메뉴 건너뛰기




Volumn 20, Issue 20, 2014, Pages 3338-3359

Methods for docking small molecules to macromolecules: A user's perspective. 1. The theory

Author keywords

Bridging water molecules; Docking algorithm; Protein flexibility; Scoring function; Structure based drug design; Virtual screening

Indexed keywords

LIGAND; PROTEIN; MACROMOLECULE; MOLECULAR LIBRARY;

EID: 84903745256     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/13816128113199990605     Document Type: Article
Times cited : (17)

References (161)
  • 1
    • 84889844714 scopus 로고    scopus 로고
    • In: Computer Applications in Pharmaceutical Research and Development. John Wiley & Sons, Inc
    • Kubinyi H. Success Stories of Computer-Aided Design. In: Computer Applications in Pharmaceutical Research and Development. John Wiley & Sons, Inc 2006; pp. 377-424.
    • (2006) Success Stories of Computer-Aided Design. , pp. 377-424
    • Kubinyi, H.1
  • 2
    • 73449113916 scopus 로고    scopus 로고
    • Modeling reality for optimal docking of small molecules to biological targets
    • Corbeil CR, Therrien E, Moitessier N. Modeling reality for optimal docking of small molecules to biological targets. Curr Computer-Aided Drug Des 2009; 5: 241-263.
    • (2009) Curr Computer-Aided Drug Des , vol.5 , pp. 241-263
    • Corbeil, C.R.1    Therrien, E.2    Moitessier, N.3
  • 3
    • 35348906680 scopus 로고    scopus 로고
    • DNA minor groove binders: An overview on molecular modeling and QSAR approaches
    • Lauria A, Montalbano A, Barraja P, Dattolo G, Almerico AM. DNA minor groove binders: An overview on molecular modeling and QSAR approaches. Curr Med Chem 2007; 14: 2136-60.
    • (2007) Curr Med Chem , vol.14 , pp. 2136-2160
    • Lauria, A.1    Montalbano, A.2    Barraja, P.3    Dattolo, G.4    Almerico, A.M.5
  • 4
    • 58149263185 scopus 로고    scopus 로고
    • Mycotoxin detection plays "cops and robbers": Cyclodextrin chemosensors as specialized police?
    • Cozzini P, Ingletto G, Singh R, Dall'Asta C. Mycotoxin detection plays "cops and robbers": Cyclodextrin chemosensors as specialized police? Int J Mol Sci 2008; 9: 2474-94.
    • (2008) Int J Mol Sci , vol.9 , pp. 2474-2494
    • Cozzini, P.1    Ingletto, G.2    Singh, R.3    Dall'Asta, C.4
  • 6
    • 76249106208 scopus 로고    scopus 로고
    • Let's not forget tautomers
    • Martin YC. Let's not forget tautomers. J Comput-Aided Mol Des 2009; 23: 693-704.
    • (2009) J Comput-Aided Mol Des , vol.23 , pp. 693-704
    • Martin, Y.C.1
  • 7
    • 79551571786 scopus 로고    scopus 로고
    • Predicting Novel Binding Modes of Agonists to beta Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations
    • Vanni S, Neri M, Tavernelli I, Rothlisberger U. Predicting Novel Binding Modes of Agonists to beta Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations. Plos Comput Biol 7(1): e1001053.
    • Plos Comput Biol , vol.7 , Issue.1
    • Vanni, S.1    Neri, M.2    Tavernelli, I.3    Rothlisberger, U.4
  • 8
    • 40349087133 scopus 로고    scopus 로고
    • Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
    • Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol 2008; 153: S7-S26
    • (2008) Br J Pharmacol , vol.153
    • Moitessier, N.1    Englebienne, P.2    Lee, D.3    Lawandi, J.4    Corbeil, C.R.5
  • 9
    • 44449103763 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 2. Development and application of FITTED 1.5 to the virtual screening of potential HCV polymerase inhibitors
    • Corbeil CR, Englebienne P, Yannopoulos CG, et al. Docking ligands into flexible and solvated macromolecules. 2. Development and application of FITTED 1.5 to the virtual screening of potential HCV polymerase inhibitors. J Chem Inf Model 2008; 48: 902-9.
    • (2008) J Chem Inf Model , vol.48 , pp. 902-909
    • Corbeil, C.R.1    Englebienne, P.2    Yannopoulos, C.G.3
  • 10
    • 13844312649 scopus 로고    scopus 로고
    • ZINC-A free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK. ZINC-A free database of commercially available compounds for virtual screening. J Chem Inf Model 2005; 45: 177-82.
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 11
    • 76149120388 scopus 로고    scopus 로고
    • Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
    • Trott O, Olson AJ. Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading. J Comp Chem 2010; 31: 455-61.
    • (2010) J Comp Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 12
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris GM, Goodsell DS, Halliday RS, et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem 1998; 19: 1639-62.
    • (1998) J Comp Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3
  • 13
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Sci 1998; 7: 938-50.
    • (1998) Protein Sci , vol.7 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 15
    • 34247197110 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0
    • Corbeil CR, Englebienne P, Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J Chem Inf Model 2007; 47: 435-49.
    • (2007) J Chem Inf Model , vol.47 , pp. 435-449
    • Corbeil, C.R.1    Englebienne, P.2    Moitessier, N.3
  • 16
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996; 261: 470-489.
    • (1996) J Mol Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 18
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004; 47: 1739-49.
    • (2004) J Med Chem , vol.47 , pp. 1739-1749
    • Friesner, R.A.1    Banks, J.L.2    Murphy, R.B.3
  • 19
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones G, Willett P, Glen RC. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 1995; 245: 43-53.
    • (1995) J Mol Biol , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 20
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997; 267: 727-748.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 21
    • 84986522918 scopus 로고
    • Icm-a New Method for Protein Modeling and Design-Applications to Docking and Structure Prediction from the Distorted Native Conformation
    • Abagyan R, Totrov M, Kuznetsov D. Icm-a New Method for Protein Modeling and Design-Applications to Docking and Structure Prediction from the Distorted Native Conformation. J Comp Chem 1994; 15: 488-506.
