40. Belubbi AV, Martis EAF (2017) Advanced techniques in bimolecular simulations. In:
Bharati SK (ed) Handbook of research on medicinal chemistry, Apple Academic Press (in
Press)
41. Berne BJ, Straub JE (1997) Novel methods of sampling phase space in the simulation of
biological systems. Curr Opin Struct Biol 7(2):181–189
42. Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: a
promising and efficient simulation method for biomolecules. J Chem Phys 120(24):11919–
11929
43. Lei H, Duan Y (2007) Improved sampling methods for molecular simulation. Curr Opin
Struct Biol 17(2):187–191
44. Zuckerman DM (2011) Equilibrium sampling in biomolecular simulation. Annu Rev
Biophys 40:41–62
45. Böhm HJ, Klebe G (1996) What can we learn from molecular recognition in protein-ligand
complexes for the design of new drugs? Angew Chem Int Ed 35(22):2588–2614
46. Homans S (2007) Dynamics and thermodynamics of ligand–protein interactions. In: Peters T
(ed) Bioactive Conformation I. Springer, Berlin, Heidelberg, pp 51–82
47. Whitesides GM, Krishnamurthy VM (2005) Designing ligands to bind proteins. Q Rev
Biophys 38(4):385–396
48. Bronowska, A. K. (2011). Thermodynamics of ligand-protein interactions: implications for
molecular design. In: Moreno-Pirajan JC (ed) Thermodynamics—Interaction Studies—
Solids, Liquids and Gases. INTECH Open Access Publisher, Croatia, pp 1–48
49. Datar PA, Khedkar SA, Malde AK, Coutinho EC (2006) Comparative residue interaction
analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site
residues with ligands. J Comput Aided Mol Des 20(6):343–360
50. Martis EA, Chandarana RC, Shaikh MS, Ambre PK, D’Souza JS, Iyer KR, Coutinho EC,
Nandan SR, Pissurlenkar RR (2015) Quantifying ligand–receptor interactions for
gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease.
J Biomol Struct Dyn 33(5):1107–1125
51. Verma J, Khedkar VM, Prabhu AS, Khedkar SA, Malde AK, Coutinho EC (2008) A
comprehensive analysis of the thermodynamic events involved in ligand–receptor binding
using CoRIA and its variants. J Comput Aided Mol Des 22(2):91–104
52. Wang T, Wade RC (2001) Comparative binding energy (COMBINE) analysis of influenza
neuraminidase—inhibitor complexes. J Med Chem 44(6):961–971
53. van Gunsteren WF (1993) Molecular dynamics studies of proteins. Curr Opin Struct Biol 3
(2):277–281
54. Mennucci B (2012) Polarizable continuum model. Wiley Interdisc Rev Comput Mol Sci 2
(3):386–404
55. Klamt A, Schuurmann G (1993) COSMO: a new approach to dielectric screening in solvents
with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans
2(5):799–805
56. Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute
electron density and on a continuum model of the solvent defined by the bulk dielectric
constant and atomic surface tensions. J Phy Chem 113(18):6378–6396
57. Hou T, Wang J, Li Y, Wang W (2010) Assessing the performance of the MM/PBSA and
MM/GBSA methods. 1. the accuracy of binding free energy calculations based on molecular
dynamics simulations. J Chem Inf Model 51(1):69–82
58. Hou T, Wang J, Li Y, Wang W (2011) Assessing the performance of the molecular
mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born
surface area methods. II. The accuracy of ranking poses generated from docking. J Comput
Chem 32(5):866–877
59. Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y, Hou T (2014) Assessing the
performance of MM/PBSA and MM/GBSA methods. 5. improved docking performance
using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Phys Chem
Chem Phys 16(40):22035–22045
Free Energy-Based Methods to Understand Drug Resistance Mutations
21
Bharati SK (ed) Handbook of research on medicinal chemistry, Apple Academic Press (in
Press)
41. Berne BJ, Straub JE (1997) Novel methods of sampling phase space in the simulation of
biological systems. Curr Opin Struct Biol 7(2):181–189
42. Hamelberg D, Mongan J, McCammon JA (2004) Accelerated molecular dynamics: a
promising and efficient simulation method for biomolecules. J Chem Phys 120(24):11919–
11929
43. Lei H, Duan Y (2007) Improved sampling methods for molecular simulation. Curr Opin
Struct Biol 17(2):187–191
44. Zuckerman DM (2011) Equilibrium sampling in biomolecular simulation. Annu Rev
Biophys 40:41–62
45. Böhm HJ, Klebe G (1996) What can we learn from molecular recognition in protein-ligand
complexes for the design of new drugs? Angew Chem Int Ed 35(22):2588–2614
46. Homans S (2007) Dynamics and thermodynamics of ligand–protein interactions. In: Peters T
(ed) Bioactive Conformation I. Springer, Berlin, Heidelberg, pp 51–82
47. Whitesides GM, Krishnamurthy VM (2005) Designing ligands to bind proteins. Q Rev
Biophys 38(4):385–396
48. Bronowska, A. K. (2011). Thermodynamics of ligand-protein interactions: implications for
molecular design. In: Moreno-Pirajan JC (ed) Thermodynamics—Interaction Studies—
Solids, Liquids and Gases. INTECH Open Access Publisher, Croatia, pp 1–48
49. Datar PA, Khedkar SA, Malde AK, Coutinho EC (2006) Comparative residue interaction
analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site
residues with ligands. J Comput Aided Mol Des 20(6):343–360
50. Martis EA, Chandarana RC, Shaikh MS, Ambre PK, D’Souza JS, Iyer KR, Coutinho EC,
Nandan SR, Pissurlenkar RR (2015) Quantifying ligand–receptor interactions for
gorge-spanning acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease.
J Biomol Struct Dyn 33(5):1107–1125
51. Verma J, Khedkar VM, Prabhu AS, Khedkar SA, Malde AK, Coutinho EC (2008) A
comprehensive analysis of the thermodynamic events involved in ligand–receptor binding
using CoRIA and its variants. J Comput Aided Mol Des 22(2):91–104
52. Wang T, Wade RC (2001) Comparative binding energy (COMBINE) analysis of influenza
neuraminidase—inhibitor complexes. J Med Chem 44(6):961–971
53. van Gunsteren WF (1993) Molecular dynamics studies of proteins. Curr Opin Struct Biol 3
(2):277–281
54. Mennucci B (2012) Polarizable continuum model. Wiley Interdisc Rev Comput Mol Sci 2
(3):386–404
55. Klamt A, Schuurmann G (1993) COSMO: a new approach to dielectric screening in solvents
with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans
2(5):799–805
56. Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute
electron density and on a continuum model of the solvent defined by the bulk dielectric
constant and atomic surface tensions. J Phy Chem 113(18):6378–6396
57. Hou T, Wang J, Li Y, Wang W (2010) Assessing the performance of the MM/PBSA and
MM/GBSA methods. 1. the accuracy of binding free energy calculations based on molecular
dynamics simulations. J Chem Inf Model 51(1):69–82
58. Hou T, Wang J, Li Y, Wang W (2011) Assessing the performance of the molecular
mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born
surface area methods. II. The accuracy of ranking poses generated from docking. J Comput
Chem 32(5):866–877
59. Sun H, Li Y, Shen M, Tian S, Xu L, Pan P, Guan Y, Hou T (2014) Assessing the
performance of MM/PBSA and MM/GBSA methods. 5. improved docking performance
using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. Phys Chem
Chem Phys 16(40):22035–22045
Free Energy-Based Methods to Understand Drug Resistance Mutations
21