535
15 (How to) Profit from Molecular Dynamics-based Ensemble Docking
69. Rueda M, Bottegoni G, Abagyan R (2009) Consistent improvement of cross-docking results
using binding site ensembles generated with elastic network normal modes. J Chem Inf Model 49(3):716–725. doi:10.1021/ci8003732
70. Tran HT, Zhang S (2011) Accurate prediction of the bound form of the akt pleckstrin homology domain using normal mode analysis to explore structural flexibility. J Chem Inf Model
51(9):2352–2360. doi:10.1021/ci2001742
71. Cavasotto CN, Abagyan RA (2004) Protein flexibility in ligand docking and virtual screening
to protein kinases. J Mol Biol 337(1):209–225. doi:10.1016/j.jmb.2004.01.003
72. Davis IW, Baker D (2009) ROSETTALIGAND docking with full ligand and receptor flexibility. J Mol Biol 385(2):381–392. doi:10.1016/j.jmb.2008.11.010
73. Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full
side-chain flexibility. Proteins: Str, Funct, Bioinform 65(3):538–548. doi:10.1002/prot.21086
74. Alonso H, Bliznyuk AA, Gready JE (2006) Combining docking and molecular dynamic simulations in drug design. Med Res Rev 26(5):531–568. doi:10.1002/med.20067
75. Knegtel RMA, Kuntz ID, Oshiro CM (1997) Molecular docking to ensembles of protein
structures. J Mol Biol 266(2):424–440. doi:10.1006/jmbi.1996.0776
76. Polgar T, Keseru GM (2006) Ensemble docking into flexible active sites. Critical evaluation
of flexE against JNK-3 and beta-secretase. J Chem Inf Model 46(4):1795–1805. doi:10.1021/
ci050412x
77. Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS (2002) Automated docking to
multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins: Str, Funct, Genet 46(1):34–40. doi:10.1002/prot.10028
78. Broughton HB (2000) A method for including protein flexibility in protein-ligand docking:
improving tools for database mining and virtual screening. J Mol Graphics Modell 18(3):247–
257. doi:10.1016/s1093-3263(00)00036-x
79. Cosconati S, Marinelli L, Di Leva FS, La Pietra V, De Simone A, Mancini F, Andrisano
V, Novellino E, Goodsell DS, Olson AJ (2012) Protein flexibility in virtual screening: the
BACE-1 case study. J Chem Inf Model 52(10):2697–2704. doi:10.1021/ci300390h
80. Lin JH, Perryman AL, Schames JR, McCammon JA (2003) The relaxed complex method:
accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68(1):47–62. doi:10.1002/bip.10218
81. Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni HH, McCammon JA (2004) Discovery of a novel binding trench in HIV integrase. J Med Chem 47(8):1879–1881. doi:10.1021/
jm0341913
82. Perryman AL, Lin J-H, McCammon JA (2006) Optimization and computational evaluation
of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1
protease: an application of the relaxed complex method of structure-based drug design. Chem
Biol Drug Des 67(5):336–345. doi:10.1111/j.1747-0285.2006.00382.x
83. Trott O, Olson AJ (2010) Software news and update autodock vina: improving the speed and
accuracy of docking with a new scoring function, efficient optimization, and multithreading.
J Comput Chem 31(2):455–461. doi:10.1002/jcc.21334
84. Amaro RE, Baron R, McCammon JA (2008) An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput-Aided Mol Des 22(9):693–705.
doi:10.1007/s10822-007-9159-2
85. Sivanesan D, Rajnarayanan RV, Doherty J, Pattabiraman N (2005) In-silico screening using
flexible ligand binding pockets: a molecular dynamics-based approach. J Comput-Aided Mol
Des 19(4):213–228. doi:10.1007/s10822-005-4788-9
86. Paulsen JL, Anderson AC (2009) Scoring ensembles of docked protein: ligand interactions
for virtual lead optimization. J Chem Inf Model 49(12):2813–2819. doi:10.1021/ci9003078
87. Korb O, Olsson TSG, Bowden SJ, Hall RJ, Verdonk ML, Liebeschuetz JW, Cole JC (2012)
Potential and limitations of ensemble docking. J Chem Inf Model 52(5):1262–1274.
