메뉴 건너뛰기




Volumn 49, Issue 8, 2006, Pages 2417-2430

Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking

Author keywords

[No Author keywords available]

Indexed keywords

AMIFLAMINE; AMIODARONE; AZELASTINE; BUFURALOL; BUNITROLOL; CARTEOLOL; CHLORPROMAZINE; CINNARIZINE; CITALOPRAM; CLOZAPINE; CYTOCHROME P450 2D6; DEBRISOQUINE; DESIPRAMINE; DEXTROMETHORPHAN; DIPHENHYDRAMINE; FLUOXETINE; IMIPRAMINE; METOPROLOL; MIANSERIN; NORTRIPTYLINE; PHENFORMIN; PROMETHAZINE; PROPRANOLOL; SPARTEINE; TAMOXIFEN; TERFENADINE; TIMOLOL; TOLTERODINE; VENLAFAXINE; WATER;

EID: 33646107162     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm0508538     Document Type: Article
Times cited : (130)

References (82)
  • 1
    • 1642350394 scopus 로고    scopus 로고
    • Recent development and application of virtual screening in drug discovery: An overview
    • Hou, T.; Xu, X. Recent development and application of virtual screening in drug discovery: an overview. Curr. Pharm. Des. 2004, 10, 1011-1033.
    • (2004) Curr. Pharm. Des. , vol.10 , pp. 1011-1033
    • Hou, T.1    Xu, X.2
  • 2
    • 21544474149 scopus 로고    scopus 로고
    • Keynote review: Structural biology and drug discovery
    • Congreve, M.; Murray, C. W.; Blundell, T. L. Keynote review: Structural biology and drug discovery. Drug Discoverv Today 2005, 10, 895-907.
    • (2005) Drug Discoverv Today , vol.10 , pp. 895-907
    • Congreve, M.1    Murray, C.W.2    Blundell, T.L.3
  • 4
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. I. Evaluation of different docking/scoring combinations
    • Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases. I. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-4767.
    • (2000) J. Med. Chem. , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 7
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
    • (2004) J. Med. Chem. , vol.47 , pp. 1739-1749
    • Friesner, R.A.1    Banks, J.L.2    Murphy, R.B.3    Halgren, T.A.4    Klicic, J.J.5
  • 8
    • 1642310340 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
    • Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47, 1750-1759.
    • (2004) J. Med. Chem. , vol.47 , pp. 1750-1759
    • Halgren, T.A.1    Murphy, R.B.2    Friesner, R.A.3    Beard, H.S.4    Frye, L.L.5
  • 9
    • 4544367743 scopus 로고    scopus 로고
    • Comparative evaluation of eight docking tools for docking and virtual screening accuracy
    • Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 2004, 57, 225-242.
    • (2004) Proteins , vol.57 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4
  • 10
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of docking performance: comparative data on docking algorithms. J. Med. Chem. 2004, 47, 558-565.
    • (2004) J. Med. Chem. , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 11
    • 11144255694 scopus 로고    scopus 로고
    • Evaluation of library ranking efficacy in virtual screening
    • Kontoyianni, M.; Sokol, G. S.; McClellan, L. M. Evaluation of library ranking efficacy in virtual screening. J. Comput. Chem. 2005, 26, 11-22.
    • (2005) J. Comput. Chem. , vol.26 , pp. 11-22
    • Kontoyianni, M.1    Sokol, G.S.2    McClellan, L.M.3
  • 12
    • 13944253576 scopus 로고    scopus 로고
    • Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors
    • Mozziconacci, J. C.; Arnoult, E.; Bernard, P.; Do, Q. T.; Marot, C.; et al. Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors. J. Med. Chem. 2005, 48, 1055-1068.
    • (2005) J. Med. Chem. , vol.48 , pp. 1055-1068
    • Mozziconacci, J.C.1    Arnoult, E.2    Bernard, P.3    Do, Q.T.4    Marot, C.5
  • 13
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004, 56, 235-249.
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 16
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R. X.; Lu, Y. P.; Wang, S. M. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46, 2287-2303.
