60. Sun H, Li Y, Tian S, Xu L, Hou T (2014) Assessing the performance of MM/PBSA and
MM/GBSA methods. 4. accuracies of MM/PBSA and MM/GBSA methodologies evaluated
by various simulation protocols using PDBbind data set. Phys Chem Chem Phys 16
(31):16719–16729
61. Xu L, Sun H, Li Y, Wang J, Hou T (2013) Assessing the performance of MM/PBSA and
MM/GBSA methods. 3. the impact of force fields and ligand charge models. J Phy Chem B
117(28):8408–8421
62. Dominy BN, Brooks CL (1999) Development of a generalized born model parametrization
for proteins and nucleic acids. J Phy Chem B 103(18):3765–3773
63. Jayaram B, Sprous D, Beveridge D (1998) Solvation free energy of biomacromolecules:
parameters for a modified generalized born model consistent with the AMBER force field.
J Phy Chem B 102(47):9571–9576
64. Onufriev A, Bashford D, Case DA (2000) Modification of the generalized Born model
suitable for macromolecules. J Phy Chem B 104(15):3712–3720
65. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale
conformational changes with a modified generalized born model. Proteins Struct Funct
Bioinf 55(2):383–394
66. Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson
—Boltzmann surface area method. Mol Inform 31(2):114–122
67. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y,
Wang W (2000) Calculating structures and free energies of complex molecules: combining
molecular mechanics and continuum models. Acc Chem Res 33(12):889–897
68. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent
studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc
120(37):9401–9409
69. Edinger SR, Cortis C, Shenkin PS, Friesner RA (1997) Solvation free energies of peptides:
comparison of approximate continuum solvation models with accurate solution of the
Poisson-Boltzmann equation. J Phy Chem B 101(7):1190–1197
70. Gilson MK, Davis ME, Luty BA, McCammon JA (1993) Computation of electrostatic forces
on solvated molecules using the Poisson-Boltzmann equation. J Phy Chem 97(14):3591–
3600
71. Im W, Beglov D, Roux B (1998) Continuum solvation model: computation of electrostatic
forces from numerical solutions to the Poisson-Boltzmann equation. Comput Phys Commun
111(1):59–75
72. Baron R, van Gunsteren WF, Hünenberger PH (2006) Estimating the configurational entropy
from molecular dynamics simulations: anharmonicity and correlation corrections to the
quasi-harmonic approximation. Trends Phys Chem 11:87–122
73. Harris S, Laughton C (2007) A simple physical description of DNA dynamics:
quasi-harmonic analysis as a route to the configurational entropy. J Phys: Condens Matter
19(7):076103
74. Case DA (1994) Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4
(2):285–290
75. Karplus M, Kushick JN (1981) Method for estimating the configurational entropy of
macromolecules. Macromolecules 14(2):325–332
76. Tidor B, Karplus M (1993) The contribution of cross-links to protein stability: a normal
mode analysis of the configurational entropy of the native state. Proteins Struct Funct Bioinf
15(1):71–79
77. Aqvist J, Marelius J (2001) The linear interaction energy method for predicting ligand
binding free energies. Comb Chem High Throughput Screen 4(8):613–626
78. Åqvist J, Medina C, Samuelsson J-E (1994) A new method for predicting binding affinity in
computer-aided drug design. Protein Eng 7(3):385–391
79. Hansson T, Marelius J, Åqvist J (1998) Ligand binding affinity prediction by linear
interaction energy methods. J Comput Aided Mol Des 12(1):27–35
22
E. A. F. Martis and E. C. Coutinho
MM/GBSA methods. 4. accuracies of MM/PBSA and MM/GBSA methodologies evaluated
by various simulation protocols using PDBbind data set. Phys Chem Chem Phys 16
(31):16719–16729
61. Xu L, Sun H, Li Y, Wang J, Hou T (2013) Assessing the performance of MM/PBSA and
MM/GBSA methods. 3. the impact of force fields and ligand charge models. J Phy Chem B
117(28):8408–8421
62. Dominy BN, Brooks CL (1999) Development of a generalized born model parametrization
for proteins and nucleic acids. J Phy Chem B 103(18):3765–3773
63. Jayaram B, Sprous D, Beveridge D (1998) Solvation free energy of biomacromolecules:
parameters for a modified generalized born model consistent with the AMBER force field.
J Phy Chem B 102(47):9571–9576
64. Onufriev A, Bashford D, Case DA (2000) Modification of the generalized Born model
suitable for macromolecules. J Phy Chem B 104(15):3712–3720
65. Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale
conformational changes with a modified generalized born model. Proteins Struct Funct
Bioinf 55(2):383–394
66. Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson
—Boltzmann surface area method. Mol Inform 31(2):114–122
67. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y,
Wang W (2000) Calculating structures and free energies of complex molecules: combining
molecular mechanics and continuum models. Acc Chem Res 33(12):889–897
68. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent
studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J Am Chem Soc
120(37):9401–9409
69. Edinger SR, Cortis C, Shenkin PS, Friesner RA (1997) Solvation free energies of peptides:
comparison of approximate continuum solvation models with accurate solution of the
Poisson-Boltzmann equation. J Phy Chem B 101(7):1190–1197
70. Gilson MK, Davis ME, Luty BA, McCammon JA (1993) Computation of electrostatic forces
on solvated molecules using the Poisson-Boltzmann equation. J Phy Chem 97(14):3591–
3600
71. Im W, Beglov D, Roux B (1998) Continuum solvation model: computation of electrostatic
forces from numerical solutions to the Poisson-Boltzmann equation. Comput Phys Commun
111(1):59–75
72. Baron R, van Gunsteren WF, Hünenberger PH (2006) Estimating the configurational entropy
from molecular dynamics simulations: anharmonicity and correlation corrections to the
quasi-harmonic approximation. Trends Phys Chem 11:87–122
73. Harris S, Laughton C (2007) A simple physical description of DNA dynamics:
quasi-harmonic analysis as a route to the configurational entropy. J Phys: Condens Matter
19(7):076103
74. Case DA (1994) Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4
(2):285–290
75. Karplus M, Kushick JN (1981) Method for estimating the configurational entropy of
macromolecules. Macromolecules 14(2):325–332
76. Tidor B, Karplus M (1993) The contribution of cross-links to protein stability: a normal
mode analysis of the configurational entropy of the native state. Proteins Struct Funct Bioinf
15(1):71–79
77. Aqvist J, Marelius J (2001) The linear interaction energy method for predicting ligand
binding free energies. Comb Chem High Throughput Screen 4(8):613–626
78. Åqvist J, Medina C, Samuelsson J-E (1994) A new method for predicting binding affinity in
computer-aided drug design. Protein Eng 7(3):385–391
79. Hansson T, Marelius J, Åqvist J (1998) Ligand binding affinity prediction by linear
interaction energy methods. J Comput Aided Mol Des 12(1):27–35
22
E. A. F. Martis and E. C. Coutinho