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103. Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H (2012) Three-dimensional
reconstruction of protein networks provides insight into human genetic disease. Nat
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drug reactions from a chemical-protein interactome. PLoS Comput Biol 5(7):e1000441
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Biophys Chem 10(1–102):309–319
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109. Zhang L, Yang Y, Kao YT, Wang L, Zhong D (2009) Protein hydration dynamics and
molecular mechanism of coupled water-protein fluctuations. J Am Chem Soc 131(30):
10677–10691
110. Schutz CN, Warshel A (2001) What are the dielectric “constants” of proteins and how to
validate electrostatic models? Proteins 44(4):400–417
111. Bernal JD, Fowler RH (1933) A theory of water and ionic solution, with particular reference
to hydrogen and hydroxyl ions. J Chem Phys 1(8):515–548
112. Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular
dynamics. J Chem Phys 60(4):1545–1557
113. Berendsen HJ, Postma JP, van Gunsteren WF, Hermans J (1981) Interaction models for
water in relation to protein hydration. In: Intermolecular forces. Springer, Netherlands,
pp 331–342
114. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of
simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935
115. Mahoney MW, Jorgensen WL (2000) A five-site model for liquid water and the reproduction
of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys 112(20):
8910–8922
116. Klamt A, Schüürmann GJGJ (1993) COSMO: a new approach to dielectric screening in
solvents with explicit expressions for the screening energy and its gradient. J Chem Soc,
Perkin Trans 2(5):799–805
117. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semianalytical treatment of
solvation for molecular mechanics and dynamics. J Am Chem Soc 112(16):6127–6129
118. Bashford D, Case DA (2000) Generalized born models of macromolecular solvation effects.
Annu Rev Phys Chem 51(1):129–152
119. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) Rapid
grid-based construction of the molecular surface and the use of induced surface charge to
calculate reaction field energies: applications to the molecular systems and geometric
objects. J Comput Chem 23(1):128–137
120. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK,
Bagheri B, Scott LR, McCammon JA (1995) Electrostatics and diffusion of molecules in
solution: simulations with the University of Houston Brownian Dynamics program. Comput
Phys Commun 91(1–3):57–95
300
D. Velmurugan et al.
scoring application in protein-protein docking. Biophys Chem 134(3):111–118
101. del Sol A, O’Meara P (2005) Small-world network approach to identify key residues in
protein-protein interaction. Proteins 58(3):672–682
102. Hammad N, Jingdong J (2013) Structure-based protein-protein interaction networks and
drug design. Quant Biol 1(Issue 3):183–191
103. Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H (2012) Three-dimensional
reconstruction of protein networks provides insight into human genetic disease. Nat
Biotechnol 30(2):159–164
104. Mestres J, Gregori-Puigjane E, Valverde S, Sole RV (2009) The topology of drug-target
interaction networks: implicit dependence on drug properties and target families. Mol
BioSyst 5(9):1051–1057
105. Xie L, Xie L, Bourne PE (2011) Structure-based systems biology for analyzing off-target
binding. Curr Opin Struct Biol 21(2):189–199
106. Yang L, Chen J, He L (2009) Harvesting candidate genes responsible for serious adverse
drug reactions from a chemical-protein interactome. PLoS Comput Biol 5(7):e1000441
107. Ben-Naim A (2002) Molecular recognition—viewed through the eyes of the solvent.
Biophys Chem 10(1–102):309–319
108. Bienstock RJ (2015) Solvation methods for protein-ligand docking. Methods Mol Biol
1289:3–12
109. Zhang L, Yang Y, Kao YT, Wang L, Zhong D (2009) Protein hydration dynamics and
molecular mechanism of coupled water-protein fluctuations. J Am Chem Soc 131(30):
10677–10691
110. Schutz CN, Warshel A (2001) What are the dielectric “constants” of proteins and how to
validate electrostatic models? Proteins 44(4):400–417
111. Bernal JD, Fowler RH (1933) A theory of water and ionic solution, with particular reference
to hydrogen and hydroxyl ions. J Chem Phys 1(8):515–548
112. Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular
dynamics. J Chem Phys 60(4):1545–1557
113. Berendsen HJ, Postma JP, van Gunsteren WF, Hermans J (1981) Interaction models for
water in relation to protein hydration. In: Intermolecular forces. Springer, Netherlands,
pp 331–342
114. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of
simple potential functions for simulating liquid water. J Chem Phys 79(2):926–935
115. Mahoney MW, Jorgensen WL (2000) A five-site model for liquid water and the reproduction
of the density anomaly by rigid, nonpolarizable potential functions. J Chem Phys 112(20):
8910–8922
116. Klamt A, Schüürmann GJGJ (1993) COSMO: a new approach to dielectric screening in
solvents with explicit expressions for the screening energy and its gradient. J Chem Soc,
Perkin Trans 2(5):799–805
117. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990) Semianalytical treatment of
solvation for molecular mechanics and dynamics. J Am Chem Soc 112(16):6127–6129
118. Bashford D, Case DA (2000) Generalized born models of macromolecular solvation effects.
Annu Rev Phys Chem 51(1):129–152
119. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) Rapid
grid-based construction of the molecular surface and the use of induced surface charge to
calculate reaction field energies: applications to the molecular systems and geometric
objects. J Comput Chem 23(1):128–137
120. Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK,
Bagheri B, Scott LR, McCammon JA (1995) Electrostatics and diffusion of molecules in
solution: simulations with the University of Houston Brownian Dynamics program. Comput
Phys Commun 91(1–3):57–95
300
D. Velmurugan et al.