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.X.1    Lu, Y.P.2    Wang, S.M.3
  • 17
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • Wang, R.; Lu, Y.; Fang, X.; Wang, S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 2004, 44, 2114-2125.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 2114-2125
    • Wang, R.1    Lu, Y.2    Fang, X.3    Wang, S.4
  • 18
    • 0036606204 scopus 로고    scopus 로고
    • ConsDock: A new program for the consensus analysis of protein-ligand interactions
    • Paul, N.; Rognan, D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins 2002, 47, 521-533.
    • (2002) Proteins , vol.47 , pp. 521-533
    • Paul, N.1    Rognan, D.2
  • 19
    • 0042307528 scopus 로고    scopus 로고
    • The performance of current methods in ligand-protein docking
    • McConkey, B. J.; Sobolev, V.; Edelman, M. The performance of current methods in ligand-protein docking. Curr. Sci. 2002, 83, 845-856.
    • (2002) Curr. Sci. , vol.83 , pp. 845-856
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 20
    • 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, N. P. 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, 2308-2318.
    • (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.5
  • 21
    • 0025895757 scopus 로고
    • Reactions and significance of cytochrome P-450 enzymes
    • Guengerich, F. P. Reactions and significance of cytochrome P-450 enzymes. J. Biol. Chem. 1991, 266, 10019-10022.
    • (1991) J. Biol. Chem. , vol.266 , pp. 10019-10022
    • Guengerich, F.P.1
  • 22
    • 0028876897 scopus 로고
    • Oxygen and xenobiotic reductase activities of cytochrome P450
    • Goeptar, A. R.; Scheerens, H.; Vermeulen, N. P. Oxygen and xenobiotic reductase activities of cytochrome P450. Crit. Rev. Toxicol. 1995, 25, 25-65.
    • (1995) Crit. Rev. Toxicol. , vol.25 , pp. 25-65
    • Goeptar, A.R.1    Scheerens, H.2    Vermeulen, N.P.3
  • 24
  • 25
    • 0036204756 scopus 로고    scopus 로고
    • Molecular genetics of CYP2D6: Clinical relevance with focus on psychotropic drugs
    • Bertilsson, L.; Dahl, M. L.; Dalen, P.; Al-Shurbaji, A. Molecular genetics of CYP2D6: clinical relevance with focus on psychotropic drugs. Br. J. Clin. Pharmacol. 2002, 53, 111-122.
    • (2002) Br. J. Clin. Pharmacol. , vol.53 , pp. 111-122
    • Bertilsson, L.1    Dahl, M.L.2    Dalen, P.3    Al-Shurbaji, A.4
  • 26
    • 0038294345 scopus 로고    scopus 로고
    • Pharmacogenetics of drug metabolising enzymes: Importance for personalised medicine
    • Oscarson, M. Pharmacogenetics of drug metabolising enzymes: importance for personalised medicine. Clin. Chem. Lab. Med. 2003, 41, 573-580.
    • (2003) Clin. Chem. Lab. Med. , vol.41 , pp. 573-580
    • Oscarson, M.1
  • 27
    • 1942421701 scopus 로고    scopus 로고
    • Pharmacogenetics of cytochrome P450 and its applications in drug therapy: The past, present and future
    • Ingelman-Sundberg, M. Pharmacogenetics of cytochrome P450 and its applications in drug therapy: the past, present and future. Trends Pharmacol. Sci. 2004, 25, 193-200.
    • (2004) Trends Pharmacol. Sci. , vol.25 , pp. 193-200
    • Ingelman-Sundberg, M.1
  • 28
    • 17444411955 scopus 로고    scopus 로고
    • Cytochrome p450 in silico: An integrative modeling approach
    • de Graaf, C.; Vermeulen, N. P.; Feenstra, K. A. Cytochrome p450 in silico: an integrative modeling approach. J. Med. Chem. 2005, 48, 2725-2755.
    • (2005) J. Med. Chem. , vol.48 , pp. 2725-2755
    • De Graaf, C.1    Vermeulen, N.P.2    Feenstra, K.A.3
  • 29
    • 0036836542 scopus 로고    scopus 로고
    • Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6
    • Kirton, S. B.; Kemp, C, A.; Tomkinson, N. P.; St-Gallay, S.; Sutcliffe, M. J. Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6. Proteins 2002, 49, 216-231.
