4. Kubinyi H (2003) Drug research: myths, hype and reality. Nat Rev Drug Discov 2(8):665–
668
5. Hodgson John (2001) ADMET-turning chemicals into drugs. Nat Biotechnol 19(8):722
6. Caldwell GW (2000) Compound optimization in early-and late-phase drug discovery:
acceptable pharmacokinetic properties utilizing combined physicochemical, in vitro and
in vivo screens. Curr Opin Drug Discov Devel 3(1):30–41
7. Zamora I, Oprea T, Cruciani G, Pastor M, Ungell AL (2003) Surface descriptors for protein
— ligand affinity prediction. J Med Chem 46(1):25–33
8. De Waterbeemd Van, Han Eric Gifford (2003) ADMET in silico modelling: towards
prediction paradise. Nat Rev Drug Discov 2(3):192–204
9. Colmenarejo G (2003) Insilico prediction of drug-binding strengths to human serum albumin.
Med Res Rev 23(3):275–301
10. Guengerich FP (2006) Cytochrome P450 s and other enzymes in drug metabolism and
toxicity. AAPS J 8(1):E101–E111
11. Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jorgensen FS, Vermeulen NPE,
Oostenbrink C (2009) Virtual screening and prediction of site of metabolism for cytochrome
P450 1A2 ligands. J Chem Inf Model 49:43–52
12. Vasanthanathan P, Olsen L, Jorgensen FS, Vermeulen NPE, Oostenbrink C (2010)
Calculation of Binding Free Energy for CYP1A2 Ligands by Using Empirical Free Energy
Method. Drug Metab Dispos 38:1347–1354
13. Leung SS, Mijalkovic J, Borrelli K, Jacobson MP (2012) Testing physical models of passive
membrane permeation. J Chem Inf Model 52(6):1621–1636
14. Westergren J, Lindfors L, Höglund T, Lüder K, Nordholm S, Kjellander R (2007) In silico
prediction of drug solubility: 1. Free energy of hydration. J Phys Chem 111(7):1872–1882
15. Rossi Sebastiano M, Doak BC, Backlund M, Poongavanam V, Over B, Ermondi G, Caron G,
Matsson P, Kihlberg J (2018) Impact of dynamically exposed polarity on permeability and
solubility of chameleonic drugs beyond the rule of 5. J Med Chem 61(9):4189–4202
16. Wan J, Zhang L, Yang GF, Zhan CG (2004) Quantitative structure-activity relationship for
cyclic imide derivatives of protoporphyrinogen oxidase inhibitors: a study of quantum
chemical descriptors from density functional theory. J Chem Inf Comput Sci 44:20
17. Hopfinger AJ, Pearlstein RA (1984) Molecular mechanics force-field parameterization
procedures. J Comput Chem 5(5):486–99.99–2105
18. Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y,
Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating
structures and free energies of complex molecules: Combining molecular mechanics and
continuum models. Acc Chem Res 33:889–897
19. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate
ligand-binding affinities. Expert Opin Drug Discov 10:449–461
20. Wang W, Donini O, Reyes CM, Kollman PA (2001) Biomolecular simulations: Recent
developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein,
and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 30:211–243
21. Massova I, Kollman PA (2000) Combined molecular mechanical and continuum solvent
approach (MM-PBSA/GBSA) to predict ligand binding. Perspect Drug Discov 18:113–135
