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Volumn 11, Issue 1, 2004, Pages 71-90

Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design

Author keywords

Computer aided drug design; De Novo design; Docking; Lead generation; Pharmacophore fingerprints; Pharmacophore mapping; Pharmacophore modeling; Pharmacophore searching; Receptor based pharmacophore; Virtual screening

Indexed keywords

DRUG; LIGAND; RECEPTOR PROTEIN;

EID: 0347755449     PISSN: 09298673     EISSN: None     Source Type: Journal    
DOI: 10.2174/0929867043456287     Document Type: Review
Times cited : (138)

References (144)
  • 2
    • 5244326376 scopus 로고
    • Berichte der Deutschen chemischen Gesellschaft
    • In German
    • Ehrlich, P. Berichte der Deutschen chemischen Gesellschaft 1909, 42, 17-47, In German.
    • (1909) , vol.42 , pp. 17-47
    • Ehrlich, P.1
  • 4
    • 0348058950 scopus 로고    scopus 로고
    • Pharmacophore and Drug Discovery
    • Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P. R., Eds.; John Wiley & Sons: Chichester, UK
    • Milne, G. W.A. Pharmacophore and Drug Discovery. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P. R., Eds.; John Wiley & Sons: Chichester, UK: 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Milne, G.W.A.1
  • 5
    • 0348126978 scopus 로고    scopus 로고
    • Molecular Superposition
    • Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P. R., Eds.; John Wiley & Sons: Chichester, UK: Online available at
    • Miller, M. Molecular Superposition. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P. R., Eds.; John Wiley & Sons: Chichester, UK: 1998 Online available at: http://www.wiley.com/legacy/wileychi/ecc/layout.html.
    • (1998) Encyclopedia of Computational Chemistry
    • Miller, M.1
  • 6
    • 0347428532 scopus 로고    scopus 로고
    • Structure-Activity Relationships in Modeling Nucleic Acid Ligand Interactions
    • Schleyer P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, ; J., Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Leclerc, F.; Cedergren, R. Structure-Activity Relationships in Modeling Nucleic Acid Ligand Interactions. In Encyclopedia of Computational Chemistry; Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, ; J., Kollman, P. A.; Schaefer, III, H. F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Leclerc, F.1    Cedergren, R.2
  • 9
    • 0000460468 scopus 로고
    • The Conformational Parameter in Drug Design: The Active Analog Approach
    • Olson, E.; Christoffersen, R., Eds.; ACS, Washington, DC
    • Marshall, G.; Barry, C.; Bosshard, H.; Dammkoehler, R.; Dunn, D. The Conformational Parameter in Drug Design: The Active Analog Approach. In Computer-Assisted Drug Design, Vol. 112; Olson, E.; Christoffersen, R., Eds.; ACS, Washington, DC: 1979.
    • (1979) Computer-Assisted Drug Design , vol.112
    • Marshall, G.1    Barry, C.2    Bosshard, H.3    Dammkoehler, R.4    Dunn, D.5
  • 10
    • 0007864877 scopus 로고    scopus 로고
    • Pharmacophore Perception, Development, and Use in Drug Design
    • International University Line: La Jolla, CA, USA, Chapter Pharmacophore Definition Using the Active Analog Approach
    • Beusen, D.D.; Marshall, G.R. Pharmacophore Perception, Development, and Use in Drug Design. In ; International University Line: La Jolla, CA, USA, 2000; Chapter Pharmacophore Definition Using the Active Analog Approach, 21-45.
    • (2000) , pp. 21-45
    • Beusen, D.D.1    Marshall, G.R.2
  • 11
    • 0346798070 scopus 로고    scopus 로고
    • Tripos Inc., "Receptor"
    • Tripos Inc., "Receptor", http://www.tripos.com/sciTech/inSilicoDisc/pharmaPerception/receptor.html
  • 16
    • 0002212887 scopus 로고    scopus 로고
    • International University Line: La Jolla, CA, USA, Chapter HipHop: Pharmacophores Based on Multiple Common-Feature Alignments
    • Clement, O.A.; Mehl, A.T. Pharmacophore Perception, Development, and Use in Drug Design. In International University Line: La Jolla, CA, USA, 2000; Chapter HipHop: Pharmacophores Based on Multiple Common-Feature Alignments, 69-84.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Design , pp. 69-84
    • Clement, O.A.1    Mehl, A.T.2
  • 19
    • 0013122190 scopus 로고    scopus 로고
    • International University Line: La Jolla, CA, USA, Chapter DISCO: What We Did Right and What We Missed
    • Martin, Y.C. Pharmacophore Perception, Development, and Use in Drug Design. In International University Line: La Jolla, CA, USA, 2000; Chapter DISCO: What We Did Right and What We Missed, 49-68.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Design , pp. 49-68
    • Martin, Y.C.1
  • 21
    • 0001383234 scopus 로고    scopus 로고
