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Volumn 46, Issue 6, 2006, Pages 2684-2691

Pocket v.2: Further developments on receptor-based pharmacophore modeling

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DRUG PRODUCTS; ENZYMES; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; PROTEINS;

EID: 33845727607     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci600246s     Document Type: Article
Times cited : (119)

References (42)
  • 1
    • 0001462919 scopus 로고
    • Three-dimensional pharmacophoric pattern searching
    • Gund, P. Three-dimensional Pharmacophoric Pattern Searching. Prog. Mol. Subcell. Biol. 1977, 5, 117-143.
    • (1977) Prog. Mol. Subcell. Biol. , vol.5 , pp. 117-143
    • Gund, P.1
  • 3
    • 0141882047 scopus 로고    scopus 로고
    • History and evolution of the pharmacophore model concept in computer-aided drug design
    • Güner, O. F. History and evolution of the pharmacophore model concept in computer-aided drug design. Curr. Top. Med. Chem. 2002, 2, 1321-1332.
    • (2002) Curr. Top. Med. Chem. , vol.2 , pp. 1321-1332
    • Güner, O.F.1
  • 4
    • 0347755449 scopus 로고    scopus 로고
    • Predicting molecular interactions in silico: 1. A guide to pharmacophore identification and its applications to drug design
    • Dror, O.; Shulman-Peleg, A.; Nussinov R.; Wolfson, H. J. Predicting Molecular Interactions in silico: 1. A Guide to Pharmacophore Identification and its Applications to Drug Design. Curr. Med. Chem. 2004, 11, 71-90.
    • (2004) Curr. Med. Chem. , vol.11 , pp. 71-90
    • Dror, O.1    Shulman-Peleg, A.2    Nussinov, R.3    Wolfson, H.J.4
  • 5
    • 0027548454 scopus 로고
    • A fast new approach to pharmacophore model mapping and its application to dopaminergic and benzodiazepine agonists
    • Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. A fast new approach to pharmacophore model mapping and its application to dopaminergic and benzodiazepine agonists. J. Comput.-Aided Mol. Des. 1993, 7, 83-102.
    • (1993) J. Comput.-aided Mol. Des. , vol.7 , pp. 83-102
    • Martin, Y.C.1    Bures, M.G.2    Danaher, E.A.3    Delazzer, J.4    Lico, I.5    Pavlik, P.A.6
  • 6
    • 0030137662 scopus 로고    scopus 로고
    • Identification of common functional configurations among molecules
    • Barnum, D.; Greene, J.; Smellie, A.; Sprague, P. Identification of common functional configurations among molecules. J. Chem. Inf. Comput. Sci. 1996, 36, 563-571.
    • (1996) J. Chem. Inf. Comput. Sci. , vol.36 , pp. 563-571
    • Barnum, D.1    Greene, J.2    Smellie, A.3    Sprague, P.4
  • 8
    • 84986522856 scopus 로고
    • Poling: Promoting conformational variation
    • Smellie, A.; Teig, S. L.; Towbin, P. Poling: Promoting conformational variation. J. Comput. Chem. 1995, 16, 171-187.
    • (1995) J. Comput. Chem. , vol.16 , pp. 171-187
    • Smellie, A.1    Teig, S.L.2    Towbin, P.3
  • 9
    • 0029444383 scopus 로고
    • A genetic algorithm for flexible molecular overlay and pharmacophore model elucidation
    • Jones, G.; Willett, P.; Glen, R. C. A genetic algorithm for flexible molecular overlay and pharmacophore model elucidation. J. Comput.-Aided Mol. Des. 1995, 9, 532-549.
    • (1995) J. Comput.-aided Mol. Des. , vol.9 , pp. 532-549
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 10
    • 0041488802 scopus 로고    scopus 로고
    • Pharmacophore discovery -Lessons learned
    • John H. V. D. Pharmacophore discovery -Lessons learned. Curr. Pharm. Des. 2003, 9, 1649-1664.
    • (2003) Curr. Pharm. Des. , vol.9 , pp. 1649-1664
    • John, H.V.D.1
  • 11
    • 0036706746 scopus 로고    scopus 로고
    • A comparison of the pharmacophore model identification programs: Catalyst, DISCO and GASP
    • Patel, Y.; Gillet, V. J.; Bravi, G.; Leach, A. R. A comparison of the pharmacophore model identification programs: Catalyst, DISCO and GASP. J. Comput. -Aided Mol. Des. 2002, 16, 653-681.
    • (2002) J. Comput. -aided Mol. Des. , vol.16 , pp. 653-681
    • Patel, Y.1    Gillet, V.J.2    Bravi, G.3    Leach, A.R.4
  • 13
    • 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
  • 14
    • 0024566942 scopus 로고
    • New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
    • Boobbyer, D. N.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J. Med. Chem. 1989, 32, 1083-1094.
    • (1989) J. Med. Chem. , vol.32 , pp. 1083-1094
    • Boobbyer, D.N.1    Goodford, P.J.2    McWhinnie, P.M.3    Wade, R.C.4
  • 15
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt, S.; Kuhn, D.; Klebe, G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol Biol. 2002, 323, 387-406.
    • (2002) J. Mol Biol. , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 16
    • 0141482410 scopus 로고    scopus 로고
    • Common structural cliques: A tool for protein structure and function analysis
    • Mariusz M.; SaǍndor S.; Krzysztof A. O. Common Structural Cliques: a tool for protein structure and function analysis. Protein Eng. 2003, 16, 543-552.
    • (2003) Protein Eng. , vol.16 , pp. 543-552
    • Mariusz, M.1    Saǎndor, S.2    Krzysztof, A.O.3
  • 17
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Bohm, H. J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J. Comput.-Aided Mol. Des. 1992, 6, 61-78.
    • (1992) J. Comput.-aided Mol. Des. , vol.6 , pp. 61-78
    • Bohm, H.J.1
  • 18