    • (1994) J Comp Chem , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 22
    • 0037434582 scopus 로고    scopus 로고
    • Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
    • Jain AN. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 2003; 46: 499-511.
    • (2003) J Med Chem , vol.46 , pp. 499-511
    • Jain, A.N.1
  • 23
    • 84865214371 scopus 로고    scopus 로고
    • Surflex-Dock: Docking benchmarks and realworld application
    • Spitzer R, Jain AN. Surflex-Dock: Docking benchmarks and realworld application. J Comput-Aided Mol Design 2012; 26: 687-99.
    • (2012) J Comput-Aided Mol Design , vol.26 , pp. 687-699
    • Spitzer, R.1    Jain, A.N.2
  • 25
    • 62449330667 scopus 로고    scopus 로고
    • Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
    • Korb O, Stutzle T, Exner TE. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS. J Chem Inf Model 2009; 49: 84-96.
    • (2009) J Chem Inf Model , vol.49 , pp. 84-96
    • Korb, O.1    Stutzle, T.2    Exner, T.E.3
  • 26
    • 0032190489 scopus 로고    scopus 로고
    • Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
    • Schnecke V, Swanson CA, Getzoff ED, Tainer JA, Kuhn LA. Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 1998; 33: 74-87.
    • (1998) Proteins , vol.33 , pp. 74-87
    • Schnecke, V.1    Swanson, C.A.2    Getzoff, E.D.3    Tainer, J.A.4    Kuhn, L.A.5
  • 28
    • 37249065124 scopus 로고    scopus 로고
    • Generating conformer ensembles using a multiobjective genetic algorithm
    • Vainio MJ, Johnson MS. Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model 2007; 47: 2462-74.
    • (2007) J Chem Inf Model , vol.47 , pp. 2462-2474
    • Vainio, M.J.1    Johnson, M.S.2
  • 31
    • 77954274184 scopus 로고    scopus 로고
    • Frog2: Efficient 3D conformation ensemble generator for small compounds
    • Miteva MA, Guyon F, Tuffery P. Frog2: Efficient 3D conformation ensemble generator for small compounds. Nucleic Acids Res 2010; 38: W622-7.
    • (2010) Nucleic Acids Res , vol.38
    • Miteva, M.A.1    Guyon, F.2    Tuffery, P.3
  • 33
    • 84855757480 scopus 로고    scopus 로고
    • 2013.08; Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7
    • Molecular Operating Environment (MOE), 2013.08; Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2013.
    • (2013) Molecular Operating Environment (MOE)
  • 34
    • 84861498479 scopus 로고    scopus 로고
    • Freely Available Conformer Generation Methods: How Good Are They?
    • Ebejer JP, Morris GM, Deane CM. Freely Available Conformer Generation Methods: How Good Are They? J Chem Inf Model 2012; 52: 1146-58.
    • (2012) J Chem Inf Model , vol.52 , pp. 1146-1158
    • Ebejer, J.P.1    Morris, G.M.2    Deane, C.M.3
  • 35
    • 77957899529 scopus 로고    scopus 로고
    • Advances and Challenges in Protein-Ligand Docking
    • Huang SY, Zou XQ. Advances and Challenges in Protein-Ligand Docking. Int J Mol Sci 2010; 11: 3016-34.
    • (2010) Int J Mol Sci , vol.11 , pp. 3016-3034
    • Huang, S.Y.1    Zou, X.Q.2
  • 36
    • 0028466540 scopus 로고
    • Comparison of automatic threedimensional model builders using 639 X-ray structures
    • Sadowski J, Gasteiger J, Klebe G. Comparison of automatic threedimensional model builders using 639 X-ray structures. J Chem Inf Comp Sci 1994; 34: 1000-8.
    • (1994) J Chem Inf Comp Sci , vol.34 , pp. 1000-1008
    • Sadowski, J.1    Gasteiger, J.2    Klebe, G.3
  • 37
    • 23844444239 scopus 로고    scopus 로고
    • Hierarchical docking of databases of multiple ligand conformations
    • Lorber DM, Shoichet BK. Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem 2005; 5: 739-49.
    • (2005) Curr Top Med Chem , vol.5 , pp. 739-749
    • Lorber, D.M.1    Shoichet, B.K.2
  • 38
    • 6344294057 scopus 로고    scopus 로고
    • FlexX-Scan: Fast, structure-based virtual screening
    • Schellhammer I, Rarey M. FlexX-Scan: fast, structure-based virtual screening. Proteins 2004; 57: 504-17.
    • (2004) Proteins , vol.57 , pp. 504-517
    • Schellhammer, I.1    Rarey, M.2
  • 39
    • 66149087635 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs
    • Corbeil CR, Moitessier N. Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs. J Chem Inf Model 2009; 49: 997-1009.
    • (2009) J Chem Inf Model , vol.49 , pp. 997-1009
    • Corbeil, C.R.1    Moitessier, N.2
  • 41
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility
    • Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. J Comp Chem 2009; 30: 2785-91.
    • (2009) J Comp Chem , vol.30 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3
  • 42
    • 26444586139 scopus 로고    scopus 로고
    • Modeling water molecules in protein-ligand docking using GOLD
    • Verdonk ML, Chessari G, Cole JC, et al. Modeling water molecules in protein-ligand docking using GOLD. J Med Chem 2005; 48: 6504-15.
    • (2005) J Med Chem , vol.48 , pp. 6504-6515
    • Verdonk, M.L.1    Chessari, G.2    Cole, J.C.3
  • 43
    • 33846630833 scopus 로고    scopus 로고
    • SODOCK: Swarm optimization for highly flexible protein-ligand docking
    • Chen HM, Liu BF, Huang HL, Hwang SF, Ho SY. SODOCK: Swarm optimization for highly flexible protein-ligand docking. J Comp Chem 2007; 28: 612-23.
    • (2007) J Comp Chem , vol.28 , pp. 612-623
    • Chen, H.M.1    Liu, B.F.2    Huang, H.L.3    Hwang, S.F.4    Ho, S.Y.5
  • 44
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
    • Murray CW, Baxter CA, Frenkel AD. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des 1999; 13: 547-62.