doi:10.1021/ci2005934
88. Nichols SE, Swift RV, Amaro RE (2012) Rational prediction with molecular dynamics for hit
identification. Curr Top Med Chem 12(18):2002–2012
15 (How to) Profit from Molecular Dynamics-based Ensemble Docking
69. Rueda M, Bottegoni G, Abagyan R (2009) Consistent improvement of cross-docking results
using binding site ensembles generated with elastic network normal modes. J Chem Inf Model 49(3):716–725. doi:10.1021/ci8003732
70. Tran HT, Zhang S (2011) Accurate prediction of the bound form of the akt pleckstrin homology domain using normal mode analysis to explore structural flexibility. J Chem Inf Model
51(9):2352–2360. doi:10.1021/ci2001742
71. Cavasotto CN, Abagyan RA (2004) Protein flexibility in ligand docking and virtual screening
to protein kinases. J Mol Biol 337(1):209–225. doi:10.1016/j.jmb.2004.01.003
72. Davis IW, Baker D (2009) ROSETTALIGAND docking with full ligand and receptor flexibility. J Mol Biol 385(2):381–392. doi:10.1016/j.jmb.2008.11.010
73. Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full
side-chain flexibility. Proteins: Str, Funct, Bioinform 65(3):538–548. doi:10.1002/prot.21086
74. Alonso H, Bliznyuk AA, Gready JE (2006) Combining docking and molecular dynamic simulations in drug design. Med Res Rev 26(5):531–568. doi:10.1002/med.20067
75. Knegtel RMA, Kuntz ID, Oshiro CM (1997) Molecular docking to ensembles of protein
structures. J Mol Biol 266(2):424–440. doi:10.1006/jmbi.1996.0776
76. Polgar T, Keseru GM (2006) Ensemble docking into flexible active sites. Critical evaluation
of flexE against JNK-3 and beta-secretase. J Chem Inf Model 46(4):1795–1805. doi:10.1021/
ci050412x
77. Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS (2002) Automated docking to
multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins: Str, Funct, Genet 46(1):34–40. doi:10.1002/prot.10028
78. Broughton HB (2000) A method for including protein flexibility in protein-ligand docking:
improving tools for database mining and virtual screening. J Mol Graphics Modell 18(3):247–
257. doi:10.1016/s1093-3263(00)00036-x
79. Cosconati S, Marinelli L, Di Leva FS, La Pietra V, De Simone A, Mancini F, Andrisano
V, Novellino E, Goodsell DS, Olson AJ (2012) Protein flexibility in virtual screening: the
BACE-1 case study. J Chem Inf Model 52(10):2697–2704. doi:10.1021/ci300390h
80. Lin JH, Perryman AL, Schames JR, McCammon JA (2003) The relaxed complex method:
accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68(1):47–62. doi:10.1002/bip.10218
81. Schames JR, Henchman RH, Siegel JS, Sotriffer CA, Ni HH, McCammon JA (2004) Discovery of a novel binding trench in HIV integrase. J Med Chem 47(8):1879–1881. doi:10.1021/
jm0341913
82. Perryman AL, Lin J-H, McCammon JA (2006) Optimization and computational evaluation
of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1
protease: an application of the relaxed complex method of structure-based drug design. Chem
Biol Drug Des 67(5):336–345. doi:10.1111/j.1747-0285.2006.00382.x
83. Trott O, Olson AJ (2010) Software news and update autodock vina: improving the speed and
accuracy of docking with a new scoring function, efficient optimization, and multithreading.
J Comput Chem 31(2):455–461. doi:10.1002/jcc.21334
84. Amaro RE, Baron R, McCammon JA (2008) An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput-Aided Mol Des 22(9):693–705.
doi:10.1007/s10822-007-9159-2
85. Sivanesan D, Rajnarayanan RV, Doherty J, Pattabiraman N (2005) In-silico screening using
flexible ligand binding pockets: a molecular dynamics-based approach. J Comput-Aided Mol
Des 19(4):213–228. doi:10.1007/s10822-005-4788-9
86. Paulsen JL, Anderson AC (2009) Scoring ensembles of docked protein: ligand interactions
for virtual lead optimization. J Chem Inf Model 49(12):2813–2819. doi:10.1021/ci9003078
87. Korb O, Olsson TSG, Bowden SJ, Hall RJ, Verdonk ML, Liebeschuetz JW, Cole JC (2012)
Potential and limitations of ensemble docking. J Chem Inf Model 52(5):1262–1274.
doi:10.1021/ci2005934
88. Nichols SE, Swift RV, Amaro RE (2012) Rational prediction with molecular dynamics for hit
identification. Curr Top Med Chem 12(18):2002–2012