83. Vishveshwara S, Ghosh A, Hansia P (2009) Intra and inter-molecular communications
through protein structure network. Curr Protein Pept Sci 10:146–160
84. Sathyapriya R, Vishveshwara S (2007) Structure networks of E-coli glutaminyl-tRNA
synthetase: effects of ligand binding. Proteins 68:541–550
85. Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S (2010) Allostery and conformational
free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and
structure networks. Proteins 78:506–517
86. Hansia P, Ghosh A, Vishveshwara S (2009) Ligand dependent intra and inter subunit
communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of
structure networks. Mol Bio Syst 5:1860–1872
87. Fanelli F, Felline A (2011) Dimerization and ligand binding affect the structure network of
A 2A adenosine receptor. Biochim Biophys Acta 1808:1256–1266
88. Lee Y, Choi S, Hyeon C (2014) Mapping the intramolecular signal transduction of G-protein
coupled receptors. Proteins 82:727–743
89. Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA (2013) Activation and
dynamic network of the M2 muscarinic receptor. PNAS 110:10982–10987
90. Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B (2007) Ligand
binding and circular permutation modify residue interaction network in DHFR. PLoS Comput
Biol 3:1097–1107
91. Li Y, Wen Z, Xiao J, Yin H, Yu L, Yang L, Li M (2011) Predicting disease-associated
substitution of a single amino acid by analyzing residue interactions. BMC Bioinform 12:14
92. Tse A, Verkhivker GM (2015) Small-world networks of residue interactions in the Abl kinase
complexes with cancer drugs: topology of allosteric communication pathways can determine
drug resistance effects. Mol Biosyst 11:2082–2095
93. Shcherbinin DS, RubtsovaMYu Grigorenko VG, Uporov IV, Veselovsky AV, Egorov AM
(2017) The study of the role of mutations M182T and Q39K in the TEM-72 b-lactamase
structure by the molecular dynamics method. Biochem (Moscow), Suppl B: Biomed Chem
11:120–127
94. Grigorenko VG, RubtsovaMYu Uporov IV, Ishtubaev IV, Andreeva IP, Shcherbinin DS,
Veselovsky AV, Egorov AM (2018) Bacterial TEM-type serine beta-lactamases: structure and
analysis of mutations. biochemistry (Moscow). Suppl B: Biomed Chem 12:87–95
95. Nwaka S, Hudson A (2006) Innovative lead discovery strategies for tropical diseases. Nat Rev
Drug Discov 5:941–955
96. Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S, Hamon J,
Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL (2009) Gaining insight into off-target
mediated effects of drug candidates with a comprehensive systems chemical biology analysis.
J Chem Inf Model 49:308–317
Analysis of Protein Structures Using Residue Interaction …
69
through protein structure network. Curr Protein Pept Sci 10:146–160
84. Sathyapriya R, Vishveshwara S (2007) Structure networks of E-coli glutaminyl-tRNA
synthetase: effects of ligand binding. Proteins 68:541–550
85. Bhattacharyya M, Ghosh A, Hansia P, Vishveshwara S (2010) Allostery and conformational
free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and
structure networks. Proteins 78:506–517
86. Hansia P, Ghosh A, Vishveshwara S (2009) Ligand dependent intra and inter subunit
communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of
structure networks. Mol Bio Syst 5:1860–1872
87. Fanelli F, Felline A (2011) Dimerization and ligand binding affect the structure network of
A 2A adenosine receptor. Biochim Biophys Acta 1808:1256–1266
88. Lee Y, Choi S, Hyeon C (2014) Mapping the intramolecular signal transduction of G-protein
coupled receptors. Proteins 82:727–743
89. Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA (2013) Activation and
dynamic network of the M2 muscarinic receptor. PNAS 110:10982–10987
90. Hu Z, Bowen D, Southerland WM, del Sol A, Pan Y, Nussinov R, Ma B (2007) Ligand
binding and circular permutation modify residue interaction network in DHFR. PLoS Comput
Biol 3:1097–1107
91. Li Y, Wen Z, Xiao J, Yin H, Yu L, Yang L, Li M (2011) Predicting disease-associated
substitution of a single amino acid by analyzing residue interactions. BMC Bioinform 12:14
92. Tse A, Verkhivker GM (2015) Small-world networks of residue interactions in the Abl kinase
complexes with cancer drugs: topology of allosteric communication pathways can determine
drug resistance effects. Mol Biosyst 11:2082–2095
93. Shcherbinin DS, RubtsovaMYu Grigorenko VG, Uporov IV, Veselovsky AV, Egorov AM
(2017) The study of the role of mutations M182T and Q39K in the TEM-72 b-lactamase
structure by the molecular dynamics method. Biochem (Moscow), Suppl B: Biomed Chem
11:120–127
94. Grigorenko VG, RubtsovaMYu Uporov IV, Ishtubaev IV, Andreeva IP, Shcherbinin DS,
Veselovsky AV, Egorov AM (2018) Bacterial TEM-type serine beta-lactamases: structure and
analysis of mutations. biochemistry (Moscow). Suppl B: Biomed Chem 12:87–95
95. Nwaka S, Hudson A (2006) Innovative lead discovery strategies for tropical diseases. Nat Rev
Drug Discov 5:941–955
96. Scheiber J, Chen B, Milik M, Sukuru SC, Bender A, Mikhailov D, Whitebread S, Hamon J,
Azzaoui K, Urban L, Glick M, Davies JW, Jenkins JL (2009) Gaining insight into off-target
mediated effects of drug candidates with a comprehensive systems chemical biology analysis.
J Chem Inf Model 49:308–317
Analysis of Protein Structures Using Residue Interaction …
69