    • (2002) Proteins , vol.49 , pp. 216-231
    • Kirton, S.B.1    Kemp, C.A.2    Tomkinson, N.P.3    St-Gallay, S.4    Sutcliffe, M.J.5
  • 30
    • 0037413558 scopus 로고    scopus 로고
    • Homology modeling of rat and human cytochrome P450 2D (CYP2D) isoforms and computational rationalization of experimental ligand-binding specificities
    • Venhorst, J.; ter Laak, A. M.; Commandeur, J. N.; Funae, Y.; Hiroi, T.; et al. Homology modeling of rat and human cytochrome P450 2D (CYP2D) isoforms and computational rationalization of experimental ligand-binding specificities. J. Med. Chem. 2003, 46, 74-86.
    • (2003) J. Med. Chem. , vol.46 , pp. 74-86
    • Venhorst, J.1    Ter Laak, A.M.2    Commandeur, J.N.3    Funae, Y.4    Hiroi, T.5
  • 31
    • 24944529052 scopus 로고    scopus 로고
    • Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: In silico predictions and experimental validation
    • Keizers, P. H.; de Graaf, C.; de Kanter, F. J.; Oostenbrink, C.; Feenstra, K. A.; et al. Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation. J. Med. Chem. 2005, 48, 6117-6127.
    • (2005) J. Med. Chem. , vol.48 , pp. 6117-6127
    • Keizers, P.H.1    De Graaf, C.2    De Kanter, F.J.3    Oostenbrink, C.4    Feenstra, K.A.5
  • 32
    • 0034962557 scopus 로고    scopus 로고
    • Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites
    • Ekins, S.; de Groot, M. J.; Jones, J. P. Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites. Drug Metab. Dispos. 2001, 29, 936-944.
    • (2001) Drug Metab. Dispos. , vol.29 , pp. 936-944
    • Ekins, S.1    De Groot, M.J.2    Jones, J.P.3
  • 33
    • 0141611170 scopus 로고    scopus 로고
    • Prediction of drug metabolism: The case of cytochrome P450 2D6
    • Vermeulen, N. P. E. Prediction of drug metabolism: the case of cytochrome P450 2D6. Curr. Top. Med. Chem. 2003, 3, 1227-1239.
    • (2003) Curr. Top. Med. Chem. , vol.3 , pp. 1227-1239
    • Vermeulen, N.P.E.1
  • 34
    • 13944260141 scopus 로고    scopus 로고
    • Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins
    • Kirton, S. B.; Murray, C. W.; Verdonk, M. L.; Taylor, R. D. Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins. Proteins 2005, 58, 836-844.
    • (2005) Proteins , vol.58 , pp. 836-844
    • Kirton, S.B.1    Murray, C.W.2    Verdonk, M.L.3    Taylor, R.D.4
  • 35
    • 0034791141 scopus 로고    scopus 로고
    • A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism
    • Keseru, G. M. A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. J. Comput.-Aided Mol. Des. 2001, 15, 649-657.
    • (2001) J. Comput.-Aided Mol. Des. , vol.15 , pp. 649-657
    • Keseru, G.M.1
  • 36
    • 0030749297 scopus 로고    scopus 로고
    • Substrate docking algorithms and prediction of the substrate specificity of cytochrome P450(cam) and its L244A mutant
    • DeVoss, J. J.; Sibbesen, O.; Zhang, Z. P.; deMontellano, P. R. O. Substrate docking algorithms and prediction of the substrate specificity of cytochrome P450(cam) and its L244A mutant. J. Am. Chem. Soc. 1997, 119, 5489-5498.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 5489-5498
    • DeVoss, J.J.1    Sibbesen, O.2    Zhang, Z.P.3    Demontellano, P.R.O.4
  • 37
    • 3042645255 scopus 로고    scopus 로고
    • Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes
    • Verras, A.; Kuntz, I. D.; de Montellano, P. R. O. Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes. J. Med. Chem. 2004, 47, 3572-3579.
