332
X. Yang et al.
50. Yang XH, Liu HH, Liu JN, Li F, Li XH, Shi LL, Chen JW (2016) Rational selection of the 3D
structure of biomacromolecules for molecular docking studies on the mechanism of endocrine
disruptor action. Chem Res Toxicol 29(9):1565–1570
51. Xiang ZX (2006) Advances in homology protein structure modeling. Curr Protein Pept Sci
7(3):217–227
52. Guo JT, Ellrott K, Xu Y (2008) A historical perspective of template-based protein structure
prediction. Methods Mol Biol 413:3–42
53. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili
D, Hunter T, Maniatis T, Califano A, Honig B (2012) Structure-based prediction of proteinprotein interactions on a genome-wide scale. Nature 490(7421):556–560
54. Keskin O, Tuncbag N, Gursoy A (2016) Predicting protein-protein interactions from the
molecular to the proteome level. Chem Rev 116(8):4884–4909
55. Orry A, Abagyan R (eds) (2012) Homology modeling: methods and protocols, methods in
molecular biology, vol 857. Humana Press
56. Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr
Protoc Bioinform 54(1):5.6.1–5.6.37
57. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for
comparative protein modeling. Electrophoresis 18(15):2714–2723
58. Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, Engström O, Ohman L, Greene
GL, Gustafsson JA, Carlquist M (1997) Molecular basis of agonism and antagonism in the
oestrogen receptor. Nature 389(6652):753–758
59. Furukawa A, Konuma T, Yanaka S, Sugase K (2016) Quantitative analysis of protein-ligand
interactions by NMR. Prog Nucl Magn Reson Spectrosc 96:47–57
60. Nitsche C, Otting G (2018) NMR studies of ligand binding. Curr Opin Struct Biol 48:16–22
61. Morris GM, Lim-Wilby M (2008) Molecular docking. In: Kukol A. (eds) Molecular modeling
of proteins. Methods molecular biology™, vol 443. Humana Press
62. Sousa SF, Fernandes PA, Ramos MJ (2006) Protein-ligand docking: current status and future
challenges. Proteins 65(1):15–26
63. Bortolato A, Fanton M, Mason JS, Moro S (2013) Molecular Docking Methodologies. In:
Monticelli L, Salonen E (eds) Biomolecular simulations. Methods in molecular biology (methods and protocols), vol 924. Humana Press, Totowa
64. Trisciuzzi D, Alberga D, Leonetti F, Novellino E, Nicolotti O, Mangiatordi GF (2018) Molecular docking for predictive toxicology. In: Nicolotti O (ed) Computational toxicology. Methods
in molecular biology, vol 1800. Humana Press, New York
65. Taylor RD, Jewsbury PJ, Essex JW (2002) A review of protein-small molecule docking
methods. J Comput Aided Mol Des 16(3):151–166
66. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening
for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):935–949
67. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of search
algorithms and a guide to scoring functions. Proteins 47(4):409–443
68. Chen YC (2015) Beware of docking! Trends Pharmacol Sci 36(2):78–95
69. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009)
AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J
Comput Chem 30(16):2785–2791
70. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Improved protein-ligand
docking using GOLD. Proteins 52(4):609–623
71. Ng HW, Zhang W, Shu M, Luo H, Ge W, Perkins R, Tong W, Hong H (2014) Competitive
molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists. BMC Bioinform 15(Suppl 11):S4
72. Celik L, Davey J, Lund D, Schiøtt B (2008) Exploring interactions of endocrine-disrupting
compounds with different conformations of the human estrogen receptor alpha ligand binding
domain: a molecular docking study. Chem Res Toxicol 21(11):2195–2206
73. Lindahl E (2015) Molecular dynamics simulations. In: Kukol A (eds) Molecular modeling of
proteins. Methods in molecular biology (Methods and protocols), vol 1215. Humana Press,
New York
X. Yang et al.
50. Yang XH, Liu HH, Liu JN, Li F, Li XH, Shi LL, Chen JW (2016) Rational selection of the 3D
structure of biomacromolecules for molecular docking studies on the mechanism of endocrine
disruptor action. Chem Res Toxicol 29(9):1565–1570
51. Xiang ZX (2006) Advances in homology protein structure modeling. Curr Protein Pept Sci
7(3):217–227
52. Guo JT, Ellrott K, Xu Y (2008) A historical perspective of template-based protein structure
prediction. Methods Mol Biol 413:3–42
53. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili
D, Hunter T, Maniatis T, Califano A, Honig B (2012) Structure-based prediction of proteinprotein interactions on a genome-wide scale. Nature 490(7421):556–560
54. Keskin O, Tuncbag N, Gursoy A (2016) Predicting protein-protein interactions from the
molecular to the proteome level. Chem Rev 116(8):4884–4909
55. Orry A, Abagyan R (eds) (2012) Homology modeling: methods and protocols, methods in
molecular biology, vol 857. Humana Press
56. Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr
Protoc Bioinform 54(1):5.6.1–5.6.37
57. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for
comparative protein modeling. Electrophoresis 18(15):2714–2723
58. Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, Engström O, Ohman L, Greene
GL, Gustafsson JA, Carlquist M (1997) Molecular basis of agonism and antagonism in the
oestrogen receptor. Nature 389(6652):753–758
59. Furukawa A, Konuma T, Yanaka S, Sugase K (2016) Quantitative analysis of protein-ligand
interactions by NMR. Prog Nucl Magn Reson Spectrosc 96:47–57
60. Nitsche C, Otting G (2018) NMR studies of ligand binding. Curr Opin Struct Biol 48:16–22
61. Morris GM, Lim-Wilby M (2008) Molecular docking. In: Kukol A. (eds) Molecular modeling
of proteins. Methods molecular biology™, vol 443. Humana Press
62. Sousa SF, Fernandes PA, Ramos MJ (2006) Protein-ligand docking: current status and future
challenges. Proteins 65(1):15–26
63. Bortolato A, Fanton M, Mason JS, Moro S (2013) Molecular Docking Methodologies. In:
Monticelli L, Salonen E (eds) Biomolecular simulations. Methods in molecular biology (methods and protocols), vol 924. Humana Press, Totowa
64. Trisciuzzi D, Alberga D, Leonetti F, Novellino E, Nicolotti O, Mangiatordi GF (2018) Molecular docking for predictive toxicology. In: Nicolotti O (ed) Computational toxicology. Methods
in molecular biology, vol 1800. Humana Press, New York
65. Taylor RD, Jewsbury PJ, Essex JW (2002) A review of protein-small molecule docking
methods. J Comput Aided Mol Des 16(3):151–166
66. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening
for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):935–949
67. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of search
algorithms and a guide to scoring functions. Proteins 47(4):409–443
68. Chen YC (2015) Beware of docking! Trends Pharmacol Sci 36(2):78–95
69. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009)
AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J
Comput Chem 30(16):2785–2791
70. Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Improved protein-ligand
docking using GOLD. Proteins 52(4):609–623
71. Ng HW, Zhang W, Shu M, Luo H, Ge W, Perkins R, Tong W, Hong H (2014) Competitive
molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists. BMC Bioinform 15(Suppl 11):S4
72. Celik L, Davey J, Lund D, Schiøtt B (2008) Exploring interactions of endocrine-disrupting
compounds with different conformations of the human estrogen receptor alpha ligand binding
domain: a molecular docking study. Chem Res Toxicol 21(11):2195–2206
73. Lindahl E (2015) Molecular dynamics simulations. In: Kukol A (eds) Molecular modeling of
proteins. Methods in molecular biology (Methods and protocols), vol 1215. Humana Press,
New York