10 Applications of Molecular Dynamics Simulations …
211
65. Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R (2007) Structural dynamics of the
cooperative binding of organic molecules in the human cytochrome P450 3A4. J Am Chem
Soc 129(6):1602–1611
66. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W,
Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd (2000) Calculating structures and
free energies of complex molecules: combining molecular mechanics and continuum models.
Acc Chem Res 33(12):889–897
67. Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC (2012) Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 52(3):617–648
68. Shu M, Hui Wen N, Michael O, Heng L, Hao Y, Weigong G, Weida T, Huixiao H (2016)
Homology model and ligand binding interactions of the extracellular domain of the human
α4β2 nicotinic acetylcholine receptor. J Biomed Sci Eng 09:41–100
69. Shen J, Zhang W, Fang H, Perkins R, Tong W, Hong H (2013) Homology modeling, molecular
docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. BMC
Bioinform 14(Suppl 14):S6–S6
70. Heitz F, Van Mau N (2002) Protein structural changes induced by their uptake at interfaces.
Biochimica et Biophysica Acta (BBA)—Protein Struct Mol Enzym 1597(1):1–11
71. Hong H, Branham WS, Dial SL, Moland CL, Fang H, Shen J, Perkins R, Sheehan D, Tong
W (2012) Rat α-fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities. Chem Res Toxicol
25(11):2553–2566
72. Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ,
Xu H, Trbovic N, Friesner RA, Palmer AG, Shaw DE (2008) Microsecond molecular dynamics
simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.
J Phys Chem B 112(19):6155–6158
73. Lange OF, Lakomek N-A, Farès C, Schröder GF, Walter KFA, Becker S, Meiler J, Grubmüller
H, Griesinger C, de Groot BL (2008) Recognition dynamics up to microseconds revealed from
an RDC-derived ubiquitin ensemble in solution. Science 320(5882):1471
74. Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson
MA, Petsko GA, Karplus M, Hübner CG, Kern D (2007) Intrinsic motions along an enzymatic
reaction trajectory. Nature 450:838
75. Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) How fast-folding proteins fold. Science
334(6055):517
76. Gibson JB, Goland AN, Milgram M, Vineyard GH (1960) Dynamics of radiation damage.
physical. Review 120(4):1229–1253
Suguna Devi Sakkiah is Research Scientist in the Division of Bioinformatics and Biostatistics of
FDA’s National Center for Toxicological Research, Jefferson, Arkansas. She received her Ph.D.
in computational chemistry from Gyeongsang National University, South Korea, and M.Sc. from
Bharathiar University, Coimbatore, India. In 2010, she received a young scientist award during her
Ph.D. She conducted postdoctoral researches on computer-aided drug design and structure–activity relationships studies using various modeling tools in Gwangju Institute of Science and technology, South Korea, University of California, Cedars-Sinai Medical Center, and FDA/National
Center for Toxicological Research, USA. Currently, she is working on computational modeling of
endocrine receptors. She developed multiple predictive models to predict chemicals binding with
estrogen and androgen receptors to assist safety evaluation of FDA-regulated products. She published more than 50 articles in scientific journals.
211
65. Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R (2007) Structural dynamics of the
cooperative binding of organic molecules in the human cytochrome P450 3A4. J Am Chem
Soc 129(6):1602–1611
66. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W,
Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE 3rd (2000) Calculating structures and
free energies of complex molecules: combining molecular mechanics and continuum models.
Acc Chem Res 33(12):889–897
67. Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC (2012) Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 52(3):617–648
68. Shu M, Hui Wen N, Michael O, Heng L, Hao Y, Weigong G, Weida T, Huixiao H (2016)
Homology model and ligand binding interactions of the extracellular domain of the human
α4β2 nicotinic acetylcholine receptor. J Biomed Sci Eng 09:41–100
69. Shen J, Zhang W, Fang H, Perkins R, Tong W, Hong H (2013) Homology modeling, molecular
docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. BMC
Bioinform 14(Suppl 14):S6–S6
70. Heitz F, Van Mau N (2002) Protein structural changes induced by their uptake at interfaces.
Biochimica et Biophysica Acta (BBA)—Protein Struct Mol Enzym 1597(1):1–11
71. Hong H, Branham WS, Dial SL, Moland CL, Fang H, Shen J, Perkins R, Sheehan D, Tong
W (2012) Rat α-fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities. Chem Res Toxicol
25(11):2553–2566
72. Maragakis P, Lindorff-Larsen K, Eastwood MP, Dror RO, Klepeis JL, Arkin IT, Jensen MØ,
Xu H, Trbovic N, Friesner RA, Palmer AG, Shaw DE (2008) Microsecond molecular dynamics
simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins.
J Phys Chem B 112(19):6155–6158
73. Lange OF, Lakomek N-A, Farès C, Schröder GF, Walter KFA, Becker S, Meiler J, Grubmüller
H, Griesinger C, de Groot BL (2008) Recognition dynamics up to microseconds revealed from
an RDC-derived ubiquitin ensemble in solution. Science 320(5882):1471
74. Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson
MA, Petsko GA, Karplus M, Hübner CG, Kern D (2007) Intrinsic motions along an enzymatic
reaction trajectory. Nature 450:838
75. Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) How fast-folding proteins fold. Science
334(6055):517
76. Gibson JB, Goland AN, Milgram M, Vineyard GH (1960) Dynamics of radiation damage.
physical. Review 120(4):1229–1253
Suguna Devi Sakkiah is Research Scientist in the Division of Bioinformatics and Biostatistics of
FDA’s National Center for Toxicological Research, Jefferson, Arkansas. She received her Ph.D.
in computational chemistry from Gyeongsang National University, South Korea, and M.Sc. from
Bharathiar University, Coimbatore, India. In 2010, she received a young scientist award during her
Ph.D. She conducted postdoctoral researches on computer-aided drug design and structure–activity relationships studies using various modeling tools in Gwangju Institute of Science and technology, South Korea, University of California, Cedars-Sinai Medical Center, and FDA/National
Center for Toxicological Research, USA. Currently, she is working on computational modeling of
endocrine receptors. She developed multiple predictive models to predict chemicals binding with
estrogen and androgen receptors to assist safety evaluation of FDA-regulated products. She published more than 50 articles in scientific journals.