메뉴 건너뛰기




Volumn 49, Issue 6, 2009, Pages 1330-1346

Use of reduced graphs to encode bioisosterism for similarity-based virtual screening

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; ENCODING (SYMBOLS); SCAFFOLDS;

EID: 67650086695     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900078h     Document Type: Article
Times cited : (28)

References (41)
  • 3
    • 46249099840 scopus 로고    scopus 로고
    • From Chemical Documentation to Chemoinformatics: Fifty Years of Chemical Information Science
    • Willett, P. From Chemical Documentation to Chemoinformatics: Fifty Years of Chemical Information Science. J. Inf. Sci. 2008, 34, 477-499.
    • (2008) J. Inf. Sci , vol.34 , pp. 477-499
    • Willett, P.1
  • 5
    • 0006908514 scopus 로고
    • Isosterism and Molecular Modification in Drug Design
    • Thornber, C. W. Isosterism and Molecular Modification in Drug Design. Quart. Rev. Chem. 1979, 8, 563-579.
    • (1979) Quart. Rev. Chem , vol.8 , pp. 563-579
    • Thornber, C.W.1
  • 6
    • 0025995750 scopus 로고
    • Isosterism and Bioisosterism in Drug Design
    • Burger, A. Isosterism and Bioisosterism in Drug Design. Prog. Drug Res. 1991, 37, 287-367.
    • (1991) Prog. Drug Res , vol.37 , pp. 287-367
    • Burger, A.1
  • 7
    • 7744243992 scopus 로고    scopus 로고
    • Patani, G. A.; LaVoie, E. J. Bioisosterism: A Rational Approach in Drug Design. Chem. Rev. 1996, 96, 3147-3176.
    • Patani, G. A.; LaVoie, E. J. Bioisosterism: A Rational Approach in Drug Design. Chem. Rev. 1996, 96, 3147-3176.
  • 8
    • 0000166488 scopus 로고    scopus 로고
    • Similarity and Dissimilarity: A Medicinal Chemist's View
    • Kubinyi, H. Similarity and Dissimilarity: A Medicinal Chemist's View. Perspect. Drug Discovery Des. 1998, 9-11, 225-232.
    • (1998) Perspect. Drug Discovery Des , vol.9-11 , pp. 225-232
    • Kubinyi, H.1
  • 9
    • 0034924558 scopus 로고    scopus 로고
    • The Use of Bioisosteric Groups in Lead Optimisation
    • Olesen, P. H. The Use of Bioisosteric Groups in Lead Optimisation. Curr. Opin. Drug Discovery Dev. 2001, 4, 471-478.
    • (2001) Curr. Opin. Drug Discovery Dev , vol.4 , pp. 471-478
    • Olesen, P.H.1
  • 11
    • 11844255399 scopus 로고    scopus 로고
    • Lima, L. M.; Barreiro, E. J. Bioisosterism: A Useful Strategy for Molecular Modification and Drug Design. Curr. Med. Chem. 2005, 12, 23-49.
    • Lima, L. M.; Barreiro, E. J. Bioisosterism: A Useful Strategy for Molecular Modification and Drug Design. Curr. Med. Chem. 2005, 12, 23-49.
  • 12
  • 13
    • 33750701141 scopus 로고    scopus 로고
    • On Scaffolds and Hopping in Medicinal Chemistry
    • Brown, N.; Jacoby, E. On Scaffolds and Hopping in Medicinal Chemistry. Mini-Rev. Med. Chem. 2006, 6, 1217-1229.
    • (2006) Mini-Rev. Med. Chem , vol.6 , pp. 1217-1229
    • Brown, N.1    Jacoby, E.2
  • 14
    • 0004489584 scopus 로고    scopus 로고
    • a Database of Structurally Analogous Compounds
    • Ujváry, I. Bioster - a Database of Structurally Analogous Compounds. Pest. Sci. 1997, 51, 92-95.
