210
S. Sakkiah et al.
46. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem
26(16):1781–1802
47. Ponder JW, Richards FM (1987) An efficient newton-like method for molecular mechanics
energy minimization of large molecules. J Comput Chem 8(7):1016–1024
48. 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
49. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys
117(1):1–19
50. Smith W, Forester TR. (1996) DL_POLY_2.0: a general-purpose parallel molecular dynamics
simulation package. J Mol Graph 14(3):136–141
51. Refson K (2000) Moldy: a portable molecular dynamics simulation program for serial and
parallel computers. Comput Phys Commun 126(3):310–329
52. Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I,
Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the 2006 ACM/IEEE
conference on Supercomputing; Tampa, Florida. 1188544: ACM. p 84
53. MacKerell AD, Brooks CL, Nilsson L, Roux B, Won Y, Karplus M (1998) {CHARMM}: the
energy function and its parameterization with an overview of the program. In: Schleyer, editor.
1: John Wiley & Sons: Chichester p 271–277
54. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T,
Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins,
nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197
55. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF (2004) A biomolecular force field based
on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5
and 53A6. J Comput Chem 25(13):1656–1676
56. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS allatom force field on conformational energetics and properties of organic liquids. J Am Chem
Soc 118(45):11225–11236
57. Nelson MT, Humphrey W, Gursoy A, Dalke A, Kalé LV, Skeel RD, Schulten K (1996) NAMD:
a parallel, object-oriented molecular dynamics program. Int J Supercomput Appl High Perform
Computing 10(4):251–268
58. Lippert RA, Bowers KJ, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I,
Shaw DE (2007) A common, avoidable source of error in molecular dynamics integrators. J
Chem Phys 126(4):046101
59. Bowers KJ, Dror RO, Shaw DE (2006) The midpoint method for parallelization of particle
simulations. J Chem Phys 124(18):184109
60. Meharenna YT, Poulos TL (2010) Using molecular dynamics to probe the structural basis for
enhanced stability in thermal stable cytochromes P450. Biochemistry 49(31):6680–6686
61. Skopalik J, Anzenbacher P, Otyepka M (2008) Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their
substrate preferences. J Phys Chem B 112(27):8165–8173
62. Hendrychova T, Anzenbacherova E, Hudecek J, Skopalik J, Lange R, Hildebrandt P, Otyepka
M, Anzenbacher P (1814) Flexibility of human cytochrome P450 enzymes: molecular dynamics
and spectroscopy reveal important function-related variations. Biochim Biophys Acta 1:58–68
63. Lampe JN, Brandman R, Sivaramakrishnan S, de Montellano PR (2010) Two-dimensional
NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates. J Biol Chem 285(13):9594–9603
64. Park H, Lee S, Suh J (2005) Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc
127(39):13634–13642
S. Sakkiah et al.
46. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem
26(16):1781–1802
47. Ponder JW, Richards FM (1987) An efficient newton-like method for molecular mechanics
energy minimization of large molecules. J Comput Chem 8(7):1016–1024
48. 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
49. Plimpton S (1995) Fast parallel algorithms for short-range molecular dynamics. J Comput Phys
117(1):1–19
50. Smith W, Forester TR. (1996) DL_POLY_2.0: a general-purpose parallel molecular dynamics
simulation package. J Mol Graph 14(3):136–141
51. Refson K (2000) Moldy: a portable molecular dynamics simulation program for serial and
parallel computers. Comput Phys Commun 126(3):310–329
52. Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I,
Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the 2006 ACM/IEEE
conference on Supercomputing; Tampa, Florida. 1188544: ACM. p 84
53. MacKerell AD, Brooks CL, Nilsson L, Roux B, Won Y, Karplus M (1998) {CHARMM}: the
energy function and its parameterization with an overview of the program. In: Schleyer, editor.
1: John Wiley & Sons: Chichester p 271–277
54. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T,
Caldwell JW, Kollman PA (1995) A second generation force field for the simulation of proteins,
nucleic acids, and organic molecules. J Am Chem Soc 117(19):5179–5197
55. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF (2004) A biomolecular force field based
on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5
and 53A6. J Comput Chem 25(13):1656–1676
56. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS allatom force field on conformational energetics and properties of organic liquids. J Am Chem
Soc 118(45):11225–11236
57. Nelson MT, Humphrey W, Gursoy A, Dalke A, Kalé LV, Skeel RD, Schulten K (1996) NAMD:
a parallel, object-oriented molecular dynamics program. Int J Supercomput Appl High Perform
Computing 10(4):251–268
58. Lippert RA, Bowers KJ, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I,
Shaw DE (2007) A common, avoidable source of error in molecular dynamics integrators. J
Chem Phys 126(4):046101
59. Bowers KJ, Dror RO, Shaw DE (2006) The midpoint method for parallelization of particle
simulations. J Chem Phys 124(18):184109
60. Meharenna YT, Poulos TL (2010) Using molecular dynamics to probe the structural basis for
enhanced stability in thermal stable cytochromes P450. Biochemistry 49(31):6680–6686
61. Skopalik J, Anzenbacher P, Otyepka M (2008) Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their
substrate preferences. J Phys Chem B 112(27):8165–8173
62. Hendrychova T, Anzenbacherova E, Hudecek J, Skopalik J, Lange R, Hildebrandt P, Otyepka
M, Anzenbacher P (1814) Flexibility of human cytochrome P450 enzymes: molecular dynamics
and spectroscopy reveal important function-related variations. Biochim Biophys Acta 1:58–68
63. Lampe JN, Brandman R, Sivaramakrishnan S, de Montellano PR (2010) Two-dimensional
NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates. J Biol Chem 285(13):9594–9603
64. Park H, Lee S, Suh J (2005) Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc
127(39):13634–13642