    • (1999) J Comput Aided Mol Des , vol.13 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 46
    • 84874310966 scopus 로고    scopus 로고
    • The application of quantum mechanics in structure-based drug design
    • Mucs, D, Bryce, RA The application of quantum mechanics in structure-based drug design. Exp Opin Drug Discov 2013; 8: 263-76.
    • (2013) Exp Opin Drug Discov , vol.8 , pp. 263-276
    • Mucs, D.1    Bryce, R.A.2
  • 47
    • 0029633186 scopus 로고
    • Amber, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules
    • Pearlman DA, Case DA, Caldwell JW, et al. Amber, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules. Comp Phys Comm 1995; 91: 1-41.
    • (1995) Comp Phys Comm , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3
  • 48
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge I, Martin YC. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 1999; 42: 791-804.
    • (1999) J Med Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 49
    • 0037046545 scopus 로고    scopus 로고
    • Docking into Knowledge-Based Potential Fields: A Comparative Evaluation of DrugScore
    • Sotriffer CA, Gohlke H, Klebe G. Docking into Knowledge-Based Potential Fields: A Comparative Evaluation of DrugScore. J Med Chem 2002; 45: 1967-70.
    • (2002) J Med Chem , vol.45 , pp. 1967-1970
    • Sotriffer, C.A.1    Gohlke, H.2    Klebe, G.3
  • 50
    • 26944499806 scopus 로고    scopus 로고
    • POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions
    • Antes I, Merkwirth C, Lengauer T. POEM: Parameter optimization using ensemble methods: Application to target specific scoring functions. J Chem Inf Model 2005; 45: 1291-302.
    • (2005) J Chem Inf Model , vol.45 , pp. 1291-1302
    • Antes, I.1    Merkwirth, C.2    Lengauer, T.3
  • 51
    • 33749266178 scopus 로고    scopus 로고
    • A Method for Induced-Fit Docking, Scoring, and Ranking of Flexible Ligands. Application to Peptidic and Pseudopeptidic beta-secretase (BACE 1) Inhibitors
    • Moitessier N, Therrien E, Hanessian S. A Method for Induced-Fit Docking, Scoring, and Ranking of Flexible Ligands. Application to Peptidic and Pseudopeptidic beta-secretase (BACE 1) Inhibitors. J Med Chem 2006; 49: 5885-94.
    • (2006) J Med Chem , vol.49 , pp. 5885-5894
    • Moitessier, N.1    Therrien, E.2    Hanessian, S.3
  • 52
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • Charifson PS, Corkery JJ, Murcko MA, Walters WP. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999; 42: 5100-9.
    • (1999) J Med Chem , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 54
    • 0038185582 scopus 로고    scopus 로고
    • Binding site characteristics in structurebased virtual screening: Evaluation of current docking tools
    • Schulz-Gasch T, Stahl M. Binding site characteristics in structurebased virtual screening: evaluation of current docking tools. J Mol Model 2003; 9: 47-57.
    • (2003) J Mol Model , vol.9 , pp. 47-57
    • Schulz-Gasch, T.1    Stahl, M.2
  • 55
    • 0001664118 scopus 로고    scopus 로고
    • A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments
    • Murphy RB, Philipp DM, Friesner RA. A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments. J Comp Chem 2000; 21: 1442-57.
    • (2000) J Comp Chem , vol.21 , pp. 1442-1457
    • Murphy, R.B.1    Philipp, D.M.2    Friesner, R.A.3
  • 56
    • 0001420061 scopus 로고    scopus 로고
    • Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide
    • Philipp DM, Friesner RA. Mixed ab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. J Comp Chem 1999; 20: 1468-94.
    • (1999) J Comp Chem , vol.20 , pp. 1468-1494
    • Philipp, D.M.1    Friesner, R.A.2
  • 57
    • 20344403522 scopus 로고    scopus 로고
    • Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach
    • Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach. J Comp Chem 2005; 26: 915-31.
    • (2005) J Comp Chem , vol.26 , pp. 915-931
    • Cho, A.E.1    Guallar, V.2    Berne, B.J.3    Friesner, R.4
  • 58
    • 77953325281 scopus 로고    scopus 로고
    • Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles
    • Abagyan R, Park SJ, Kufareva I. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput-Aided Mol Des 2010; 24: 459-71.
    • (2010) J Comput-Aided Mol Des , vol.24 , pp. 459-471
    • Abagyan, R.1    Park, S.J.2    Kufareva, I.3
  • 62
    • 77950207644 scopus 로고    scopus 로고
    • Tackling the challenges posed by target flexibility in drug design
    • Beier C, Zacharias M. Tackling the challenges posed by target flexibility in drug design. Exp Opin Drug Discov 2010; 5: 347-59.
    • (2010) Exp Opin Drug Discov , vol.5 , pp. 347-359
    • Beier, C.1    Zacharias, M.2
  • 63
    • 63149162777 scopus 로고    scopus 로고
    • Managing protein flexibility in docking and its applications
    • B-Rao C, Subramanian J, Sharma SD. Managing protein flexibility in docking and its applications. Drug Discov Today 2009; 14: 394-400.
    • (2009) Drug Discov Today , vol.14 , pp. 394-400
    • B-Rao, C.1    Subramanian, J.2    Sharma, S.D.3
  • 65
    • 84867743951 scopus 로고    scopus 로고
    • Modeling loop backbone flexibility in receptor-ligand docking simulations
    • Flick J, Tristram F, Wenzel W. Modeling loop backbone flexibility in receptor-ligand docking simulations. J Comp Chem 2012; 33: 2504-15.
    • (2012) J Comp Chem , vol.33 , pp. 2504-2515
    • Flick, J.1    Tristram, F.2    Wenzel, W.3
  • 66
    • 84861499934 scopus 로고    scopus 로고
    • Potential and limitations of ensemble docking
    • Korb O, Olsson TS, Bowden SJ, et al. Potential and limitations of ensemble docking. J Chem Inf Model 2012; 52: 1262-74.
    • (2012) J Chem Inf Model , vol.52 , pp. 1262-1274
    • Korb, O.1    Olsson, T.S.2    Bowden, S.J.3
  • 67
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson HA, McCammon JA. Accommodating protein flexibility in computational drug design. Mol Pharmacol 2000; 57: 213-8.