    • (1997) Pest. Sci , vol.51 , pp. 92-95
    • Ujváry, I.B.1
  • 15
    • 0001696622 scopus 로고    scopus 로고
    • Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the Bioster Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors
    • Schuffenhauer, A.; Gillet, V. J.; Willett, P. Similarity Searching in Files of Three-Dimensional Chemical Structures: Analysis of the Bioster Database Using Two-Dimensional Fingerprints and Molecular Field Descriptors. J. Chem. Inf. Comput. Sci. 2000, 40, 295-307.
    • (2000) J. Chem. Inf. Comput. Sci , vol.40 , pp. 295-307
    • Schuffenhauer, A.1    Gillet, V.J.2    Willett, P.3
  • 16
    • 0037365304 scopus 로고    scopus 로고
    • Calculation of Intersubstutuent Similarity Using R-Group Descriptors
    • Holliday, J. D.; Jelfs, S. P.; Willett, P. Calculation of Intersubstutuent Similarity Using R-Group Descriptors. J. Chem. Inf. Comput. Sci. 2003, 43, 406-411.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 406-411
    • Holliday, J.D.1    Jelfs, S.P.2    Willett, P.3
  • 17
    • 33646237557 scopus 로고    scopus 로고
    • The Quest for Bioisosteric Replacements
    • Wagener, M.; Lommerse, J. P. M. The Quest for Bioisosteric Replacements. J. Chem. Inf. Model. 2006, 46, 677-685.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 677-685
    • Wagener, M.1    Lommerse, J.P.M.2
  • 18
    • 33845379303 scopus 로고
    • Atom Pairs as Molecular-Features in Structure Activity Studies - Definition and Applications
    • Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom Pairs as Molecular-Features in Structure Activity Studies - Definition and Applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
    • (1985) J. Chem. Inf. Comput. Sci , vol.25 , pp. 64-73
    • Carhart, R.E.1    Smith, D.H.2    Venkataraghavan, R.3
  • 19
    • 0036025428 scopus 로고    scopus 로고
    • The Most Common Chemical Replacements in Drug-Like Compounds
    • Sheridan, R. P. The Most Common Chemical Replacements in Drug-Like Compounds. J. Chem. Inf. Comput. Sci. 2002, 42, 103-108.
    • (2002) J. Chem. Inf. Comput. Sci , vol.42 , pp. 103-108
    • Sheridan, R.P.1
  • 20
    • 34547659363 scopus 로고    scopus 로고
    • A Database of Historically-Observed Chemical Replacements
    • Haubertin, D. Y.; Bruneau, P. A Database of Historically-Observed Chemical Replacements. J. Chem. Inf. Model. 2007, 47, 1294-1302.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1294-1302
    • Haubertin, D.Y.1    Bruneau, P.2
  • 21
    • 33750976700 scopus 로고    scopus 로고
    • Matched Molecular Pairs as a Guide Inthe Optimization of Pharmaceutical Properties: A Study of Aqueous Solubility, Plasma Protein Binding and Oral Exposure
    • Leach, A. G.; Jones, H. D.; Cosgrove, D. A.; Kenny, P. W.; Ruston, L.; MacFaul, P.; Wood, J. M.; Colclough, N.; Law, B. Matched Molecular Pairs as a Guide Inthe Optimization of Pharmaceutical Properties: A Study of Aqueous Solubility, Plasma Protein Binding and Oral Exposure. J. Med. Chem. 2006, 49, 6672-6682.
    • (2006) J. Med. Chem , vol.49 , pp. 6672-6682
    • Leach, A.G.1    Jones, H.D.2    Cosgrove, D.A.3    Kenny, P.W.4    Ruston, L.5    MacFaul, P.6    Wood, J.M.7    Colclough, N.8    Law, B.9
  • 22
    • 33244456816 scopus 로고    scopus 로고
    • Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR
    • Sheridan, R. P.; Hunt, P.; Culbertson, J. C. Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR. J. Chem. Inf. Model. 2006, 46, 180-192.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 180-192
    • Sheridan, R.P.1    Hunt, P.2    Culbertson, J.C.3
  • 23
    • 0035207623 scopus 로고    scopus 로고
    • Calculating the Knowledge-Based Similarity of Functional Groups Using Crystallographic Data
    • Watson, P.; Willett, P.; Gillet, V. J.; Verdonk, M. L. Calculating the Knowledge-Based Similarity of Functional Groups Using Crystallographic Data. J. Comput.-Aided Mol. Des. 2001, 15, 835-857.
