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Volumn 49, Issue 6, 2009, Pages 1359-1368

Molecular formal concept analysis for compound selectivity profiling in biologically annotated databases

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; INFORMATION ANALYSIS; INFORMATION THEORY;

EID: 67650088856     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900095v     Document Type: Article
Times cited : (12)

References (36)
  • 1
    • 0036835460 scopus 로고    scopus 로고
    • Integration of Virtual and High-Throughput Screening
    • Bajorath, J. Integration of Virtual and High-Throughput Screening. Nat. Rev. Drug Discovery 2002, 1, 882-894.
    • (2002) Nat. Rev. Drug Discovery , vol.1 , pp. 882-894
    • Bajorath, J.1
  • 2
    • 43949145741 scopus 로고    scopus 로고
    • Computational Analysis of Ligand Relationships within Target Families
    • Bajorath, J. Computational Analysis of Ligand Relationships within Target Families. Curr. Opin. Chem. Biol. 2008, 12, 352-358.
    • (2008) Curr. Opin. Chem. Biol , vol.12 , pp. 352-358
    • Bajorath, J.1
  • 3
    • 1842532337 scopus 로고    scopus 로고
    • Bredel, M.; Jacoby, E. Chemogenomics: An Emerging Strategy for Rapid Target and Drug Discovery. Nat. Rev. Genet. 2004, 5, 262-275.
    • Bredel, M.; Jacoby, E. Chemogenomics: An Emerging Strategy for Rapid Target and Drug Discovery. Nat. Rev. Genet. 2004, 5, 262-275.
  • 4
    • 34548317031 scopus 로고    scopus 로고
    • Chemogenomic Approaches to Rational Drug Design
    • Rognan, D. Chemogenomic Approaches to Rational Drug Design. Br. J. Pharmacol. 2007, 152, 38-52.
    • (2007) Br. J. Pharmacol , vol.152 , pp. 38-52
    • Rognan, D.1
  • 6
    • 19744365702 scopus 로고    scopus 로고
    • Fabian, M. A.; Biggs, W. H.; Treiber, D. K.; Atteridge, C. E.; Azimioara, M. D.; Benedetti, M. G.; Carter, T. A.; Ciceri, P.; Edeen, P. T.; Floyd, M.; Ford, J. M.; Galvin, M.; Gerlach, J. L.; Grotzfeld, R. M.; Herrgard, S.; Insko, D. E.; Insko, M. A.; Lai, A. G.; Lélias, J.; Mehta, S. A.; Milanov, Z. V.; Velasco, A. M.; Wodicka, L. M.; Patel, H. K.; Zarrinkar, P. P.; Lockhart, D. J. A Small Molecule-Kinase Interaction Map for Clinical Kinase Inhibitors. Nat. Biotechnol. 2005, 23, 329-336.
    • Fabian, M. A.; Biggs, W. H.; Treiber, D. K.; Atteridge, C. E.; Azimioara, M. D.; Benedetti, M. G.; Carter, T. A.; Ciceri, P.; Edeen, P. T.; Floyd, M.; Ford, J. M.; Galvin, M.; Gerlach, J. L.; Grotzfeld, R. M.; Herrgard, S.; Insko, D. E.; Insko, M. A.; Lai, A. G.; Lélias, J.; Mehta, S. A.; Milanov, Z. V.; Velasco, A. M.; Wodicka, L. M.; Patel, H. K.; Zarrinkar, P. P.; Lockhart, D. J. A Small Molecule-Kinase Interaction Map for Clinical Kinase Inhibitors. Nat. Biotechnol. 2005, 23, 329-336.
  • 11
    • 33745391215 scopus 로고    scopus 로고
    • Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases
    • Nidhi; Glick, M.; Davies, J. W.; Jenkins, J. L. Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases. J. Chem. Inf. Model. 2006, 46, 1124-1233.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1124-1233
    • Nidhi1    Glick, M.2    Davies, J.W.3    Jenkins, J.L.4
  • 12
    • 33645422011 scopus 로고    scopus 로고
    • Are Target-Family- Privileged Substructures Truly Privileged
    • Schnur, D. M.; Hermsmeier, M. A.; Tebben, A. J. Are Target-Family- Privileged Substructures Truly Privileged. J. Med. Chem. 2006, 49, 2000-2009.