    • (2000) Mol Pharmacol , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 68
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel RMA, Kuntz ID, Oshiro CM. Molecular docking to ensembles of protein structures. J Mol Biol 1997; 266: 424-40.
    • (1997) J Mol Biol , vol.266 , pp. 424-440
    • Knegtel, R.M.A.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 69
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock. Prot Struct Funct Bioinf 2002; 46: 34-40.
    • (2002) Prot Struct Funct Bioinf , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 70
    • 60549086155 scopus 로고    scopus 로고
    • Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
    • Bottegoni G, Kufareva I, Totrov M, Abagyan R. Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking. J Med Chem 2009; 52: 397-406.
    • (2009) J Med Chem , vol.52 , pp. 397-406
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 71
    • 34548119525 scopus 로고    scopus 로고
    • FlexE ensemble docking approach to virtual screening for CDK2 inhibitors
    • Chong Y, Kim J, Park JG. FlexE ensemble docking approach to virtual screening for CDK2 inhibitors. Mol Simulation 2007; 33: 667-676.
    • (2007) Mol Simulation , vol.33 , pp. 667-676
    • Chong, Y.1    Kim, J.2    Park, J.G.3
  • 73
    • 78650667884 scopus 로고    scopus 로고
    • Accounting for water molecules in drug design
    • Wong SE, Lightstone FC. Accounting for water molecules in drug design. Exp Opin Drug Discov 2011; 6: 65-74.
    • (2011) Exp Opin Drug Discov , vol.6 , pp. 65-74
    • Wong, S.E.1    Lightstone, F.C.2
  • 74
    • 0032961895 scopus 로고    scopus 로고
    • The particle concept: Placing discrete water molecules during protein-ligand docking predictions
    • Rarey M, Kramer B, Lengauer T. The particle concept: Placing discrete water molecules during protein-ligand docking predictions. Prot Struct Funct Genet 1999; 34: 17-28.
    • (1999) Prot Struct Funct Genet , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 75
    • 0033674405 scopus 로고    scopus 로고
    • Virtual screening with solvation and ligand-induced complementarity
    • Schnecke V, Kuhn LA. Virtual screening with solvation and ligand-induced complementarity. Perspectives Drug Discov Des 2000; 20: 171-90.
    • (2000) Perspectives Drug Discov Des , vol.20 , pp. 171-190
    • Schnecke, V.1    Kuhn, L.A.2
  • 76
    • 50249094315 scopus 로고    scopus 로고
    • Exploiting ordered waters in molecular docking
    • Huang N, Shoichet BK. Exploiting ordered waters in molecular docking. J Med Chem 2008; 51: 4862-5.
    • (2008) J Med Chem , vol.51 , pp. 4862-4865
    • Huang, N.1    Shoichet, B.K.2
  • 77
    • 40949163431 scopus 로고    scopus 로고
    • Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
    • Abel R, Young T, Farid R, Berne BJ, Friesner RA. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc 2008; 130: 2817-31.
    • (2008) J Am Chem Soc , vol.130 , pp. 2817-2831
    • Abel, R.1    Young, T.2    Farid, R.3    Berne, B.J.4    Friesner, R.A.5
  • 78
    • 67749099405 scopus 로고    scopus 로고
    • High-energy water sites determine peptide binding affinity and specificity of PDZ domains
    • Beuming T, Farid R, Sherman W. High-energy water sites determine peptide binding affinity and specificity of PDZ domains. Protein Sci 2009; 18: 1609-19.
    • (2009) Protein Sci , vol.18 , pp. 1609-1619
    • Beuming, T.1    Farid, R.2    Sherman, W.3
  • 79
    • 17844388776 scopus 로고    scopus 로고
    • SZMAP 1.2.0.7: Santa Fe, NM
    • SZMAP 1.2.0.7: OpenEye Scientific Software, Santa Fe, NM. http://www.eyesopen.com (2013).
    • (2013) OpenEye Scientific Software
  • 80
    • 70349683018 scopus 로고    scopus 로고
    • Prediction of the water content in protein binding sites
    • Michel J, Tirado-Rives J, Jorgensen WL. Prediction of the water content in protein binding sites. J Phys Chem B 2009; 113: 13337-46.
    • (2009) J Phys Chem B , vol.113 , pp. 13337-13346
    • Michel, J.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 81
    • 41549091964 scopus 로고    scopus 로고
    • Ligand-protein docking with water molecules
    • Roberts BC, Mancera RL. Ligand-protein docking with water molecules. J Chem Inf Model 2008; 48: 397-408.
    • (2008) J Chem Inf Model , vol.48 , pp. 397-408
    • Roberts, B.C.1    Mancera, R.L.2
  • 82
    • 34548304863 scopus 로고    scopus 로고
    • Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: A comparison with crystallography
    • Englebienne P, Fiaux H, Kuntz DA, et al. Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: A comparison with crystallography. Prot Struct Funct Bioinf 2007; 69: 160-76.
    • (2007) Prot Struct Funct Bioinf , vol.69 , pp. 160-176
    • Englebienne, P.1    Fiaux, H.2    Kuntz, D.A.3
  • 83
    • 17144368025 scopus 로고    scopus 로고
    • Binding mode prediction of cytochrome P450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking
    • De Graaf C, Pospisil P, Pos W, Folkers G, Vermeulen NPE. Binding mode prediction of cytochrome P450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking. J Med Chem 2005; 48: 2308-18.
    • (2005) J Med Chem , vol.48 , pp. 2308-2318
    • De Graaf, C.1    Pospisil, P.2    Pos, W.3    Folkers, G.4    Vermeulen, N.P.E.5
  • 84
    • 77949797550 scopus 로고    scopus 로고
    • Ligand-Protein Cross-Docking with Water Molecules
    • Thilagavathi R, Mancera RL. Ligand-Protein Cross-Docking with Water Molecules. J Chem Inf Model 2010; 50: 415-21.
