60. Reichmann D, Rahat O, Albeck S, Meged R, Dym O, Schreiber G (2005) The modular
architecture of protein–protein binding interfaces. PNAS 102:57–62
61. Brinda KV, Surolia A, Vishveshwara S (2005) Insights into the quaternary association of
proteins through structure graphs: a case study of lectins. Biochem J J391:1–15
62. Kannan N, Chander P, Ghosh P, Vishveshwara S, Chatterji D (2001) Stabilizing interactions
in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral
and point mutation study. Protein Sci 10:46–54
63. Soni N, Madhusudhan MS (2017) Computational modeling of protein assemblies. Curr Opin
Struct Biol 44:179–189
64. Zhang Q, Feng T, Xu L, Sun H, Pan P, Li Y, Li D, Hou T (2016) Recent advances in
protein-protein docking. Curr Drug Targets 17:1586–1594
65. Chang S, Jiao X, Li CH, Gong XQ, Chen WZ, Wang CX (2008) Amino acid network and its
scoring application in protein–protein docking. Biophys Chem 134:111–118
66. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003)
Protein–protein docking with simultaneous optimization of rigid-body displacement and
side-chain conformations. J Mol Biol 33(1):281–299
67. Shih ESC, Hwang M-J (2015) NPPD: a protein-protein docking scoring function based on
dyadic differences in networks of hydrophobic and hydrophilic amino acid residues. Biology
4:282–297
68. Gong X, Wang P, Yang F, Chang S, Liu B, He H, Cao L, Xu X, Li C, Chen W, Wang C
(2010) Protein-protein docking with binding site patch prediction and network-based terms
enhanced combinatorial scoring. Proteins 78:3150–3155
69. Jiao X, Chang S (2011) Scoring function based on weighted residue network. Int J Mol Sci
12:8773–8786
70. Luo Q, Hamer R, Reinert G, Deane CM (2013) Local network patterns in protein-protein
interfaces. PLoS ONE 8:e57031
71. Greener JG, Sternberg MJ (2018) Structure-based prediction of protein allostery. Curr Opin
Struct Biol 50:1–8
72. Nussinov R, Tsai CJ (2013) Allostery in disease and in drug discovery. Cell 153:293–305
73. Lu S, Li S, Zhang J (2014) Harnessing allostery: a novel approach to drug discovery. Med
Res Rev 34:1242–1285
74. Ghosh A, Vishveshwara S (2007) A study of communication pathways in methionyl-tRNA
synthetase by molecular dynamics simulations and structure network analysis. PNAS
104:15711–15716
75. del Sol A, Arauzo-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
76. Angelova K, Felline A, Lee M, Patel M, Puett D, Fanelli F (2011) Conserved amino acids
participate in the structure networks deputed to intramolecular communication in the lutropin
receptor. Cell Mol Life Sci 68:1227–1239
77. Süel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved networks
of residues mediate allosteric communication in proteins. Nat Struct Biol 10:59–69
78. Tang S, Liao JC, Dunn AR, Altman RB, Spudich JA, Schmidt JP (2007) Predicting allosteric
communication in myosin via a pathway of conserved residues. J Mol Biol 373:1361–1373
79. del Sol A, Tsai CJ, Ma B, Nussinov R (2009) The origin of allosteric functional modulation:
multiple pre-existing pathways. Structure 17:1042–1050
80. Sethi A, Eargle J, Black AA, Luthey-Schulten Z (2009) Dynamical networks in tRNA:
protein complexes. PNAS 106:6620–6625
81. Dixit A, Verkhivker GM (2011) Computational modeling of allosteric communication reveals
organizing principles of mutation-induced signaling in ABL and EGFR kinases. PLoS
Comput Biol 7:e1002179
82. Kong Y, Karplus M (2009) Signaling pathways of PDZ2 domain: a molecular dynamics
interaction correlation analysis. Proteins 74:145–154