    • (2006) J. Med. Chem , vol.49 , pp. 2000-2009
    • Schnur, D.M.1    Hermsmeier, M.A.2    Tebben, A.J.3
  • 13
    • 41649105837 scopus 로고    scopus 로고
    • Kinase-Likeness and Kinase-Privileged Fragments: Toward Virtual Polypharmacology
    • Aronov, A. M.; McClain, B.; Moody, C. S.; Murcko, M. A. Kinase-Likeness and Kinase-Privileged Fragments: Toward Virtual Polypharmacology. J. Med. Chem. 2008, 51, 1214-1222.
    • (2008) J. Med. Chem , vol.51 , pp. 1214-1222
    • Aronov, A.M.1    McClain, B.2    Moody, C.S.3    Murcko, M.A.4
  • 14
    • 34547678010 scopus 로고    scopus 로고
    • Mining of Randomly Generated Molecular Fragment Populations Uncovers Activity-Specific Fragment Hierarchies
    • Batista, J.; Bajorath, J. Mining of Randomly Generated Molecular Fragment Populations Uncovers Activity-Specific Fragment Hierarchies. J. Chem. Inf. Model. 2007, 47, 1405-1413.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 1405-1413
    • Batista, J.1    Bajorath, J.2
  • 15
    • 51849102040 scopus 로고    scopus 로고
    • Formal Concept Analysis for the Identification of Molecular Fragment Combinations Specific for Active and Highly Potent Compounds
    • Lounkine, E.; Auer, J.; Bajorath, J. Formal Concept Analysis for the Identification of Molecular Fragment Combinations Specific for Active and Highly Potent Compounds. J. Med. Chem. 2008, 51, 5342-5348.
    • (2008) J. Med. Chem , vol.51 , pp. 5342-5348
    • Lounkine, E.1    Auer, J.2    Bajorath, J.3
  • 16
    • 28844441336 scopus 로고    scopus 로고
    • Formal Concept Analysis in Information Science
    • Priss, U. Formal Concept Analysis in Information Science. Annu. Rev. Inform. Sci. Technol. 2006, 40, 521-543.
    • (2006) Annu. Rev. Inform. Sci. Technol , vol.40 , pp. 521-543
    • Priss, U.1
  • 17
    • 0032802397 scopus 로고    scopus 로고
    • Structure-Activity Relationship Homology (SARAH): A Conceptual Framework for Drug Discovery in the Genomic Era
    • Frye, S. V. Structure-Activity Relationship Homology (SARAH): a Conceptual Framework for Drug Discovery in the Genomic Era. Chem. Biol. 1999, 6, R3-R7.
    • (1999) Chem. Biol , vol.6
    • Frye, S.V.1
  • 18
    • 0038170311 scopus 로고    scopus 로고
    • Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins
    • Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins. J. Chem. Inf. Comput. Sci. 2003, 43, 391-405.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 391-405
    • Schuffenhauer, A.1    Floersheim, P.2    Acklin, P.3    Jacoby, E.4
  • 19
    • 4143122120 scopus 로고    scopus 로고
    • Classification of Kinase Inhibitors Using a Bayesian Model
    • Xia, X.; Maliski, E. G.; Gallant, P.; Rogers, D. Classification of Kinase Inhibitors Using a Bayesian Model. J. Med. Chem. 2004, 47, 4463-4470.
    • (2004) J. Med. Chem , vol.47 , pp. 4463-4470
    • Xia, X.1    Maliski, E.G.2    Gallant, P.3    Rogers, D.4
  • 20
    • 34548180374 scopus 로고    scopus 로고
    • Methods for Computer-Aided Chemical Biology. Part 1: Design of a Benchmark System for the Evaluation of Compound Selectivity
    • Stumpfe, D.; Ahmed, H. E. A.; Vogt, I.; Bajorath, J. Methods for Computer-Aided Chemical Biology. Part 1: Design of a Benchmark System for the Evaluation of Compound Selectivity. Chem. Biol. Drug. Des. 2007, 70, 182-194.