    • (2010) J Chem Inf Model , vol.50 , pp. 415-421
    • Thilagavathi, R.1    Mancera, R.L.2
  • 85
    • 34248596450 scopus 로고    scopus 로고
    • Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes
    • Jain T, Jayaram B. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes. Prot Struct Funct Bioinf 2007; 67: 1167-78.
    • (2007) Prot Struct Funct Bioinf , vol.67 , pp. 1167-1178
    • Jain, T.1    Jayaram, B.2
  • 86
    • 42449105721 scopus 로고    scopus 로고
    • Modeling of metal interaction geometries for protein-ligand docking
    • Seebeck B, Reulecke I, Kamper A, Rarey M. Modeling of metal interaction geometries for protein-ligand docking. Prot Struct Funct Bioinf 2008; 71: 1237-54.
    • (2008) Prot Struct Funct Bioinf , vol.71 , pp. 1237-1254
    • Seebeck, B.1    Reulecke, I.2    Kamper, A.3    Rarey, M.4
  • 87
    • 13944260141 scopus 로고    scopus 로고
    • Prediction of binding modes for ligands in the cytochromes p450 and other heme-containing proteins
    • Kirton SB, Murray CW, Verdonk ML, Taylor RD. Prediction of binding modes for ligands in the cytochromes p450 and other heme-containing proteins. Prot Struct Funct Bioinf 2005; 58: 836-44.
    • (2005) Prot Struct Funct Bioinf , vol.58 , pp. 836-844
    • Kirton, S.B.1    Murray, C.W.2    Verdonk, M.L.3    Taylor, R.D.4
  • 88
    • 0041654899 scopus 로고    scopus 로고
    • Docking studies of matrix metalloproteinase inhibitors: Zinc parameter optimization to improve the binding free energy prediction
    • Hu X, Shelver WH. Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction. J Mol Graph Model 2003; 22: 115-26.
    • (2003) J Mol Graph Model , vol.22 , pp. 115-126
    • Hu, X.1    Shelver, W.H.2
  • 89
    • 60649120008 scopus 로고    scopus 로고
    • Molecular modelling for transition metal complexes: Dealing with d-electron effects
    • Deeth RJ, Anastasi A, Diedrich C, Randell K. Molecular modelling for transition metal complexes: Dealing with d-electron effects. Coord Chem Rev 2009; 253: 795-816.
    • (2009) Coord Chem Rev , vol.253 , pp. 795-816
    • Deeth, R.J.1    Anastasi, A.2    Diedrich, C.3    Randell, K.4
  • 91
    • 24944529911 scopus 로고    scopus 로고
    • Virtual screening against metalloenzymes for inhibitors and substrates
    • Irwin JJ, Raushel FM, Shoichet BK. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry 2005; 44: 12316-28.
    • (2005) Biochemistry , vol.44 , pp. 12316-12328
    • Irwin, J.J.1    Raushel, F.M.2    Shoichet, B.K.3
  • 92
    • 33845873363 scopus 로고    scopus 로고
    • Development and validation of a modular, extensible docking program: DOCK 5
    • Moustakas DT, Lang PT, Pegg S, et al. Development and validation of a modular, extensible docking program: DOCK 5. J Comput-Aided Mol Des 2006; 20: 601-19.
    • (2006) J Comput-Aided Mol Des , vol.20 , pp. 601-619
    • Moustakas, D.T.1    Lang, P.T.2    Pegg, S.3
  • 93
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola E, Walters WP, Charifson PS. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Prot Struct Funct Bioinf 2004; 56: 235-49.
    • (2004) Prot Struct Funct Bioinf , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 94
    • 0032464349 scopus 로고    scopus 로고
    • Analysis of zinc binding sites in protein crystal structures
    • Alberts IL, Nadassy K, Wodak SJ. Analysis of zinc binding sites in protein crystal structures. Prot Sci 1998; 7: 1700-1716.
    • (1998) Prot Sci , vol.7 , pp. 1700-1716
    • Alberts, I.L.1    Nadassy, K.2    Wodak, S.J.3
  • 95
    • 77957920876 scopus 로고    scopus 로고
    • Metals in protein structures: A review of their principal features
    • Harding MM, Nowicki MW, Walkinshaw MD. Metals in protein structures: a review of their principal features. Crystallography Rev 2010; 16: 247-302.
    • (2010) Crystallography Rev , vol.16 , pp. 247-302
    • Harding, M.M.1    Nowicki, M.W.2    Walkinshaw, M.D.3
  • 96
    • 60449094541 scopus 로고    scopus 로고
    • Beyond Picomolar Affinities: Quantitative Aspects of Noncovalent and Covalent Binding of Drugs to Proteins
    • Smith AJT, Zhang XY, Leach AG, Houk KN. Beyond Picomolar Affinities: Quantitative Aspects of Noncovalent and Covalent Binding of Drugs to Proteins. J Med Chem 2009; 52: 225-33.
    • (2009) J Med Chem , vol.52 , pp. 225-233
    • Smith, A.J.T.1    Zhang, X.Y.2    Leach, A.G.3    Houk, K.N.4
  • 98
    • 71049143154 scopus 로고    scopus 로고
    • Constrained Peptidomimetics Reveal Detailed Geometric Requirements of Covalent Prolyl Oligopeptidase Inhibitors
    • Lawandi J, Toumieux S, Seyer V, et al. Constrained Peptidomimetics Reveal Detailed Geometric Requirements of Covalent Prolyl Oligopeptidase Inhibitors. J Med Chem 2009; 52: 6672-84.
    • (2009) J Med Chem , vol.52 , pp. 6672-6684
    • Lawandi, J.1    Toumieux, S.2    Seyer, V.3
  • 99
    • 36949007602 scopus 로고    scopus 로고
    • Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
    • Katritch V, Byrd CM, Tseitin V, et al. Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches. J Comput-Aided Mol Des 2007; 21: 549-58.
    • (2007) J Comput-Aided Mol Des , vol.21 , pp. 549-558
    • Katritch, V.1    Byrd, C.M.2    Tseitin, V.3
  • 100
    • 13944274970 scopus 로고    scopus 로고
    • Unsupervised guided docking of covalently bound ligands
    • Fradera X, Kaur J, Mestres J. Unsupervised guided docking of covalently bound ligands. J Comput-Aided Mol Des 2004; 18: 635-50.
