS ONE 7:e41430
56. Poirrette AR, Artymiuk PJ, Grindley HM, Rice DW, Willett P (1994) Structural similarity
between binding sites in influenza sialidase and isocitrate dehydrogenase: implications for an
alternative approach to rational drug design. Protein Sci 3:1128–1130
57. Liu ZP, Wu LY, Wang Y, Zhang XS, Chen L (2008) Analysis of protein surface patterns by
pocket similarity network. Prot Pept Lett 15:448–455
58. Yan W, Hu G, Liang Z, Zhou J, Yang Y, Chen J, Shen B (2018) Node-weighted amino acid
network strategy for characterization and identification of protein functional residues. J Chem
Inf Model. (in press). https://doi.org/10.1021/acs.jcim.8b00146
59. Brinda KV, Kannan N, Vishveshwara S (2002) Analysis of homodimeric protein interfaces by
graph-spectral methods. Protein Eng 15:265–277
Analysis of Protein Structures Using Residue Interaction …
67