    • (2007) Chem. Biol. Drug. Des , vol.70 , pp. 182-194
    • Stumpfe, D.1    Ahmed, H.E.A.2    Vogt, I.3    Bajorath, J.4
  • 21
    • 34548168343 scopus 로고    scopus 로고
    • Methods for Computer-Aided Chemical Biology. Part 2: Evaluation of Compound Selectivity Using 2D Molecular Fingerprints
    • Vogt, I.; Stumpfe, D.; Ahmed, H. E. A.; Bajorath, J. Methods for Computer-Aided Chemical Biology. Part 2: Evaluation of Compound Selectivity Using 2D Molecular Fingerprints. Chem. Biol. Drug. Des. 2007, 70, 195-205.
    • (2007) Chem. Biol. Drug. Des , vol.70 , pp. 195-205
    • Vogt, I.1    Stumpfe, D.2    Ahmed, H.E.A.3    Bajorath, J.4
  • 22
    • 43949101012 scopus 로고    scopus 로고
    • Methods for Computer-Aided Chemical Biology. Part 3: Analysis of Structure-Selectivity Relationships Through Single- or Dual-Step Selectivity Searching and Bayesian Classification
    • Stumpfe, D.; Geppert, H.; Bajorath, J. Methods for Computer-Aided Chemical Biology. Part 3: Analysis of Structure-Selectivity Relationships Through Single- or Dual-Step Selectivity Searching and Bayesian Classification. Chem. Biol. Drug. Des. 2008, 71, 518-528.
    • (2008) Chem. Biol. Drug. Des , vol.71 , pp. 518-528
    • Stumpfe, D.1    Geppert, H.2    Bajorath, J.3
  • 23
    • 60349100337 scopus 로고    scopus 로고
    • Methods for Computer-Aided Chemical Biology. Part 4: Selectivity Searching for Ion Channel Ligands and Mapping of Molecular Fragments as Selectivity Markers
    • Ahmed, H. E. A.; Geppert, H.; Stumpfe, D.; Lounkine, E.; Bajorath, J. Methods for Computer-Aided Chemical Biology. Part 4: Selectivity Searching for Ion Channel Ligands and Mapping of Molecular Fragments as Selectivity Markers. Chem. Biol. Drug. Des. 2009, 73, 273-282.
    • (2009) Chem. Biol. Drug. Des , vol.73 , pp. 273-282
    • Ahmed, H.E.A.1    Geppert, H.2    Stumpfe, D.3    Lounkine, E.4    Bajorath, J.5
  • 24
    • 33846108633 scopus 로고    scopus 로고
    • Binding DB: A Web-Accessible Database of Experimentally Determined Protein-Ligand Binding Affinities
    • Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. Binding DB: a Web-Accessible Database of Experimentally Determined Protein-Ligand Binding Affinities. Nucleic Acids Res. 2007, 35, D198-D201.
    • (2007) Nucleic Acids Res , vol.35
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 26
    • 57749170458 scopus 로고    scopus 로고
    • The Many Roles of Histone Deacetylases in Development and Physiology: Implications for Disease and Therapy
    • Haberland, M.; Montgomery, R. L.; Olson, E. N. The Many Roles of Histone Deacetylases in Development and Physiology: Implications for Disease and Therapy. Nat. Rev. Genet. 2009, 10, 32-42.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 32-42
    • Haberland, M.1    Montgomery, R.L.2    Olson, E.N.3
  • 27
    • 0034942625 scopus 로고    scopus 로고
    • Giembycz, M. A. Cilomilast: A Second Generation Phosphodiesterase 4 Inhibitor for Asthma and Chronic Obstructive Pulmonary Disease. Expert Opin. Invest. Drugs 2001, 10, 1361-1379.