    • (2004) J Comput-Aided Mol Des , vol.18 , pp. 635-650
    • Fradera, X.1    Kaur, J.2    Mestres, J.3
  • 101
    • 84864219812 scopus 로고    scopus 로고
    • Virtual screening and computational optimization for the discovery of covalent prolyl oligopeptidase inhibitors with activity in human cells
    • De Cesco S, Deslandes S, Therrien E, et al. Virtual screening and computational optimization for the discovery of covalent prolyl oligopeptidase inhibitors with activity in human cells. J Med Chem 2012; 55: 6306-15.
    • (2012) J Med Chem , vol.55 , pp. 6306-6315
    • De Cesco, S.1    Deslandes, S.2    Therrien, E.3
  • 102
    • 33845762914 scopus 로고    scopus 로고
    • Prediction of multiple binding modes of the CDK2 inhibitors, anilinopyrazoles, using the automated docking programs GOLD, FlexX, and LigandFit: An evaluation of performance
    • Sato H, Shewchuk LM, Tang J. Prediction of multiple binding modes of the CDK2 inhibitors, anilinopyrazoles, using the automated docking programs GOLD, FlexX, and LigandFit: an evaluation of performance. J Chem Inf Model 2006; 46: 2552-62.
    • (2006) J Chem Inf Model , vol.46 , pp. 2552-2562
    • Sato, H.1    Shewchuk, L.M.2    Tang, J.3
  • 103
    • 41349106542 scopus 로고    scopus 로고
    • Recommendations for evaluation of computational methods
    • Jain AN, Nicholls A. Recommendations for evaluation of computational methods. J Comput Aided Mol Des 2008; 22: 133-9.
    • (2008) J Comput Aided Mol Des , vol.22 , pp. 133-139
    • Jain, A.N.1    Nicholls, A.2
  • 104
    • 41449114598 scopus 로고    scopus 로고
    • Community benchmarks for virtual screening
    • Irwin JJ. Community benchmarks for virtual screening. J Comput Aided Mol Des 2008; 22: 193-9.
    • (2008) J Comput Aided Mol Des , vol.22 , pp. 193-199
    • Irwin, J.J.1
  • 105
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006; 49: 6789-801.
    • (2006) J Med Chem , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 106
    • 84864264343 scopus 로고    scopus 로고
    • Directory of useful decoys, enhanced (DUD-E): Better ligands and decoys for better benchmarking
    • Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem 2012; 55: 6582-94.
    • (2012) J Med Chem , vol.55 , pp. 6582-6594
    • Mysinger, M.M.1    Carchia, M.2    Irwin, J.J.3    Shoichet, B.K.4
  • 109
  • 110
    • 34250349894 scopus 로고    scopus 로고
    • Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping
    • Richardson CM, Nunns CL, Williamson DS, et al. Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping. Bioorg Med Chem Lett 2007; 17: 3880-3885.
    • (2007) Bioorg Med Chem Lett , vol.17 , pp. 3880-3885
    • Richardson, C.M.1    Nunns, C.L.2    Williamson, D.S.3
  • 111
    • 84871082124 scopus 로고    scopus 로고
    • Los Angeles, CA
    • Chemaxon, Los Angeles, CA, 2012.
    • (2012) Chemaxon
  • 112
    • 84858044044 scopus 로고    scopus 로고
    • Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery
    • Therrien E, Englebienne P, Arrowsmith AG, et al. Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery. J Chem Inf Model 2012; 52: 210-224.
    • (2012) J Chem Inf Model , vol.52 , pp. 210-224
    • Therrien, E.1    Englebienne, P.2    Arrowsmith, A.G.3
  • 113
    • 20144385151 scopus 로고    scopus 로고
    • Design of smallsized libraries by combinatorial assembly of linkers and functional groups to a given scaffold: Application to the structure-based optimization of a phosphodiesterase 4 inhibitor
    • Krier M, de Araujo-Junior JX, Schmitt M, et al. Design of smallsized libraries by combinatorial assembly of linkers and functional groups to a given scaffold: Application to the structure-based optimization of a phosphodiesterase 4 inhibitor. J Med Chem 2005; 48: 3816-22.
    • (2005) J Med Chem , vol.48 , pp. 3816-3822
    • Krier, M.1    de Araujo-Junior, J.X.2    Schmitt, M.3
  • 117
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006; 22: 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 119
    • 0029004590 scopus 로고
    • Protein Modeling by E-Mail
    • Peitsch MC. Protein Modeling by E-Mail. Bio-Technology 1995; 13: 658-60.
    • (1995) Bio-Technology , vol.13 , pp. 658-660
    • Peitsch, M.C.1
  • 120
    • 80052841737 scopus 로고    scopus 로고
    • A quality alert and call for improved curation of public chemistry databases
    • Williams AJ, Ekins S. A quality alert and call for improved curation of public chemistry databases. Drug Discovery Today 2011; 16: 747-50.
    • (2011) Drug Discovery Today , vol.16 , pp. 747-750
    • Williams, A.J.1    Ekins, S.2
  • 122
    • 20144369541 scopus 로고    scopus 로고
    • Virtual Screening for β-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228
    • Polgár T, Keserü GM. Virtual Screening for β-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228. J Med Chem 2005; 48: 3749-55.
    • (2005) J Med Chem , vol.48 , pp. 3749-3755
    • Polgár, T.1    Keserü, G.M.2
  • 123
    • 34547593171 scopus 로고    scopus 로고
    • NQ-Flipper: Recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
    • Weichenberger CX, Sippl MJ. NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. Nucleic Acids Res 2007; 35: W403-6.
    • (2007) Nucleic Acids Res , vol.35
    • Weichenberger, C.X.1    Sippl, M.J.2
  • 124
    • 79957744584 scopus 로고    scopus 로고
    • Computer Review of ChemDraw Ultra 12.0
    • Cousins KR. Computer Review of ChemDraw Ultra 12.0. J Am Chem Soc 2011; 133: 8388-8.