    • (2004) J. Med. Chem. , vol.47 , pp. 3572-3579
    • Verras, A.1    Kuntz, I.D.2    De Montellano, P.R.O.3
  • 38
    • 6044232040 scopus 로고    scopus 로고
    • Validation of model of cytochrome P450 2D6: An in silico tool for predicting metabolism and inhibition
    • Kemp, C. A.; Flanagan, J. U.; van Eldik, A. J.; Marechal, J. D.; Wolf, C. R.; et al. Validation of model of cytochrome P450 2D6: an in silico tool for predicting metabolism and inhibition. J. Med. Chem. 2004, 47, 5340-5346.
    • (2004) J. Med. Chem. , vol.47 , pp. 5340-5346
    • Kemp, C.A.1    Flanagan, J.U.2    Van Eldik, A.J.3    Marechal, J.D.4    Wolf, C.R.5
  • 39
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5
  • 40
    • 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
  • 41
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; 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
  • 42
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
    • (1997) J. Comput.-Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 43
    • 7444225179 scopus 로고    scopus 로고
    • Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: Crucial role in 7-methoxy-4-(aminomethyl)- coumarin metabolism
    • Keizers, P. H.; Lussenburg, B. M.; de Graaf, C.; Mentink, L. M.; Vermeulen, N. P.; et al. Influence of phenylalanine 120 on cytochrome P450 2D6 catalytic selectivity and regiospecificity: crucial role in 7-methoxy-4- (aminomethyl)-coumarin metabolism. Biochem. Pharmacol. 2004, 68, 2263-2271.
    • (2004) Biochem. Pharmacol. , vol.68 , pp. 2263-2271
    • Keizers, P.H.1    Lussenburg, B.M.2    De Graaf, C.3    Mentink, L.M.4    Vermeulen, N.P.5
  • 45
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 47
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y. C. 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
  • 48
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang, R. X.; Liu, L.; Lai, L. H.; Tang, Y. Q. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Model. 1998, 4, 379-394.
    • (1998) J. Mol. Model. , vol.4 , pp. 379-394
    • Wang, R.X.1    Liu, L.2    Lai, L.H.3    Tang, Y.Q.4
  • 49
    • 0029450365 scopus 로고
    • Hydration in drug design. I. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
    • Poornima, C. S.; Dean, P. M. Hydration in drug design. I. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J. Comput.-Aided Mol. Des. 1995, 9, 500-512.
    • (1995) J. Comput.-Aided Mol. Des. , vol.9 , pp. 500-512
    • Poornima, C.S.1    Dean, P.M.2
  • 50
    • 0029444719 scopus 로고
    • Hydration in drug design. 2. Influence of local site surface shape on water binding
    • Poornima, C. S.; Dean, P. M. Hydration in drug design. 2. Influence of local site surface shape on water binding. J. Comput.-Aided Mol. Des. 1995, 9, 513-520.
    • (1995) J. Comput.-Aided Mol. Des. , vol.9 , pp. 513-520
    • Poornima, C.S.1    Dean, P.M.2
  • 51
    • 0029450636 scopus 로고
    • Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins
    • Poornima, C. S.; Dean, P. M. Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins. J. Compul.-Aided Mol. Des. 1995, 9, 521-531.
    • (1995) J. Compul.-Aided Mol. Des. , vol.9 , pp. 521-531
    • Poornima, C.S.1    Dean, P.M.2
  • 52
    • 0027027467 scopus 로고
    • LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
    • Bohm, H. J. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput.-Aided Mol. Des. 1992, 6, 593-606.
    • (1992) J. Comput.-Aided Mol. Des. , vol.6 , pp. 593-606
    • Bohm, H.J.1
  • 53
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang, R. X.; Lai, L. H.; Wang, S. M. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput.-Aided Mol. Des. 2002, 16, 11-26.
    • (2002) J. Comput.-Aided Mol. Des. , vol.16 , pp. 11-26
    • Wang, R.X.1    Lai, L.H.2    Wang, S.M.3
  • 54
    • 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. Proteins 1999, 34, 17-28.
    • (1999) Proteins , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 55
    • 0033674405 scopus 로고    scopus 로고
    • Virtual screening with solvation and ligand-induced complementarity
    • Schnecke, V.; Kuhn, L. A. Virtual screening with solvation and ligand-induced complementarity. Perspect. Drug Discovery Des. 2000, 20, 171-190.