    • Giembycz, M. A. Cilomilast: A Second Generation Phosphodiesterase 4 Inhibitor for Asthma and Chronic Obstructive Pulmonary Disease. Expert Opin. Invest. Drugs 2001, 10, 1361-1379.
  • 28
    • 56549120329 scopus 로고    scopus 로고
    • Enteric-Coated Mycophenolate Sodium: A Review of its Use in the Prevention of Renal Transplant Rejection
    • Sanford, M.; Keating, G. M. Enteric-Coated Mycophenolate Sodium: A Review of its Use in the Prevention of Renal Transplant Rejection. Drugs 2008, 68, 2505-2533.
    • (2008) Drugs , vol.68 , pp. 2505-2533
    • Sanford, M.1    Keating, G.M.2
  • 29
    • 0037342981 scopus 로고    scopus 로고
    • The Caspase Inhibitor IDN-6556 Prevents Caspase Activation and Apoptosis in Sinusoidal Endothelial Cells During Liver Preservation Injury
    • Natori, S.; Higuchi, H.; Contreras, P.; Gores, G. J. The Caspase Inhibitor IDN-6556 Prevents Caspase Activation and Apoptosis in Sinusoidal Endothelial Cells During Liver Preservation Injury. Liver Transplant 2003, 9, 278-284.
    • (2003) Liver Transplant , vol.9 , pp. 278-284
    • Natori, S.1    Higuchi, H.2    Contreras, P.3    Gores, G.J.4
  • 30
    • 0034326799 scopus 로고    scopus 로고
    • Han, J. W.; Ahn, S. H.; Park, S. H.; Wang, S. Y.; Bae, G. U.; Seo, D. W.; Kwon, H. K.; Hong, S.; Lee, H. Y.; Lee, Y. W.; Lee, H. W. Apicidin, a Histone Deacetylase Inhibitor, Inhibits Proliferation of Tumor Cells via Induction of p21WAF1/Cip1 and Gelsolin. Cancer Res. 2000, 60, 6068-6064.
    • Han, J. W.; Ahn, S. H.; Park, S. H.; Wang, S. Y.; Bae, G. U.; Seo, D. W.; Kwon, H. K.; Hong, S.; Lee, H. Y.; Lee, Y. W.; Lee, H. W. Apicidin, a Histone Deacetylase Inhibitor, Inhibits Proliferation of Tumor Cells via Induction of p21WAF1/Cip1 and Gelsolin. Cancer Res. 2000, 60, 6068-6064.
  • 31
    • 0027314528 scopus 로고
    • The Effect of Zardaverine, an Inhibitor of Phosphodiesterase Isoenzymes III and IV, on Endotoxin-Induced Airway Changes in Rats
    • Kips, J. C.; Joos, G. F.; Peleman, R. A.; Pauwels, R. A. The Effect of Zardaverine, an Inhibitor of Phosphodiesterase Isoenzymes III and IV, on Endotoxin-Induced Airway Changes in Rats. Clin. Exp. Allergy 1993, 23, 518-523.
    • (1993) Clin. Exp. Allergy , vol.23 , pp. 518-523
    • Kips, J.C.1    Joos, G.F.2    Peleman, R.A.3    Pauwels, R.A.4
  • 32
    • 52949140176 scopus 로고    scopus 로고
    • PDE4 Inhibitors: Current Status
    • Spina, D. PDE4 Inhibitors: Current Status. Br. J. Pharmacol. 2008, 155, 308-315.
    • (2008) Br. J. Pharmacol , vol.155 , pp. 308-315
    • Spina, D.1
  • 35
    • 0020693045 scopus 로고
    • Potential Antidepressant Activity of Rolipram and other Selective Cyclic Adenosine 3′,5′-Monophosphate Phosphodiesterase Inhibitors
    • Wachtel, H. Potential Antidepressant Activity of Rolipram and other Selective Cyclic Adenosine 3′,5′-Monophosphate Phosphodiesterase Inhibitors. Neuropharmacology 1983, 22, 267-272.
    • (1983) Neuropharmacology , vol.22 , pp. 267-272
    • Wachtel, H.1


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