    • (2011) J Am Chem Soc , vol.133 , pp. 8388
    • Cousins, K.R.1
  • 126
    • 67650077383 scopus 로고    scopus 로고
    • Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results
    • Brink TT, Exner TE. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J Chem Inf Model 2009; 49: 1535-46.
    • (2009) J Chem Inf Model , vol.49 , pp. 1535-1546
    • Brink, T.T.1    Exner, T.E.2
  • 127
    • 77951983882 scopus 로고    scopus 로고
    • Evaluation of pKa estimation methods on 211 druglike compounds
    • Manchester J, Walkup G, Rivin O, You Z. Evaluation of pKa estimation methods on 211 druglike compounds. J Chem Inf Model 2010; 50: 565-71.
    • (2010) J Chem Inf Model , vol.50 , pp. 565-571
    • Manchester, J.1    Walkup, G.2    Rivin, O.3    You, Z.4
  • 128
    • 0035907237 scopus 로고    scopus 로고
    • The 1.8-angstrom crystal structure of a matrix metalloproteinase 8-barbiturate inhibitor complex reveals a previously unobserved mechanism for collagenase substrate recognition
    • Brandstetter H, Grams F, Glitz D, et al. The 1.8-angstrom crystal structure of a matrix metalloproteinase 8-barbiturate inhibitor complex reveals a previously unobserved mechanism for collagenase substrate recognition J Biol Chem 2001; 276: 31474.
    • (2001) J Biol Chem , vol.276 , pp. 31474
    • Brandstetter, H.1    Grams, F.2    Glitz, D.3
  • 129
    • 79952586132 scopus 로고    scopus 로고
    • Comments on the Article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds"
    • Shelley JC, Calkins D, Sullivan AP. Comments on the Article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds". J Chem Inf Model 2011; 51: 102-4.
    • (2011) J Chem Inf Model , vol.51 , pp. 102-104
    • Shelley, J.C.1    Calkins, D.2    Sullivan, A.P.3
  • 130
    • 33645675960 scopus 로고    scopus 로고
    • Estimating the cost of new drug development: Is it really 802 million dollars?
    • Adams CP, Brantner VV. Estimating the cost of new drug development: is it really 802 million dollars? Health Aff (Millwood) 2006; 25: 420-8.
    • (2006) Health Aff (Millwood) , vol.25 , pp. 420-428
    • Adams, C.P.1    Brantner, V.V.2
  • 131
    • 67650088429 scopus 로고    scopus 로고
    • ADDME--Avoiding Drug Development Mistakes Early: Central nervous system drug discovery perspective
    • Tsaioun K, Bottlaender M, Mabondzo A. ADDME--Avoiding Drug Development Mistakes Early: central nervous system drug discovery perspective. BMC Neurol 2009; 9 Suppl 1: S1.
    • (2009) BMC Neurol , vol.9 , Issue.SUPPL. 1
    • Tsaioun, K.1    Bottlaender, M.2    Mabondzo, A.3
  • 132
    • 77958069126 scopus 로고    scopus 로고
    • Toward a Comprehensive Molecular Design Framework for Reduced Hazard
    • Voutchkova AM, Osimitz TG, Anastas PT. Toward a Comprehensive Molecular Design Framework for Reduced Hazard. Chem Rev 2010; 110: 5845-82.
    • (2010) Chem Rev , vol.110 , pp. 5845-5882
    • Voutchkova, A.M.1    Osimitz, T.G.2    Anastas, P.T.3
  • 133
    • 0035289779 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001; 46: 3-26.
    • (2001) Adv Drug Deliv Rev , vol.46 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 135
    • 79960111434 scopus 로고    scopus 로고
    • The FAF-Drugs2 server: A multistep engine to prepare electronic chemical compound collections
    • Lagorce D, Maupetit J, Baell J, et al. The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections. Bioinformatics 2011; 27: 2018-20.
    • (2011) Bioinformatics , vol.27 , pp. 2018-2020
    • Lagorce, D.1    Maupetit, J.2    Baell, J.3
  • 136
    • 84856385436 scopus 로고    scopus 로고
    • Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era
    • Taboureau O, Baell JB, Fernandez-Recio J, Villoutreix BO. Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era. Chem Biol 2012; 19: 29-41.
    • (2012) Chem Biol , vol.19 , pp. 29-41
    • Taboureau, O.1    Baell, J.B.2    Fernandez-Recio, J.3    Villoutreix, B.O.4
  • 137
    • 77950571108 scopus 로고    scopus 로고
    • New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays
    • Baell JB, Holloway GA. New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays. J Med Chem 2010; 53: 2719-40.
    • (2010) J Med Chem , vol.53 , pp. 2719-2740
    • Baell, J.B.1    Holloway, G.A.2
  • 138
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam CM, Jiang X, Oldfield T, Waldman M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graphics Modell 2003; 21: 289-307.
    • (2003) J Mol Graphics Modell , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 139
    • 84903731987 scopus 로고    scopus 로고
    • Accelerys
    • In: Accelerys: San Diego, CA
    • Accelerys. Pipeline Pilot. In: Accelerys: San Diego, CA 2009.
    • (2009) Pipeline Pilot.
  • 140
    • 3242729723 scopus 로고    scopus 로고
    • Derivation and applications of molecular descriptors based on approximate surface area
    • Labute P. Derivation and applications of molecular descriptors based on approximate surface area. Methods Mol Biol 2004; 275: 261-78.
    • (2004) Methods Mol Biol , vol.275 , pp. 261-278
    • Labute, P.1
  • 141
    • 69549118627 scopus 로고    scopus 로고
    • Testing assumptions and hypotheses for rescoring success in protein-ligand docking
    • O'Boyle NM, Liebeschuetz JW, Cole JC. Testing assumptions and hypotheses for rescoring success in protein-ligand docking. J Chem Inf Model 2009; 49: 1871-8.
    • (2009) J Chem Inf Model , vol.49 , pp. 1871-1878
    • O'Boyle, N.M.1    Liebeschuetz, J.W.2    Cole, J.C.3
  • 142
    • 0037107887 scopus 로고    scopus 로고
    • Structure-based virtual screening: An overview
    • Lyne PD. Structure-based virtual screening: An overview. Drug Discov Today 2002; 7: 1047-55.