    • (2001) J. Comput.-Aided Mol. Des , vol.15 , pp. 835-857
    • Watson, P.1    Willett, P.2    Gillet, V.J.3    Verdonk, M.L.4
  • 24
    • 0031261930 scopus 로고    scopus 로고
    • Bruno, I. J.; Cole, J. C.; Lommerse, J. P. M.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. Isostar: A Library of Information About Non-bonded Interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
    • Bruno, I. J.; Cole, J. C.; Lommerse, J. P. M.; Rowland, R. S.; Taylor, R.; Verdonk, M. L. Isostar: A Library of Information About Non-bonded Interactions. J. Comput.-Aided Mol. Des. 1997, 11, 525-537.
  • 25
    • 33750836761 scopus 로고    scopus 로고
    • Identification of Target-Specific Bioisosteric Fragments from Ligand-Protein Crystallographic Data
    • Kennewell, E. A.; Willett, P.; Ducrot, P.; Luttman, C. Identification of Target-Specific Bioisosteric Fragments from Ligand-Protein Crystallographic Data. J. Comput.-Aided Mol. Des. 2006, 20, 385-394.
    • (2006) J. Comput.-Aided Mol. Des , vol.20 , pp. 385-394
    • Kennewell, E.A.1    Willett, P.2    Ducrot, P.3    Luttman, C.4
  • 27
    • 0023401741 scopus 로고
    • Computer-Storage and Retrieval of Generic Chemical Structures in Patents. 8. Reduced Chemical Graphs and Their Applications in Generic Chemical-Structure Retrieval
    • Gillet, V. J.; Downs, G. M.; Ling, A.; Lynch, M. F.; Venkataram, P.; Wood, J. V.; Dethlefsen, W. Computer-Storage and Retrieval of Generic Chemical Structures in Patents. 8. Reduced Chemical Graphs and Their Applications in Generic Chemical-Structure Retrieval. J. Chem. Inf. Comput. Sci. 1987, 27, 126-137.
    • (1987) J. Chem. Inf. Comput. Sci , vol.27 , pp. 126-137
    • Gillet, V.J.1    Downs, G.M.2    Ling, A.3    Lynch, M.F.4    Venkataram, P.5    Wood, J.V.6    Dethlefsen, W.7
  • 28
    • 0032149905 scopus 로고    scopus 로고
    • Feature Trees: A New Molecular Similarity Measure Based on Tree Matching
    • Rarey, M.; Dixon, J. S. Feature Trees: A New Molecular Similarity Measure Based on Tree Matching. J. Comput.-Aided Mol. Des. 1998, 12, 471-490.
    • (1998) J. Comput.-Aided Mol. Des , vol.12 , pp. 471-490
    • Rarey, M.1    Dixon, J.S.2
  • 29
    • 0034923575 scopus 로고    scopus 로고
    • Similarity Searching in Large Combinatorial Chemistry Spaces
    • Rarey, M.; Stahl, M. Similarity Searching in Large Combinatorial Chemistry Spaces. J. Comput.-Aided Mol. Des. 2001, 15, 497-520.
    • (2001) J. Comput.-Aided Mol. Des , vol.15 , pp. 497-520
    • Rarey, M.1    Stahl, M.2
  • 30
    • 39149135210 scopus 로고    scopus 로고
    • Tree Query Construction for Virtual Screening: A Statistical Analysis
    • Gerlach, C.; Broughton, H.; Zaliani, A. F. Tree Query Construction for Virtual Screening: A Statistical Analysis. J. Comput.-Aided Mol. Des. 2008, 22, 111-118.