    • (2000) Perspect. Drug Discovery Des. , vol.20 , pp. 171-190
    • Schnecke, V.1    Kuhn, L.A.2
  • 56
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002, 46, 34-40.
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 58
    • 0033587105 scopus 로고    scopus 로고
    • The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: Heat-labile enterotoxin, a multivalent test case
    • Minke, W. E.; Diller, D. J.; Hol, W. G. J.; Verlinde, C. The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: Heat-labile enterotoxin, a multivalent test case. J. Med. Chem. 1999, 42, 1778-1788.
    • (1999) J. Med. Chem. , vol.42 , pp. 1778-1788
    • Minke, W.E.1    Diller, D.J.2    Hol, W.G.J.3    Verlinde, C.4
  • 59
    • 0033081482 scopus 로고    scopus 로고
    • Modelling of factor Xa-inhibitor complexes: A computational flexible docking approach
    • Rao, M. S.; Olson, A. J. Modelling of factor Xa-inhibitor complexes: a computational flexible docking approach. Proteins 1999, 34, 173-183.
    • (1999) Proteins , vol.34 , pp. 173-183
    • Rao, M.S.1    Olson, A.J.2
  • 62
    • 0036973210 scopus 로고    scopus 로고
    • Methodology and problems of protein-ligand docking: Case study of dihydroorotate dehydrogenase, thymidine kinase, and phosphodiesterase 4
    • Pospisil, P.; Kuoni, T.; Scapozza, L.; Folkers, G. Methodology and problems of protein-ligand docking: case study of dihydroorotate dehydrogenase, thymidine kinase, and phosphodiesterase 4. J. Recept. Signal Transduction 2002, 22, 141-154.
    • (2002) J. Recept. Signal Transduction , vol.22 , pp. 141-154
    • Pospisil, P.1    Kuoni, T.2    Scapozza, L.3    Folkers, G.4
  • 63
  • 64
    • 0346731234 scopus 로고    scopus 로고
    • HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases
    • Floriano, W. B.; Vaidehi, N.; Zamanakos, G.; Goddard, W. A., III. HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. J. Med. Chem. 2004, 47, 56-71.
    • (2004) J. Med. Chem. , vol.47 , pp. 56-71
    • Floriano, W.B.1    Vaidehi, N.2    Zamanakos, G.3    Goddard III, W.A.4
  • 65
    • 12844260196 scopus 로고    scopus 로고
    • Docking studies on PARP-1 inhibitors: Insights into the role of a binding pocket water molecule
    • Bellocchi, D.; Macchiarulo, A.; Costantino, G.; Pellicciari, R. Docking studies on PARP-1 inhibitors: insights into the role of a binding pocket water molecule. Bioorg. Med. Chem. 2005, 13, 1151-1157.
    • (2005) Bioorg. Med. Chem. , vol.13 , pp. 1151-1157
    • Bellocchi, D.1    Macchiarulo, A.2    Costantino, G.3    Pellicciari, R.4
  • 66
    • 20444427212 scopus 로고    scopus 로고
    • Virtual screening of 4-anilinoquinazoline analogues as EGFR kinase inhibitors: Importance of hydrogen bonds in the evaluation of poses and scoring functions
    • Aparna, V.; Rambabu, G.; Panigrahi, S. K.; Sarma, J. A.; Desiraju, G. R. Virtual screening of 4-anilinoquinazoline analogues as EGFR kinase inhibitors: importance of hydrogen bonds in the evaluation of poses and scoring functions. J. Chem. Inf. Model. 2005, 45, 725-738.
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 725-738
    • Aparna, V.1    Rambabu, G.2    Panigrahi, S.K.3    Sarma, J.A.4    Desiraju, G.R.5
  • 68
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R. X.; Lu, Y. P.; Wang, S. M. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46, 2287-2303.
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.X.1    Lu, Y.P.2    Wang, S.M.3
  • 70
    • 0041698413 scopus 로고    scopus 로고
    • Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition
    • Susnow, R. G.; Dixon, S. L. Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition. J. Chem. Inf. Comput. Sci. 2003, 43, 1308-1315.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 1308-1315
    • Susnow, R.G.1    Dixon, S.L.2
  • 71
    • 0037432069 scopus 로고    scopus 로고
    • Role of glutamic acid 216 in cytochrome P450 2D6 substrate binding and catalysis
    • Guengerich, F. P.; Hanna, I. H.; Martin, M. V.; Gillam, E. M. Role of glutamic acid 216 in cytochrome P450 2D6 substrate binding and catalysis. Biochemistry 2003, 42, 1245-1253.