    • (2002) Drug Discov Today , vol.7 , pp. 1047-1055
    • Lyne, P.D.1
  • 143
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman PA, Massova I, Reyes C, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000; 33: 889-97.
    • (2000) Acc Chem Res , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3
  • 144
    • 33748667774 scopus 로고    scopus 로고
    • Consensus scoring for protein-ligand interactions
    • Feher M. Consensus scoring for protein-ligand interactions. Drug Discov Today 2006; 11: 421-8.
    • (2006) Drug Discov Today , vol.11 , pp. 421-428
    • Feher, M.1
  • 145
    • 0346962971 scopus 로고    scopus 로고
    • Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions
    • Deng Z, Chuaqui C, Singh J. Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions. J Med Chem 2003; 47: 337-44.
    • (2003) J Med Chem , vol.47 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 146
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
    • Marcou G, Rognan D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 2007; 47: 195-207.
    • (2007) J Chem Inf Model , vol.47 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 147
    • 66249123260 scopus 로고    scopus 로고
    • APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
    • Pérez-Nueno VI, Rabal O, Borrell JI, Teixidó J. APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening. J Chem Inf Model 2009; 49: 1245-60.
    • (2009) J Chem Inf Model , vol.49 , pp. 1245-1260
    • Pérez-Nueno, V.I.1    Rabal, O.2    Borrell, J.I.3    Teixidó, J.4
  • 148
    • 0037263939 scopus 로고    scopus 로고
    • Structural quality assurance
    • Laskowski RA. Structural quality assurance. Methods Biochem Anal 2003; 44: 273-303.
    • (2003) Methods Biochem Anal , vol.44 , pp. 273-303
    • Laskowski, R.A.1
  • 149
    • 67650097331 scopus 로고    scopus 로고
    • Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
    • Cross JB, Thompson DC, Rai BK, et al. Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy. J Chem Inf Model 2009; 49: 1455-74.
    • (2009) J Chem Inf Model , vol.49 , pp. 1455-1474
    • Cross, J.B.1    Thompson, D.C.2    Rai, B.K.3
  • 151
    • 0037208312 scopus 로고    scopus 로고
    • Consideration of molecular weight during compound selection in virtual target-based database screening
    • Pan YP, Huang N, Cho S, MacKerell AD. Consideration of molecular weight during compound selection in virtual target-based database screening. J Chem Inf Comp Sci 2003; 43: 267-72.
    • (2003) J Chem Inf Comp Sci , vol.43 , pp. 267-272
    • Pan, Y.P.1    Huang, N.2    Cho, S.3    McKerell, A.D.4
  • 152
    • 34547676154 scopus 로고    scopus 로고
    • Unbiasing scoring functions: A new normalization and rescoring strategy
    • Carta G, Knox AJS, Lloyd DG. Unbiasing scoring functions: A new normalization and rescoring strategy. J Chem Inf Model 2007; 47: 1564-71.
    • (2007) J Chem Inf Model , vol.47 , pp. 1564-1571
    • Carta, G.1    Knox, A.J.S.2    Lloyd, D.G.3
  • 153
    • 69549090094 scopus 로고    scopus 로고
    • Docking studies on DNA-ligand interactions: Building and application of a protocol to identify the binding mode
    • Ricci CG, Netz PA. Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode. J Chem Inf Model 2009; 49: 1925-35.
    • (2009) J Chem Inf Model , vol.49 , pp. 1925-1935
    • Ricci, C.G.1    Netz, P.A.2
  • 155
    • 32344449937 scopus 로고    scopus 로고
    • Docking of aminoglycosides to hydrated and flexible RNA
    • Moitessier N, Westhof E, Hanessian S. Docking of aminoglycosides to hydrated and flexible RNA. J Med Chem 2006; 49: 1023-33.
    • (2006) J Med Chem , vol.49 , pp. 1023-1033
    • Moitessier, N.1    Westhof, E.2    Hanessian, S.3
  • 156
  • 157
    • 0033949057 scopus 로고    scopus 로고
    • Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
    • Filikov AV, Mohan V, Vickers TA, et al. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J Comput-Aided Mol Des 2000; 14: 593-610.
    • (2000) J Comput-Aided Mol Des , vol.14 , pp. 593-610
    • Filikov, A.V.1    Mohan, V.2    Vickers, T.A.3
  • 158
    • 0036008846 scopus 로고    scopus 로고
    • Structurebased computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA
    • Lind KE, Du ZH, Fujinaga K, Peterlin BM, James TL. Structurebased computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. Chem Biol 2002; 9: 185-93.
    • (2002) Chem Biol , vol.9 , pp. 185-193
    • Lind, K.E.1    Du, Z.H.2    Fujinaga, K.3    Peterlin, B.M.4    James, T.L.5
  • 159
    • 4043058000 scopus 로고    scopus 로고
    • Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock (R)
    • Morley SD, Afshar M. Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock (R). J Comput-Aided Mol Des 2004; 18: 189-208.
    • (2004) J Comput-Aided Mol Des , vol.18 , pp. 189-208
    • Morley, S.D.1    Afshar, M.2
  • 160
    • 84865553456 scopus 로고    scopus 로고
    • Spectroscopic and molecular docking studies on chlorambucil interaction with DNA
    • Charak S, Shandilya M, Tyagi G, Mehrotra R. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA. Int J Biol Macromol 2012; 51: 406-11.
    • (2012) Int J Biol Macromol , vol.51 , pp. 406-411
    • Charak, S.1    Shandilya, M.2    Tyagi, G.3    Mehrotra, R.4
  • 161
    • 77954071784 scopus 로고    scopus 로고
    • Accuracy Assessment of Protein-Based Docking Programs against RNA Targets
    • Li YZ, Shen J, Sun XG, Li WH, Liu GX, Tang Y. Accuracy Assessment of Protein-Based Docking Programs against RNA Targets. J Chem Inf Model 2010; 50: 1134-46.
    • (2010) J Chem Inf Model , vol.50 , pp. 1134-1146
    • Li, Y.Z.1    Shen, J.2    Sun, X.G.3    Li, W.H.4    Liu, G.X.5    Tang, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.