    • International University Line: La Jolla, CA, USA, Chapter HypGen: An automated system for generating 3D predictive pharmacophore models
    • Li, H.; Sutter, J.; Hoffmann, R. Pharmacophore Perception, Development, and Use in Drug Design. In International University Line: La Jolla, CA, USA, 2000; Chapter HypGen: An automated system for generating 3D predictive pharmacophore models, 171-189.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Design , pp. 171-189
    • Li, H.1    Sutter, J.2    Hoffmann, R.3
  • 25
    • 85050522215 scopus 로고
    • Aspects of molecular modeling
    • Lipkowitz, K.; Boyd, D.B., Eds.; VCH Publishers
    • Boyd, D.B. Aspects of molecular modeling. In Reviews in Computational Chemistry, Vol. 1; Lipkowitz, K.; Boyd, D.B., Eds.; VCH Publishers, 1990.
    • (1990) Reviews in Computational Chemistry , vol.1
    • Boyd, D.B.1
  • 35
    • 0348058948 scopus 로고    scopus 로고
    • Molecular Simulations Inc. (MSI), "Catalyst Software"
    • Molecular Simulations Inc. (MSI), "Catalyst Software", http://www.accelrys.com/about/msi.html
  • 45
    • 0002761314 scopus 로고    scopus 로고
    • Genetic Algorithms: Introduction and Applications
    • Schleyer, P.V. R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Venkatasubramanian, V.; Sundaram, A. Genetic Algorithms: Introduction and Applications. In Encyclopedia of Computational Chemistry; Schleyer, P.V. R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK: 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Venkatasubramanian, V.1    Sundaram, A.2
  • 46
    • 0007627926 scopus 로고    scopus 로고
    • Genetic and Evolutionary Algorithms
    • Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Jones, G. Genetic and Evolutionary Algorithms. In Encyclopedia of Computational Chemistry; Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK: 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Jones, G.1
  • 48
    • 64949109013 scopus 로고    scopus 로고
    • International University Line: La Jolla, CA, USA, Chapter Pharmacophores Derived from the 3D Substructure Perception
    • Handshuh, S.; Gasteiger, J. Pharmacophore Perception, Development, and Use in Drug Design. In International University Line: La Jolla, CA, USA, 2000; Chapter Pharmacophores Derived from the 3D Substructure Perception, 429-454.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Design , pp. 429-454
    • Handshuh, S.1    Gasteiger, J.2
  • 51
  • 54
    • 0346167518 scopus 로고    scopus 로고
    • Accelrys Inc., "Structure-Based Focusing"
    • Accelrys Inc., "Structure-Based Focusing", http://www.accelrys.com/cerius2/c2sbf.html.
  • 57
    • 0038179010 scopus 로고    scopus 로고
    • MultiProt - A Multiple Protein Structural Alignment Algorithm
    • Guigo, R.; Gusfield, D., Eds.; Springer Verlag: Rome, Italy, Lecture Notes in Computer Science
    • Shatsky, M.; Nussinov, R.; Wolfson, H. MultiProt - a Multiple Protein Structural Alignment Algorithm. In Workshop on Algorithms in Bioinformatics; Guigo, R.; Gusfield, D., Eds.; Springer Verlag: Rome, Italy, 2002 Lecture Notes in Computer Science 2452.
    • (2002) Workshop on Algorithms in Bioinformatics , pp. 2452
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.3
  • 58
    • 0142143332 scopus 로고    scopus 로고
    • MASS: Multiple Structural Alignment by Secondary Structures
    • Dror, O.; Benyamini, H.; Nussinov, R.; Wolfson, H. MASS: Multiple Structural Alignment by Secondary Structures, Bioinformatics 2003, 19 suppl. 95-104.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. , pp. 95-104
    • Dror, O.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.4
  • 62
    • 0346167517 scopus 로고    scopus 로고
    • Technique for developing a pharmacophore model that accommodates inherent protein flexibility: An application to HIV-1 integrase
    • Guner, O.F., Ed.; International University Line: La Jolla, CA, USA
    • Masukawa, K.M.; Carlson, H.A.; McCammon, J.A. Technique for developing a pharmacophore model that accommodates inherent protein flexibility: an application to HIV-1 integrase. In Pharmacophore Perception, Development, and Use in Drug Design; Guner, O.F., Ed.; International University Line: La Jolla, CA, USA, 2000.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Design
    • Masukawa, K.M.1    Carlson, H.A.2    McCammon, J.A.3
  • 81
    • 0344236539 scopus 로고    scopus 로고
    • International University Line: La Jolla, CA, USA, Chapter Exploring Pharmacophores with Chem-X
    • Cato, S. Pharmacophore Perception, Development, and Use in Drug Design. In International University Line: La Jolla, CA, USA, 2000; Chapter Exploring Pharmacophores with Chem-X, 107-125.
