16 Molecular Modeling Method Applications …
333
74. Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G (2015) The impact
of molecular dynamics on drug design: applications for the characterization of ligandmacromolecule complexes. Drug Discov Today 20(6):686–702
75. Steinbrecher T, Elstner M (2013) QM and QM/MM Simulations of Proteins. In: Monticelli
L, Salonen E (eds) Biomolecular simulations. Methods in molecular biology (Methods and
protocols), vol 924. Humana Press, Totowa
76. Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat
Struct Biol 9(9):646–652
77. Field MJ, Bash PA, Karplus M (1990) A combined quantum mechanical and molecular
mechanical potential for molecular dynamics simulations. J Comput Chem 11(6):700–733
78. Ng HW, Shu M, Luo H, Ye H, Ge W, Perkins R, Tong W, Hong H (2015) Estrogenic activity
data extraction and in silico prediction show the endocrine disruption potential of bisphenol
A replacement compounds. Chem Res Toxicol 28(9):1784–1795
79. Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the Amber biomolecular
simulation package. WIREs Comput Mol Sci 3(2):198–210
80. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701–1718
81. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kalé L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem
26(16):1781–1802
82. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y,
Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer
S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor
RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York
DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem
30(10):1545–1614
83. Yang XH, Xie HB, Chen JW, Li XH (2013) Anionic phenolic compounds bind stronger
with transthyretin than their neutral forms: nonnegligible mechanisms in virtual screening of
endocrine disrupting chemicals. Chem Res Toxicol 26(9):1340–1347
84. Yang XH, Lyakurwa F, Xie HB, Chen JW, Li XH, Qiao XL, Cai XY (2017) Different binding
mechanisms of neutral and anionic poly-/perfluorinated chemicals to human transthyretin
revealed by In silico models. Chemosphere 182:574–583
85. Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010)
Revealing noncovalent interactions. J Am Chem Soc 132(18):6498–6506
86. Mahadevi AS, Sastry GN (2016) Cooperativity in noncovalent interactions. Chem Rev
116(5):2775–2825
87. Klebe G (2013) Protein-ligand interactions as the basis for drug action. In: Klebe G (ed) Drug
design. Springer, Berlin, Heidelberg
88. Ferreira de Freitas R, Schapira M (2017) A systematic analysis of atomic protein-ligand
interactions in the PDB. Medchemcomm 8(10):1970–1981
89. Gallina AM, Bork P, Bordo D (2014) Structural analysis of protein-ligand interactions: the
binding of endogenous compounds and of synthetic drugs. J Mol Recognit 27(2):65–72
90. Avvakumov GV, Cherkasov A, Muller YA, Hammond GL (2010) Structural analyses of
sex hormone-binding globulin reveal novel ligands and function. Mol Cell Endocrinol
316(1):13–23
91. Rowe RK, Ho PS (2017) Relationships between hydrogen bonds and halogen bonds in biological systems. Acta Crystallogr B Struct Sci Cryst Eng Mater 73(Pt 2):255–264
92. Glättli A, Daura X, Seebach D, van Gunsteren WF (2002) Can one derive the conformational
preference of a beta-peptide from its CD spectrum? J Am Chem Soc 124:12972–12978
93. Williams SP, Sigler PB (1998) Atomic structure of progesterone complexed with its receptor.
Nature 393(6683):392–396
94. Celik L, Lund JD, Schiøtt B (2007) Conformational dynamics of the estrogen receptor alpha:
molecular dynamics simulations of the influence of binding site structure on protein dynamics.
Biochemistry 46(7):1743–1758
333
74. Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G (2015) The impact
of molecular dynamics on drug design: applications for the characterization of ligandmacromolecule complexes. Drug Discov Today 20(6):686–702
75. Steinbrecher T, Elstner M (2013) QM and QM/MM Simulations of Proteins. In: Monticelli
L, Salonen E (eds) Biomolecular simulations. Methods in molecular biology (Methods and
protocols), vol 924. Humana Press, Totowa
76. Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat
Struct Biol 9(9):646–652
77. Field MJ, Bash PA, Karplus M (1990) A combined quantum mechanical and molecular
mechanical potential for molecular dynamics simulations. J Comput Chem 11(6):700–733
78. Ng HW, Shu M, Luo H, Ye H, Ge W, Perkins R, Tong W, Hong H (2015) Estrogenic activity
data extraction and in silico prediction show the endocrine disruption potential of bisphenol
A replacement compounds. Chem Res Toxicol 28(9):1784–1795
79. Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the Amber biomolecular
simulation package. WIREs Comput Mol Sci 3(2):198–210
80. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701–1718
81. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kalé L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem
26(16):1781–1802
82. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y,
Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer
S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor
RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York
DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem
30(10):1545–1614
83. Yang XH, Xie HB, Chen JW, Li XH (2013) Anionic phenolic compounds bind stronger
with transthyretin than their neutral forms: nonnegligible mechanisms in virtual screening of
endocrine disrupting chemicals. Chem Res Toxicol 26(9):1340–1347
84. Yang XH, Lyakurwa F, Xie HB, Chen JW, Li XH, Qiao XL, Cai XY (2017) Different binding
mechanisms of neutral and anionic poly-/perfluorinated chemicals to human transthyretin
revealed by In silico models. Chemosphere 182:574–583
85. Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010)
Revealing noncovalent interactions. J Am Chem Soc 132(18):6498–6506
86. Mahadevi AS, Sastry GN (2016) Cooperativity in noncovalent interactions. Chem Rev
116(5):2775–2825
87. Klebe G (2013) Protein-ligand interactions as the basis for drug action. In: Klebe G (ed) Drug
design. Springer, Berlin, Heidelberg
88. Ferreira de Freitas R, Schapira M (2017) A systematic analysis of atomic protein-ligand
interactions in the PDB. Medchemcomm 8(10):1970–1981
89. Gallina AM, Bork P, Bordo D (2014) Structural analysis of protein-ligand interactions: the
binding of endogenous compounds and of synthetic drugs. J Mol Recognit 27(2):65–72
90. Avvakumov GV, Cherkasov A, Muller YA, Hammond GL (2010) Structural analyses of
sex hormone-binding globulin reveal novel ligands and function. Mol Cell Endocrinol
316(1):13–23
91. Rowe RK, Ho PS (2017) Relationships between hydrogen bonds and halogen bonds in biological systems. Acta Crystallogr B Struct Sci Cryst Eng Mater 73(Pt 2):255–264
92. Glättli A, Daura X, Seebach D, van Gunsteren WF (2002) Can one derive the conformational
preference of a beta-peptide from its CD spectrum? J Am Chem Soc 124:12972–12978
93. Williams SP, Sigler PB (1998) Atomic structure of progesterone complexed with its receptor.
Nature 393(6683):392–396
94. Celik L, Lund JD, Schiøtt B (2007) Conformational dynamics of the estrogen receptor alpha:
molecular dynamics simulations of the influence of binding site structure on protein dynamics.
Biochemistry 46(7):1743–1758