    • 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
  • 20
    • 0030253210 scopus 로고    scopus 로고
    • Activesite-directed 3D database searching: Pharmacophore extraction and validation of hits
    • Clark, D. E.; Westhead, D. R.; Sykes, R. A.; Murray, C. W. Activesite-directed 3D database searching: Pharmacophore extraction and validation of hits. J. Comput.-Aided Mol. Des. 1996, 10, 397-416.
    • (1996) J. Comput.-aided Mol. Des. , vol.10 , pp. 397-416
    • Clark, D.E.1    Westhead, D.R.2    Sykes, R.A.3    Murray, C.W.4
  • 21
    • 0035002051 scopus 로고    scopus 로고
    • Structure-based focusing using pharmacophore models derived from the active site of 17beta-hydroxysteroid dehydrogenase
    • Hoffren, A. M.; Murray, C. M.; Hoffmann, R. D. Structure-based focusing using pharmacophore models derived from the active site of 17beta-hydroxysteroid dehydrogenase. Curr. Pharm. Des. 2001, 7, 547-566.
    • (2001) Curr. Pharm. Des. , vol.7 , pp. 547-566
    • Hoffren, A.M.1    Murray, C.M.2    Hoffmann, R.D.3
  • 23
    • 0000217414 scopus 로고    scopus 로고
    • LigBuilder: A multi-purpose program for structure-based drug design
    • Wang, R. X.; Gao, Y.; Lai, L. H. LigBuilder: a multi-purpose program for structure-based drug design. J. Mol. Model. 2000, 6, 498-516.
    • (2000) J. Mol. Model. , vol.6 , pp. 498-516
    • Wang, R.X.1    Gao, Y.2    Lai, L.H.3
  • 24
    • 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
  • 25
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44, 1035-1042.
    • (2001) J. Med. Chem. , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 26
    • 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
  • 27
    • 0035011980 scopus 로고    scopus 로고
    • Protein ligand docking based on empirical method for binding affinity estimation
    • Tao, P.; Lai, L. H. Protein ligand docking based on empirical method for binding affinity estimation. J. Comput.-Aided Mol. Des. 2001, 5, 429-446.
    • (2001) J. Comput.-aided Mol. Des. , vol.5 , pp. 429-446
    • Tao, P.1    Lai, L.H.2
  • 28
    • 0032214649 scopus 로고    scopus 로고
    • Databases for protein-ligand complexes
    • Hendlich, M. Databases for Protein-Ligand Complexes. Acta Crystallogr. 1998, 54, 1178-1182.
    • (1998) Acta Crystallogr. , vol.54 , pp. 1178-1182
    • Hendlich, M.1
  • 29
    • 20444422149 scopus 로고    scopus 로고
    • The PDBbind database: Methodologies and updates
    • Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind Database: Methodologies and updates. J. Med. Chem. 2005, 48, 4111-4119.
    • (2005) J. Med. Chem. , vol.48 , pp. 4111-4119
    • Wang, R.1    Fang, X.2    Lu, Y.3    Yang, C.-Y.4    Wang, S.5
  • 30
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind Database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 2004, 47, 2977-2980.
    • (2004) J. Med. Chem. , vol.47 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 31
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S. J. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discovery 2003, 2, 527-541.
    • (2003) Nat. Rev. Drug Discovery , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 32
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
    • (2004) J. Med. Chem. , vol.47 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 33
    • 0036019065 scopus 로고    scopus 로고
    • Protein flexibility is an important component of structure-based drug discovery
    • Carlson, H. A. Protein flexibility is an important component of structure-based drug discovery. Curr. Pharm. Des. 2002, 8, 1571-1578.
    • (2002) Curr. Pharm. Des. , vol.8 , pp. 1571-1578
    • Carlson, H.A.1
  • 34
    • 0346022974 scopus 로고    scopus 로고
    • Understanding protein-ligand interactions: The price of protein flexibility
    • Rauh, D.; Klebe, G.; Stubbs, M. T. Understanding protein-ligand interactions: the price of protein flexibility. J. Mol. Biol. 2004, 335, 1325-1341.
    • (2004) J. Mol. Biol. , vol.335 , pp. 1325-1341
    • Rauh, D.1    Klebe, G.2    Stubbs, M.T.3
  • 35
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson, H. A.; McCammon, J. A. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 2000, 57, 213-218.
    • (2000) Mol. Pharmacol. , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 36
    • 0036680063 scopus 로고    scopus 로고
    • Protein flexibility and drug design: How to hit a moving target
    • Carlson, H. A. Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 2002, 6, 447-452.
    • (2002) Curr. Opin. Chem. Biol. , vol.6 , pp. 447-452
    • Carlson, H.A.1
  • 37
  • 38
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng E. C.; Shoichet B. K.; Kuntz I. D. Automated docking with grid-based energy evaluation. J. Comput. Chem. 1992, 13, 505-524.
    • (1992) J. Comput. Chem. , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 40
    • 0027385177 scopus 로고
    • Matching chemistry and shape in molecular docking
    • Shoichet B. K.; Kuntz I. D. Matching chemistry and shape in molecular docking. Protein Eng. 1993, 6, 723-732.
    • (1993) Protein Eng. , vol.6 , pp. 723-732
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 42
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, A. C.; Laskowski, R. A.; Thornton J. M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8, 127-134.
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.