    • (2003) Biochemistry , vol.42 , pp. 1245-1253
    • Guengerich, F.P.1    Hanna, I.H.2    Martin, M.V.3    Gillam, E.M.4
  • 72
    • 0037423276 scopus 로고    scopus 로고
    • Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6
    • Paine, M. J.; McLaughlin, L. A.; Flanagan, J. U.; Kemp, C. A.; Sutcliffe, M. J.; et al. Residues glutamate 216 and aspartate 301 are key determinants of substrate specificity and product regioselectivity in cytochrome P450 2D6. J. Biol. Chem. 2003, 278, 4021-4027.
    • (2003) J. Biol. Chem. , vol.278 , pp. 4021-4027
    • Paine, M.J.1    McLaughlin, L.A.2    Flanagan, J.U.3    Kemp, C.A.4    Sutcliffe, M.J.5
  • 73
    • 5044245324 scopus 로고    scopus 로고
    • Phe120 contributes to the regiospecificity of cytochrome P450 2D6: Mutation leads to the formation of a novel dextromethorphan metabolite
    • Flanagan, J. U.; Marechal, J. D.; Ward, R.; Kemp, C. A.; McLaughlin, L. A.; et al. Phe120 contributes to the regiospecificity of cytochrome P450 2D6: mutation leads to the formation of a novel dextromethorphan metabolite. Biochem. J. 2004, 380, 353-360.
    • (2004) Biochem. J. , vol.380 , pp. 353-360
    • Flanagan, J.U.1    Marechal, J.D.2    Ward, R.3    Kemp, C.A.4    McLaughlin, L.A.5
  • 74
    • 0034284367 scopus 로고    scopus 로고
    • Similarity-driven flexible ligand docking
    • Fradera, X.; Knegtel, R. M.; Mestres, J. Similarity-driven flexible ligand docking. Proteins 2000, 40, 623-636.
    • (2000) Proteins , vol.40 , pp. 623-636
    • Fradera, X.1    Knegtel, R.M.2    Mestres, J.3
  • 76
    • 11144244970 scopus 로고    scopus 로고
    • Ph4Dock: Pharmacophore-based protein-ligand docking
    • Goto, J.; Kataoka, R.; Hirayama, N. Ph4Dock: pharmacophore-based protein-ligand docking. J. Med. Chem. 2004, 47, 6804-6811.
    • (2004) J. Med. Chem. , vol.47 , pp. 6804-6811
    • Goto, J.1    Kataoka, R.2    Hirayama, N.3
  • 77
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
    • Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins 1999, 37, 228-241.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 78
    • 2442486800 scopus 로고    scopus 로고
    • Impact of receptor conformation on in silico screening performance
    • Merlitz, H.; Burghardt, B.; Wenzel, W. Impact of receptor conformation on in silico screening performance. Chem. Phys. Lett. 2004, 390, 500-505.
    • (2004) Chem. Phys. Lett. , vol.390 , pp. 500-505
    • Merlitz, H.1    Burghardt, B.2    Wenzel, W.3
  • 82
    • 0032876070 scopus 로고    scopus 로고
    • Design, synthesis, and characterization of 7-methoxy-4-(aminomethyl) coumarin as a novel and selective cytochrome P450 2D6 substrate suitable for high-throughput screening
    • Onderwater, R. C.; Venhorst, J.; Commandeur, J. N. M.; Vermeulen, N. P. E. Design, synthesis, and characterization of 7-methoxy-4-(aminomethyl)coumarin as a novel and selective cytochrome P450 2D6 substrate suitable for high-throughput screening. Chem. Res. Toxicol. 1999, 12, 555-559.
    • (1999) Chem. Res. Toxicol. , vol.12 , pp. 555-559
    • Onderwater, R.C.1    Venhorst, J.2    Commandeur, J.N.M.3    Vermeulen, N.P.E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.