18. Carbonell P, Trosset J-Y (2014) Overcoming drug resistance through in silico prediction.
Drug Discov Today Technol 11:101–107
19. Hao G-F, Yang G-F, Zhan C-G (2012) Structure-based methods for predicting target
mutation-induced drug resistance and rational drug design to overcome the problem. Drug
Discov Today 17(19):1121–1126
20. Martis EAF, Joseph B, Gupta SP, Coutinho EC, Hdoufane I, Bjij I, Cherqaoui D (2017)
Flexibility of important HIV-1 targets and in silico design of anti-HIV drugs. Curr Chem
Biol 12(1):23–39
21. Chandrika B-R, Subramanian J, Sharma SD (2009) Managing protein flexibility in docking
and its applications. Drug Discov Today 14(7):394–400
22. Coupez B, Lewis R (2006) Docking and scoring-theoretically easy, practically impossible?
Curr Med Chem 13(25):2995–3003
23. Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility.
J Mol Biol 385(2):381–392
24. Lin J-H (2011) Accommodating protein flexibility for structure-based drug design. Curr Top
Med Chem 11(2):171–178
25. Mohan V, Gibbs AC, Cummings MD, Jaeger EP, DesJarlais RL (2005) Docking: successes
and challenges. Curr Pharm Des 11(3):323–333
26. van Gunsteren WF (1988) The role of computer simulation techniques in protein
engineering. Protein Eng 2(1):5–13
27. Hansson T, Oostenbrink C, van Gunsteren WF (2002) Molecular dynamics simulations.
Curr Opin Struct Biol 12(2):190–196
28. Binder K, Horbach J, Kob W, Paul W, Varnik F (2004) Molecular dynamics simulations.
J Phys Condens Matter 16:S429
29. Pissurlenkar RR, Shaikh MS, Iyer RP, Coutinho EC (2009) Molecular mechanics force
fields and their applications in drug design. AntiInfect Agents Med Chem 8(2):128–150
30. Anderson JA, Lorenz CD, Travesset A (2008) General purpose molecular dynamics
simulations fully implemented on graphics processing units. J Comput Phys 227(10):5342–
5359
31. Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC (2012) Routine
microsecond molecular dynamics simulations with AMBER on GPUs. 1. generalized born.
J Chem Theory Comput 8(5):1542–1555
32. Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC (2013) Routine microsecond
molecular dynamics simulations with AMBER on GPUs. 2. explicit solvent particle mesh
Ewald. J Chem Theory Comput 9(9):3878–3888
33. Beberg AL, Ensign DL, Jayachandran G, Khaliq S, Pande VS (2009) Folding@ home:
lessons from eight years of volunteer distributed computing. In: IEEE international
symposium on parallel & distributed processing, 2009. IPDPS 2009. IEEE
34. Larson SM, Snow CD, Shirts M, Pande VS (2009) Folding@ Home and Genome@ Home:
Using distributed computing to tackle previously intractable problems in computational
biology. DOI: arXiv preprint arXiv:0901.0866
35. Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature
molecular dynamics. Biopolymers 29(14):1847–1862
36. Earl DJ, Deem MW (2005) Parallel tempering: theory, applications, and new perspectives.
Phys Chem Chem Phys 7(23):3910–3916
37. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein
folding. Chem Phys Lett 314(1):141–151
38. Huber T, Torda AE, van Gunsteren WF (1994) Local elevation: a method for improving the
searching properties of molecular dynamics simulation. J Comput Aided Mol Des 8(6):695–
708
39. Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci USA 99
(20):12562–12566
20
E. A. F. Martis and E. C. Coutinho
Drug Discov Today Technol 11:101–107
19. Hao G-F, Yang G-F, Zhan C-G (2012) Structure-based methods for predicting target
mutation-induced drug resistance and rational drug design to overcome the problem. Drug
Discov Today 17(19):1121–1126
20. Martis EAF, Joseph B, Gupta SP, Coutinho EC, Hdoufane I, Bjij I, Cherqaoui D (2017)
Flexibility of important HIV-1 targets and in silico design of anti-HIV drugs. Curr Chem
Biol 12(1):23–39
21. Chandrika B-R, Subramanian J, Sharma SD (2009) Managing protein flexibility in docking
and its applications. Drug Discov Today 14(7):394–400
22. Coupez B, Lewis R (2006) Docking and scoring-theoretically easy, practically impossible?
Curr Med Chem 13(25):2995–3003
23. Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility.
J Mol Biol 385(2):381–392
24. Lin J-H (2011) Accommodating protein flexibility for structure-based drug design. Curr Top
Med Chem 11(2):171–178
25. Mohan V, Gibbs AC, Cummings MD, Jaeger EP, DesJarlais RL (2005) Docking: successes
and challenges. Curr Pharm Des 11(3):323–333
26. van Gunsteren WF (1988) The role of computer simulation techniques in protein
engineering. Protein Eng 2(1):5–13
27. Hansson T, Oostenbrink C, van Gunsteren WF (2002) Molecular dynamics simulations.
Curr Opin Struct Biol 12(2):190–196
28. Binder K, Horbach J, Kob W, Paul W, Varnik F (2004) Molecular dynamics simulations.
J Phys Condens Matter 16:S429
29. Pissurlenkar RR, Shaikh MS, Iyer RP, Coutinho EC (2009) Molecular mechanics force
fields and their applications in drug design. AntiInfect Agents Med Chem 8(2):128–150
30. Anderson JA, Lorenz CD, Travesset A (2008) General purpose molecular dynamics
simulations fully implemented on graphics processing units. J Comput Phys 227(10):5342–
5359
31. Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC (2012) Routine
microsecond molecular dynamics simulations with AMBER on GPUs. 1. generalized born.
J Chem Theory Comput 8(5):1542–1555
32. Salomon-Ferrer R, Götz AW, Poole D, Le Grand S, Walker RC (2013) Routine microsecond
molecular dynamics simulations with AMBER on GPUs. 2. explicit solvent particle mesh
Ewald. J Chem Theory Comput 9(9):3878–3888
33. Beberg AL, Ensign DL, Jayachandran G, Khaliq S, Pande VS (2009) Folding@ home:
lessons from eight years of volunteer distributed computing. In: IEEE international
symposium on parallel & distributed processing, 2009. IPDPS 2009. IEEE
34. Larson SM, Snow CD, Shirts M, Pande VS (2009) Folding@ Home and Genome@ Home:
Using distributed computing to tackle previously intractable problems in computational
biology. DOI: arXiv preprint arXiv:0901.0866
35. Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature
molecular dynamics. Biopolymers 29(14):1847–1862
36. Earl DJ, Deem MW (2005) Parallel tempering: theory, applications, and new perspectives.
Phys Chem Chem Phys 7(23):3910–3916
37. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein
folding. Chem Phys Lett 314(1):141–151
38. Huber T, Torda AE, van Gunsteren WF (1994) Local elevation: a method for improving the
searching properties of molecular dynamics simulation. J Comput Aided Mol Des 8(6):695–
708
39. Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci USA 99
(20):12562–12566
20
E. A. F. Martis and E. C. Coutinho