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273. Lin JH, Lu AYH (1997) Role of pharmacokinetics and metabolism in drug discovery and
development. Pharmacol Rev 49:403–449
274. Gallo JM (2010) Pharmacokinetic/pharmacodynamic-driven drug development. Mt Sinai J
Med A J Transl Pers Med 77:381–388. https://doi.org/10.1002/msj.20193
275. Alavijeh MS, Chishty M, Qaiser MZ, Palmer AM (2005) Drug metabolism and
pharmacokinetics, the blood-brain barrier, and central nervous system drug discovery.
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276. Altshuler J, Flanagan A, Guy P et al (2001) A revolution in R&D: how genomics and
genetics are transforming the biopharmaceutical industry. Boston Consulting Group, Boston
174
S. K. Panday and I. Ghosh
determination of relative free energy by computer simulation. J Am Chem Soc 107:7793–
7794. https://doi.org/10.1021/ja00311a112
257. Bash P, Singh U, Langridge R, Kollman P (1987) Free energy calculations by computer
simulation. Science 236(80):564–568. https://doi.org/10.1126/science.3576184
258. Kollman P (1993) Free energy calculations: applications to chemical and biochemical
phenomena. Chem Rev 93:2395–2417. https://doi.org/10.1021/cr00023a004
259. Jorgensen WL (1989) Free energy calculations: a breakthrough for modeling organic
chemistry in solution. Acc Chem Res 22:184–189. https://doi.org/10.1021/ar00161a004
260. Aqvist J, Medina C, Samuelsson JE (1994) A new method for predicting binding affinity in
computer-aided drug design. Protein Eng 7:385–391
261. Lee FS, Chu ZT, Bolger MB, Warshel A (1992) Calculations of antibody-antigen
interactions: microscopic and semi-microscopic evaluation of the free energies of binding of
phosphorylcholine analogs to McPC603. Protein Eng 5:215–228. https://doi.org/10.1093/
protein/5.3.215
262. Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions.
J Chem Phys 69:1352. https://doi.org/10.1063/1.436761
263. Adcock SA, McCammon JA (2006) Molecular dynamics: survey of methods for simulating
the activity of proteins. Chem Rev 106:1589–1615. https://doi.org/10.1021/cr040426m
264. Bek S, Jakobsson E (1994) Brownian dynamics study of a multiply-occupied cation channel:
application to understanding permeation in potassium channels. Biophys J 66:1028–1038.
https://doi.org/10.1016/s0006-3495(94)80884-7
265. Sines J, Allison S, McCammon JA (1990) Brownian dynamics simulation of the
superoxide-superoxide dismutase reaction: iron and manganese enzymes. J Phys Chem
94:959–961
266. Northrup SH, Erickson HP (1992) Kinetics of protein–protein association explained by
Brownian dynamics computer simulation. Proc Natl Acad Sci U S A 89:3338–3342
267. Kozack RE, Subramaniam S (1993) Brownian dynamics simulations of molecular
recognition in an antibody-antigen system. Protein Sci 2:915–926. https://doi.org/10.1002/
pro.5560020605
268. Gabdoulline RR, Wade RC (1997) Simulation of the diffusional association of barnase and
barstar. Biophys J 72:1917–1929. https://doi.org/10.1016/s0006-3495(97)78838-6
269. Gabdoulline RR, Wade RC (1998) Brownian dynamics simulation of protein–protein
diffusional encounter. Methods 14:329–341. https://doi.org/10.1006/meth.1998.0588
270. Deganutti G, Cuzzolin A, Ciancetta A, Moro S (2015) Understanding allosteric interactions
in G protein-coupled receptors using supervised molecular dynamics: a prototype study
analysing the human A3 adenosine receptor positive allosteric modulator LUF6000. Bioorg
Med Chem 23:4065–4071. https://doi.org/10.1016/j.bmc.2015.03.039
271. Cuzzolin A, Sturlese M, Deganutti G et al (2016) Deciphering the complexity of
ligand-protein recognition pathways using supervised molecular dynamics (SuMD) simulations. J Chem Inf Model 56:687–705. https://doi.org/10.1021/acs.jcim.5b00702
272. Paoletta S, Sabbadin D, von Kügelgen I et al (2015) Modeling ligand recognition at the
P2Y12 receptor in light of X-ray structural information. J Comput Aided Mol Des 29:737–
756. https://doi.org/10.1007/s10822-015-9858-z
273. Lin JH, Lu AYH (1997) Role of pharmacokinetics and metabolism in drug discovery and
development. Pharmacol Rev 49:403–449
274. Gallo JM (2010) Pharmacokinetic/pharmacodynamic-driven drug development. Mt Sinai J
Med A J Transl Pers Med 77:381–388. https://doi.org/10.1002/msj.20193
275. Alavijeh MS, Chishty M, Qaiser MZ, Palmer AM (2005) Drug metabolism and
pharmacokinetics, the blood-brain barrier, and central nervous system drug discovery.
NeuroRx 2:554–571. https://doi.org/10.1602/neurorx.2.4.554
276. Altshuler J, Flanagan A, Guy P et al (2001) A revolution in R&D: how genomics and
genetics are transforming the biopharmaceutical industry. Boston Consulting Group, Boston
174
S. K. Panday and I. Ghosh