    • (2000) Pharmacophore Perception, Development, and Use in Drug Design , pp. 107-125
    • Cato, S.1
  • 88
    • 0348058892 scopus 로고    scopus 로고
    • Structure Databases
    • Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Paris, C.G. Structure Databases. In Encyclopedia of Computational Chemistry; Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Paris, C.G.1
  • 89
    • 0347428523 scopus 로고    scopus 로고
    • MDL InformationSystems, Inc. "ACD (Available Chemicals Directory )"
    • MDL InformationSystems, Inc. "ACD (Available Chemicals Directory)", 1997, http://www.daylight.com/products/databases/ACD.html.
    • (1997)
  • 90
    • 0348058942 scopus 로고    scopus 로고
    • "CSD (Cambridge Structural Database)"
    • "CSD (Cambridge Structural Database)", http://www.cmbi.kun.nl/cheminf/csd.
  • 92
    • 0001778240 scopus 로고    scopus 로고
    • Three-dimensional Structure Searching
    • Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Güner, O.F.; Henry, D.R. Three-dimensional Structure Searching. In Encyclopedia of Computational Chemistry; Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK:, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Güner, O.F.1    Henry, D.R.2
  • 94
    • 0346798067 scopus 로고    scopus 로고
    • "3D pharmacophore searching", Online available at
    • Davies, K.; Upton, R. "3D pharmacophore searching", Online available at http://www.netsci.org/Science/Cheminform/feature02.html.
    • Davies, K.1    Upton, R.2
  • 99
    • 0002336415 scopus 로고    scopus 로고
    • High-throughput 'Virtual' Chemistry
    • Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Walters, W.P.; Stahl, M.T.; A., M.M. High-throughput 'Virtual' Chemistry. In Encyclopedia of Computational Chemistry; Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK:, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Walters, W.P.1    Stahl, M.T.2    Stahl, A.M.M.3
  • 100
    • 0348058890 scopus 로고    scopus 로고
    • "3D database searching in drug discovery"
    • Online available at
    • VanDrie, J.H. "3D database searching in drug discovery", Online available at http://www.netsci.org/Science/Cheminform/featute06.html.
    • VanDrie, J.H.1
  • 105
    • 0347428474 scopus 로고    scopus 로고
    • "ConFirm, Catalyst Software"
    • Molecular Simulations Inc. (MSI)
    • Molecular Simulations Inc. (MSI), "ConFirm, Catalyst Software", http://www.accelrys.com/catalyst/confirm.html.
  • 106
    • 0346167454 scopus 로고    scopus 로고
    • Oxford Molecular Group "Chem-X Software"
    • Oxford Molecular Group, "Chem-X Software", 1998, http://www.accelrys.com/about/oxmol.html.
    • (1998)
  • 108
    • 0346798066 scopus 로고    scopus 로고
    • "UNITY Software"
    • Tripos Inc
    • Tripos Inc., "UNITY Software", http://www.tripos.com/sciTech/inSilicoDisc/chemInfo/unity.html
  • 110
    • 0348058891 scopus 로고    scopus 로고
    • "ISIS/3D"
    • MDL Information Systems, Inc
    • MDL Information Systems, Inc., "ISIS/3D", http://www..mdli.com.
  • 117
    • 0011418296 scopus 로고    scopus 로고
    • Conformational flexibility in 3D structural database searching
    • Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Henry, D.R.; Özkabak, A.G. Conformational flexibility in 3D structural database searching. In Encyclopedia of Computational Chemistry; Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK:, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Henry, D.R.1    Özkabak, A.G.2
  • 135
  • 142
    • 0002638507 scopus 로고    scopus 로고
    • Comparative Molecular Field Analysis (CoMFA)
    • Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK
    • Kubinyi, H. Comparative Molecular Field Analysis (CoMFA). In Encyclopedia of Computational Chemistry; Schleyer, P. v.R.; Allinger, N.L.; Clark, T.; Gasteiger, ; J., Kollman, P.A.; Schaefer, III, H.F.; Schreiner, P.R., Eds.; John Wiley & Sons: Chichester, UK:, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Kubinyi, H.1
  • 143
    • 0348058950 scopus 로고    scopus 로고
    • Pharmacophore and drug discovery
    • von RagueSchleyer, P., Ed.; Wiley: New York, USA
    • Milne, G. W.A. Pharmacophore and drug discovery. In Encyclopedia of computational chemistry; von RagueSchleyer, P., Ed.; Wiley: New York, USA, 1998.
    • (1998) Encyclopedia of Computational Chemistry
    • Milne, G.W.A.1
  • 144
    • 0029119568 scopus 로고
    • Manual is available on
    • Sayle, R.; Milner-White, E. Trends Biochem. Sci. 1995, 20, 374 Manual is available on http://info.bio.cmu.edu/Courses/BiochemMols/RasFrames/TOC.HTM.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 374
    • Sayle, R.1    Milner-White, E.2


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