10 Applications of Molecular Dynamics Simulations …
209
22. Luo H, Ye H, Ng HW, Shi L, Tong W, Mendrick DL, Hong H (2015) Machine learning methods
for predicting HLA-peptide binding activity. Bioinform Biol Insights 9(Suppl 3):21–29
23. Kavlock RJ, Ankley G, Blancato J, Breen M, Conolly R, Dix D, Houck K, Hubal E, Judson
R, Rabinowitz J, Richard A, Setzer RW, Shah I, Villeneuve D, Weber E (2008) Computational
toxicology–a state of the science mini review. Toxicol Sci 103(1):14–27
24. Benfenati E (2007) Predicting toxicity through computers: a changing world. Chem Cent J
1:32
25. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L, Su Z, Perkins R, Tong W (2008) Mold(2),
molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem
Inf Model 48(7):1337–1344
26. Devillers J, Doré JC, Guyot M, Poroikov V, Gloriozova T, Lagunin A, Filimonov D (2007)
Prediction of biological activity profiles of cyanobacterial secondary metabolites. SAR QSAR
Environ Res 18(7–8):629–643
27. Chen M, Bisgin H, Tong L, Hong H, Fang H, Borlak J, Tong W (2014) Toward predictive
models for drug-induced liver injury in humans: are we there yet? Biomark Med 8(2):201–213
28. Hong H, Chen M, Ng HW, Tong W (2016) QSAR Models at the US FDA/NCTR. Methods
Mol Biol 1425:431–459
29. Karplus M (2003) Molecular dynamics of biological macromolecules: a brief history and
perspective. Biopolymers 68(3):350–358
30. Fermi E, Pasta P, Ulam S, Tsingou M. Studies of the nonlinear problems. United States: 1955
1955-05-01
31. Alder BJ, Wainwright TE (1957) Phase transition for a hard sphere system. J Chem Phys.
27:1208–1209
32. Alder BJ, Wainwright TE (1959) Studies in molecular dynamics. General method. J Chem
Phys. 31:459
33. Rahman A (1964) Correlations in the motion of atoms in liquid argon. Phys Rev
136(2A):A405–A411
34. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature
267:585–590
35. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol
103(2):227–249
36. Roccatano D, Barthel A, Zacharias M (2007) Structural flexibility of the nucleosome
core particle at atomic resolution studied by molecular dynamics simulation. Biopolymers
85(5–6):407–421
37. Sharma S, Ding F, Dokholyan NV (2007) Multiscale modeling of nucleosome dynamics.
Biophys J 92(5):1457–1470
38. Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular dynamics.
J Chem Phys. 60:1545–1557
39. Clementi E, Corongiu G (1980) A theoretical study on the water structure for nucleic acids
bases and base pairs in solution at T = 300 K. J Chem Phys 72(7):3979–3992
40. Parrinello M, Rahman A (1980) Crystal structure and pair potentials: a molecular-dynamics
study. Phys Rev Lett 45(14):1196–1199
41. Andersen HC (1980) Molecular dynamics simulations at constant pressure and/or temperature.
J Chem Phys 72(4):2384–2393
42. Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature molecular
dynamics. Biopolymers 29(14):1847–1862
43. Hospital A, Goñi JR, Orozco M, Gelpí JL (2015) Molecular dynamics simulations: advances
and applications. Adv Appl Bioinform Chem: AABC. 8:37–47
44. 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
45. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling
C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem
26(16):1668–1688
209
22. Luo H, Ye H, Ng HW, Shi L, Tong W, Mendrick DL, Hong H (2015) Machine learning methods
for predicting HLA-peptide binding activity. Bioinform Biol Insights 9(Suppl 3):21–29
23. Kavlock RJ, Ankley G, Blancato J, Breen M, Conolly R, Dix D, Houck K, Hubal E, Judson
R, Rabinowitz J, Richard A, Setzer RW, Shah I, Villeneuve D, Weber E (2008) Computational
toxicology–a state of the science mini review. Toxicol Sci 103(1):14–27
24. Benfenati E (2007) Predicting toxicity through computers: a changing world. Chem Cent J
1:32
25. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L, Su Z, Perkins R, Tong W (2008) Mold(2),
molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem
Inf Model 48(7):1337–1344
26. Devillers J, Doré JC, Guyot M, Poroikov V, Gloriozova T, Lagunin A, Filimonov D (2007)
Prediction of biological activity profiles of cyanobacterial secondary metabolites. SAR QSAR
Environ Res 18(7–8):629–643
27. Chen M, Bisgin H, Tong L, Hong H, Fang H, Borlak J, Tong W (2014) Toward predictive
models for drug-induced liver injury in humans: are we there yet? Biomark Med 8(2):201–213
28. Hong H, Chen M, Ng HW, Tong W (2016) QSAR Models at the US FDA/NCTR. Methods
Mol Biol 1425:431–459
29. Karplus M (2003) Molecular dynamics of biological macromolecules: a brief history and
perspective. Biopolymers 68(3):350–358
30. Fermi E, Pasta P, Ulam S, Tsingou M. Studies of the nonlinear problems. United States: 1955
1955-05-01
31. Alder BJ, Wainwright TE (1957) Phase transition for a hard sphere system. J Chem Phys.
27:1208–1209
32. Alder BJ, Wainwright TE (1959) Studies in molecular dynamics. General method. J Chem
Phys. 31:459
33. Rahman A (1964) Correlations in the motion of atoms in liquid argon. Phys Rev
136(2A):A405–A411
34. McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature
267:585–590
35. Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol
103(2):227–249
36. Roccatano D, Barthel A, Zacharias M (2007) Structural flexibility of the nucleosome
core particle at atomic resolution studied by molecular dynamics simulation. Biopolymers
85(5–6):407–421
37. Sharma S, Ding F, Dokholyan NV (2007) Multiscale modeling of nucleosome dynamics.
Biophys J 92(5):1457–1470
38. Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular dynamics.
J Chem Phys. 60:1545–1557
39. Clementi E, Corongiu G (1980) A theoretical study on the water structure for nucleic acids
bases and base pairs in solution at T = 300 K. J Chem Phys 72(7):3979–3992
40. Parrinello M, Rahman A (1980) Crystal structure and pair potentials: a molecular-dynamics
study. Phys Rev Lett 45(14):1196–1199
41. Andersen HC (1980) Molecular dynamics simulations at constant pressure and/or temperature.
J Chem Phys 72(4):2384–2393
42. Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature molecular
dynamics. Biopolymers 29(14):1847–1862
43. Hospital A, Goñi JR, Orozco M, Gelpí JL (2015) Molecular dynamics simulations: advances
and applications. Adv Appl Bioinform Chem: AABC. 8:37–47
44. 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
45. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling
C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem
26(16):1668–1688