22. Wang C, Greene DA, Xiao L, Qi R, Luo R (2018) Recent developments and applications of
the MMPBSA method. Front Mol Biosci 10(4):87
23. Wang J, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the
binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to
HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc 123(22):5221–5230
24. Meng XY, Zhang HX, Mezei M, Cui M (2011) Molecular docking: a powerful approach for
structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–157
25. Jain AN (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7:407–
420
26. Stahl M, Rarey M (2001) Detailed analysis of scoring functions for virtual screening. J Med
Chem 44:1035–1042
244
N. A. Murugan et al.
668
5. Hodgson John (2001) ADMET-turning chemicals into drugs. Nat Biotechnol 19(8):722
6. Caldwell GW (2000) Compound optimization in early-and late-phase drug discovery:
acceptable pharmacokinetic properties utilizing combined physicochemical, in vitro and
in vivo screens. Curr Opin Drug Discov Devel 3(1):30–41
7. Zamora I, Oprea T, Cruciani G, Pastor M, Ungell AL (2003) Surface descriptors for protein
— ligand affinity prediction. J Med Chem 46(1):25–33
8. De Waterbeemd Van, Han Eric Gifford (2003) ADMET in silico modelling: towards
prediction paradise. Nat Rev Drug Discov 2(3):192–204
9. Colmenarejo G (2003) Insilico prediction of drug-binding strengths to human serum albumin.
Med Res Rev 23(3):275–301
10. Guengerich FP (2006) Cytochrome P450 s and other enzymes in drug metabolism and
toxicity. AAPS J 8(1):E101–E111
11. Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jorgensen FS, Vermeulen NPE,
Oostenbrink C (2009) Virtual screening and prediction of site of metabolism for cytochrome
P450 1A2 ligands. J Chem Inf Model 49:43–52
12. Vasanthanathan P, Olsen L, Jorgensen FS, Vermeulen NPE, Oostenbrink C (2010)
Calculation of Binding Free Energy for CYP1A2 Ligands by Using Empirical Free Energy
Method. Drug Metab Dispos 38:1347–1354
13. Leung SS, Mijalkovic J, Borrelli K, Jacobson MP (2012) Testing physical models of passive
membrane permeation. J Chem Inf Model 52(6):1621–1636
14. Westergren J, Lindfors L, Höglund T, Lüder K, Nordholm S, Kjellander R (2007) In silico
prediction of drug solubility: 1. Free energy of hydration. J Phys Chem 111(7):1872–1882
15. Rossi Sebastiano M, Doak BC, Backlund M, Poongavanam V, Over B, Ermondi G, Caron G,
Matsson P, Kihlberg J (2018) Impact of dynamically exposed polarity on permeability and
solubility of chameleonic drugs beyond the rule of 5. J Med Chem 61(9):4189–4202
16. Wan J, Zhang L, Yang GF, Zhan CG (2004) Quantitative structure-activity relationship for
cyclic imide derivatives of protoporphyrinogen oxidase inhibitors: a study of quantum
chemical descriptors from density functional theory. J Chem Inf Comput Sci 44:20
17. Hopfinger AJ, Pearlstein RA (1984) Molecular mechanics force-field parameterization
procedures. J Comput Chem 5(5):486–99.99–2105
18. Kollman PA, Massova I, Reyes C, Kuhn B, Huo SH, Chong L, Lee M, Lee T, Duan Y,
Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating
structures and free energies of complex molecules: Combining molecular mechanics and
continuum models. Acc Chem Res 33:889–897
19. Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate
ligand-binding affinities. Expert Opin Drug Discov 10:449–461
20. Wang W, Donini O, Reyes CM, Kollman PA (2001) Biomolecular simulations: Recent
developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein,
and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 30:211–243
21. Massova I, Kollman PA (2000) Combined molecular mechanical and continuum solvent
approach (MM-PBSA/GBSA) to predict ligand binding. Perspect Drug Discov 18:113–135
22. Wang C, Greene DA, Xiao L, Qi R, Luo R (2018) Recent developments and applications of
the MMPBSA method. Front Mol Biosci 10(4):87
23. Wang J, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the
binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to
HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc 123(22):5221–5230
24. Meng XY, Zhang HX, Mezei M, Cui M (2011) Molecular docking: a powerful approach for
structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–157
25. Jain AN (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7:407–
420
26. Stahl M, Rarey M (2001) Detailed analysis of scoring functions for virtual screening. J Med
Chem 44:1035–1042
244
N. A. Murugan et al.