68
D. Shcherbinin and A. Veselovsky
architecture of protein–protein binding interfaces. PNAS 102:57–62
61. Brinda KV, Surolia A, Vishveshwara S (2005) Insights into the quaternary association of
proteins through structure graphs: a case study of lectins. Biochem J J391:1–15
62. Kannan N, Chander P, Ghosh P, Vishveshwara S, Chatterji D (2001) Stabilizing interactions
in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral
and point mutation study. Protein Sci 10:46–54
63. Soni N, Madhusudhan MS (2017) Computational modeling of protein assemblies. Curr Opin
Struct Biol 44:179–189
64. Zhang Q, Feng T, Xu L, Sun H, Pan P, Li Y, Li D, Hou T (2016) Recent advances in
protein-protein docking. Curr Drug Targets 17:1586–1594
65. Chang S, Jiao X, Li CH, Gong XQ, Chen WZ, Wang CX (2008) Amino acid network and its
scoring application in protein–protein docking. Biophys Chem 134:111–118
66. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003)
Protein–protein docking with simultaneous optimization of rigid-body displacement and
side-chain conformations. J Mol Biol 33(1):281–299
67. Shih ESC, Hwang M-J (2015) NPPD: a protein-protein docking scoring function based on
dyadic differences in networks of hydrophobic and hydrophilic amino acid residues. Biology
4:282–297
68. Gong X, Wang P, Yang F, Chang S, Liu B, He H, Cao L, Xu X, Li C, Chen W, Wang C
(2010) Protein-protein docking with binding site patch prediction and network-based terms
enhanced combinatorial scoring. Proteins 78:3150–3155
69. Jiao X, Chang S (2011) Scoring function based on weighted residue network. Int J Mol Sci
12:8773–8786
70. Luo Q, Hamer R, Reinert G, Deane CM (2013) Local network patterns in protein-protein
interfaces. PLoS ONE 8:e57031
71. Greener JG, Sternberg MJ (2018) Structure-based prediction of protein allostery. Curr Opin
Struct Biol 50:1–8
72. Nussinov R, Tsai CJ (2013) Allostery in disease and in drug discovery. Cell 153:293–305
73. Lu S, Li S, Zhang J (2014) Harnessing allostery: a novel approach to drug discovery. Med
Res Rev 34:1242–1285
74. Ghosh A, Vishveshwara S (2007) A study of communication pathways in methionyl-tRNA
synthetase by molecular dynamics simulations and structure network analysis. PNAS
104:15711–15716
75. del Sol A, Arauzo-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
76. Angelova K, Felline A, Lee M, Patel M, Puett D, Fanelli F (2011) Conserved amino acids
participate in the structure networks deputed to intramolecular communication in the lutropin
receptor. Cell Mol Life Sci 68:1227–1239
77. Süel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved networks
of residues mediate allosteric communication in proteins. Nat Struct Biol 10:59–69
78. Tang S, Liao JC, Dunn AR, Altman RB, Spudich JA, Schmidt JP (2007) Predicting allosteric
communication in myosin via a pathway of conserved residues. J Mol Biol 373:1361–1373
79. del Sol A, Tsai CJ, Ma B, Nussinov R (2009) The origin of allosteric functional modulation:
multiple pre-existing pathways. Structure 17:1042–1050
80. Sethi A, Eargle J, Black AA, Luthey-Schulten Z (2009) Dynamical networks in tRNA:
protein complexes. PNAS 106:6620–6625
81. Dixit A, Verkhivker GM (2011) Computational modeling of allosteric communication reveals
organizing principles of mutation-induced signaling in ABL and EGFR kinases. PLoS
Comput Biol 7:e1002179
82. Kong Y, Karplus M (2009) Signaling pathways of PDZ2 domain: a molecular dynamics
interaction correlation analysis. Proteins 74:145–154
68
D. Shcherbinin and A. Veselovsky