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90. Daura X, van Gunsteren WF, Mark AE (1999) Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins: Str, Funct, Genet 34 (3):269–280.
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93. Ben Nasr N, Guillemain H, Lagarde N, Zagury J-F, Montes M (2013) Multiple structures
for virtual ligand screening: defining binding site properties-based criteria to optimize the
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94. Sotriffer CA, Dramburg I (2005) “In situ cross-docking” to simultaneously address multiple
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95. Huang S-Y, Zou X (2007) Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins: Str, Funct, Bioinform 66(2):399–
421. doi:10.1002/prot.21214
96. Bottegoni G, Kufareva I, Totrov M, Abagyan R (2009) Four-dimensional docking: a fast and
accurate account of discrete receptor flexibility in ligand docking. J Med Chem 52(2):397–
406. doi:10.1021/jm8009958
97. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach
to macromolecule-ligand interactions. J Mol Biol 161(2):269–288. doi:10.1016/00222836(82)90153-x
98. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Rev Drug Discov 3(11):935–949.
doi:10.1038/nrd1549
99. Jorgensen WL (2004) The many roles of computation in drug discovery. Science
303(5665):1813–1818. doi:10.1126/science.1096361
100. Rognan D (2011) Docking methods for virtual screening: principles and recent advances. In:
Sotriffer C (ed) Virtual screening: principals, challenges, and practical guidelines, vol 82.
Wiley, Weinheim, pp 153–176
101. Henzler AM, Rarey M (2011) Protein flexibility in structure-based virtual screening: from
models to algorithms. In: Sotriffer C (ed) Virtual screening: principals, challenges, and practical guidelines, vol 82. Wiley, Weinheim, pp 223–244
102. Carlson HA, Dunbar JB Jr (2011) A call to arms: what you can do for computational drug
discovery. J Chem Inf Model 51(9):2025–2026. doi:10.1021/ci200398g
103. Warren GL, Andrews CW, Capelli A-M, Clarke B, LaLonde J, Lambert MH, Lindvall
M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head
MS (2006) A critical assessment of docking programs and scoring functions. J Med Chem
49(20):5912–5931. doi:10.1021/jm050362n
104. Perola E, Charifson PS (2004) Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem 47(10):2499–
2510. doi:10.1021/jm030563w
105. Gohlke H, Hendlich M, Klebe G (2000) Predicting binding modes, binding affinities and
‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function. Perspec
Drug Discov Des 20(1):115–144. doi:10.1023/a:1008781006867
106. Velec HFG, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native
ligand poses and better affinity prediction. J Med Chem 48(20):6296–6303. doi:10.1021/
jm050436v
S. von Grafenstein et al.
89. Shao JY, Tanner SW, Thompson N, Cheatham TE (2007) Clustering molecular dynamics
trajectories: 1. characterizing the performance of different clustering algorithms. J Chem
Theory Comput 3(6):2312–2334. doi:10.1021/ct700119m
90. Daura X, van Gunsteren WF, Mark AE (1999) Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations. Proteins: Str, Funct, Genet 34 (3):269–280.
doi:10.1002/(sici)1097-0134(19990215)34:3<269::aid-prot1>3.0.co;2-3
91. Durrant JD, Hall L, Swift RV, Landon M, Schnaufer A, Amaro RE (2010) Novel naphthalene-based inhibitors of trypanosoma brucei RNA editing ligase 1. PloS Neglect Trop D
4(8):e803 doi:10.1371/journal.pntd.0000803
92. Damm-Ganamet KL, Smith RD, Dunbar JB, Stuckey JA, Carlson HA (2013) CSAR benchmark exercise 2011–2012: evaluation of results from docking and relative ranking of blinded
congeneric series. J Chem Inf Model. doi:10.1021/ci400025f
93. Ben Nasr N, Guillemain H, Lagarde N, Zagury J-F, Montes M (2013) Multiple structures
for virtual ligand screening: defining binding site properties-based criteria to optimize the
selection of the query. J Chem Inf Model 53(2):293–311. doi:10.1021/ci3004557
94. Sotriffer CA, Dramburg I (2005) “In situ cross-docking” to simultaneously address multiple
targets. J Med Chem 48(9):3122–3125. doi:10.1021/jm050075j
95. Huang S-Y, Zou X (2007) Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins: Str, Funct, Bioinform 66(2):399–
421. doi:10.1002/prot.21214
96. Bottegoni G, Kufareva I, Totrov M, Abagyan R (2009) Four-dimensional docking: a fast and
accurate account of discrete receptor flexibility in ligand docking. J Med Chem 52(2):397–
406. doi:10.1021/jm8009958
97. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach
to macromolecule-ligand interactions. J Mol Biol 161(2):269–288. doi:10.1016/00222836(82)90153-x
98. Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nature Rev Drug Discov 3(11):935–949.
doi:10.1038/nrd1549
99. Jorgensen WL (2004) The many roles of computation in drug discovery. Science
303(5665):1813–1818. doi:10.1126/science.1096361
100. Rognan D (2011) Docking methods for virtual screening: principles and recent advances. In:
Sotriffer C (ed) Virtual screening: principals, challenges, and practical guidelines, vol 82.
Wiley, Weinheim, pp 153–176
101. Henzler AM, Rarey M (2011) Protein flexibility in structure-based virtual screening: from
models to algorithms. In: Sotriffer C (ed) Virtual screening: principals, challenges, and practical guidelines, vol 82. Wiley, Weinheim, pp 223–244
102. Carlson HA, Dunbar JB Jr (2011) A call to arms: what you can do for computational drug
discovery. J Chem Inf Model 51(9):2025–2026. doi:10.1021/ci200398g
103. Warren GL, Andrews CW, Capelli A-M, Clarke B, LaLonde J, Lambert MH, Lindvall
M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head
MS (2006) A critical assessment of docking programs and scoring functions. J Med Chem
49(20):5912–5931. doi:10.1021/jm050362n
104. Perola E, Charifson PS (2004) Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem 47(10):2499–
2510. doi:10.1021/jm030563w
105. Gohlke H, Hendlich M, Klebe G (2000) Predicting binding modes, binding affinities and
‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function. Perspec
Drug Discov Des 20(1):115–144. doi:10.1023/a:1008781006867
106. Velec HFG, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native
ligand poses and better affinity prediction. J Med Chem 48(20):6296–6303. doi:10.1021/
jm050436v