    • (2008) J. Comput.-Aided Mol. Des , vol.22 , pp. 111-118
    • Gerlach, C.1    Broughton, H.2    Zaliani, A.F.3
  • 32
    • 10044265608 scopus 로고    scopus 로고
    • The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data
    • Harper, G.; Bravi, G. S.; Pickett, S. D.; Hussain, J.; Green, D. V. S. The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data. J. Chem. Inf. Comput. Sci. 2004, 44, 2145-2156.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 2145-2156
    • Harper, G.1    Bravi, G.S.2    Pickett, S.D.3    Hussain, J.4    Green, D.V.S.5
  • 33
    • 33646270382 scopus 로고    scopus 로고
    • Training Similarity Measures for Specific Activities: Application to Reduced Graphs
    • Birchall, K.; Gillet, V. J.; Harper, G.; Pickett, S. D. Training Similarity Measures for Specific Activities: Application to Reduced Graphs. J. Chem. Inf. Model. 2006, 46, 577-586.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 577-586
    • Birchall, K.1    Gillet, V.J.2    Harper, G.3    Pickett, S.D.4
  • 35
    • 33646261627 scopus 로고    scopus 로고
    • A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening
    • Stiefl, N.; Zaliani, A. A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening. J. Chem. Inf. Model. 2006, 46, 587-596.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 587-596
    • Stiefl, N.1    Zaliani, A.2
  • 36
    • 33751391841 scopus 로고
    • Automatic Identification of Molecular Similarity Using Reduced-Graph Representation of Chemical-Structure
    • Takahashi, Y.; Sukekawa, M.; Sasaki, S. Automatic Identification of Molecular Similarity Using Reduced-Graph Representation of Chemical-Structure. J. Chem. Inf. Comput. Sci. 1992, 32, 639-643.
    • (1992) J. Chem. Inf. Comput. Sci , vol.32 , pp. 639-643
    • Takahashi, Y.1    Sukekawa, M.2    Sasaki, S.3
  • 37
    • 34247257243 scopus 로고    scopus 로고
    • Representing Clusters Using a Maximum Common Edge Substructure Algorithm Applied to Reduced Graphs and Molecular Graphs
    • Gardiner, E. J.; Gillet, V. J.; Willett, P.; Cosgrove, D. A. Representing Clusters Using a Maximum Common Edge Substructure Algorithm Applied to Reduced Graphs and Molecular Graphs. J. Chem. Inf. Model. 2007, 47, 354-366.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 354-366
    • Gardiner, E.J.1    Gillet, V.J.2    Willett, P.3    Cosgrove, D.A.4
  • 38
    • 52049115881 scopus 로고    scopus 로고
    • Evolving Interpretable Structure-Activity Relationships. 1. Reduced Graph Queries
    • Birchall, K.; Gillet, V. J.; Harper, G.; Pickett, S. D. Evolving Interpretable Structure-Activity Relationships. 1. Reduced Graph Queries. J. Chem. Inf. Model. 2008, 48, 1543-1557.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 1543-1557
    • Birchall, K.1    Gillet, V.J.2    Harper, G.3    Pickett, S.D.4
  • 39
    • 52049117428 scopus 로고    scopus 로고
    • Evolving Interpretable Structure-Activity Relationship Models. 2. Using Multiobjective Optimization to Derive Multiple Models
    • Birchall, K.; Gillet, V. J.; Harper, G.; Pickett, S. D. Evolving Interpretable Structure-Activity Relationship Models. 2. Using Multiobjective Optimization to Derive Multiple Models. J. Chem. Inf. Model. 2008, 48, 1558-1570.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 1558-1570
    • Birchall, K.1    Gillet, V.J.2    Harper, G.3    Pickett, S.D.4
  • 40
    • 5444268169 scopus 로고    scopus 로고
    • Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients
    • Whittle, M.; Gillet, V. J.; Willett, P.; Alex, A.; Loesel, J. Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients. J. Chem. Inf. Comput. Sci. 2004, 44, 1840-1848.
    • (2004) J. Chem. Inf. Comput. Sci , vol.44 , pp. 1840-1848
    • Whittle, M.1    Gillet, V.J.2    Willett, P.3    Alex, A.4    Loesel, J.5
  • 41
    • 0026458378 scopus 로고
    • Amino Acid Substitution Matrices from Protein Blocks
    • Henikoff, S.; Henikoff, J. G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. U.S.A , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.