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Volumn 46, Issue 3, 2006, Pages 1124-1133

Prediction of biological targets for compounds using multiple-category bayesian models trained on chemogenomics databases

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ANALYSIS; DATABASE SYSTEMS; GENETIC ENGINEERING; LAPLACE TRANSFORMS; MATHEMATICAL MODELS; STRUCTURE (COMPOSITION);

EID: 33745391215     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci060003g     Document Type: Article
Times cited : (309)

References (50)
  • 2
    • 0034331004 scopus 로고    scopus 로고
    • Chemical genetics: Ligand-based discovery of gene function
    • Stockwell, B. R. Chemical Genetics: Ligand-Based Discovery of Gene Function. Nat. Rev. Genet. 2000, 1, 116-125.
    • (2000) Nat. Rev. Genet. , vol.1 , pp. 116-125
    • Stockwell, B.R.1
  • 3
    • 11144298973 scopus 로고    scopus 로고
    • Exploring biology with small organic molecules
    • Stockwell, B. R. Exploring Biology with Small Organic Molecules. Nature 2004, 432, 846-854.
    • (2004) Nature , vol.432 , pp. 846-854
    • Stockwell, B.R.1
  • 4
    • 13344275782 scopus 로고    scopus 로고
    • Fishing for targets: Novel approaches using small molecule baits
    • Szardenings, K.; Li, B.; Ma, L.; Wu, M. Fishing for Targets: Novel Approaches Using Small Molecule Baits. Drug Discovery Today: Targets 2004, 1, 9-15.
    • (2004) Drug Discovery Today: Targets , vol.1 , pp. 9-15
    • Szardenings, K.1    Li, B.2    Ma, L.3    Wu, M.4
  • 5
    • 1842532337 scopus 로고    scopus 로고
    • Chemogenomics: An emerging strategy for rapid target and drug discovery
    • Bredel, M.; Jacoby, E. Chemogenomics: An Emerging Strategy for Rapid Target and Drug Discovery. Nat. Rev. Genet. 2004, 5, 262-275.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 262-275
    • Bredel, M.1    Jacoby, E.2
  • 6
    • 0141521869 scopus 로고    scopus 로고
    • Biological mechanism profiling using an annotated compound library
    • Root, D. E.; Flaherty, S. P.; Kelley, B. P.; Stockwell, B. R. Biological Mechanism Profiling Using an Annotated Compound Library. Chem. Biol. 2003, 10, 881-892.
    • (2003) Chem. Biol. , vol.10 , pp. 881-892
    • Root, D.E.1    Flaherty, S.P.2    Kelley, B.P.3    Stockwell, B.R.4
  • 7
  • 8
    • 0037835538 scopus 로고    scopus 로고
    • Finding multiactivity substructures by mining databases of drug-like compounds
    • Sheridan, R. P. Finding Multiactivity Substructures by Mining Databases of Drug-Like Compounds. J. Chem. Inf. Comput. Sci. 2003, 43, 1037-1050.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 1037-1050
    • Sheridan, R.P.1
  • 9
    • 1842790495 scopus 로고    scopus 로고
    • Calculating similarities between biological activities in the MDL drug data report database
    • Sheridan, R. P.; Shpungin, J. Calculating Similarities between Biological Activities in the MDL Drug Data Report Database. J. Chem. Inf. Comput. Sci. 2004, 44, 727-740.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 727-740
    • Sheridan, R.P.1    Shpungin, J.2
  • 10
    • 0033737778 scopus 로고    scopus 로고
    • PASS: Prediction of activity spectra for biologically active substances
    • Lagunin, A.; Stepanchikova, A.; Filimonov, D.; Poroikov, V. PASS: Prediction of Activity Spectra for Biologically Active Substances. Bioinformatics 2000, 16, 747-748.
    • (2000) Bioinformatics , vol.16 , pp. 747-748
    • Lagunin, A.1    Stepanchikova, A.2    Filimonov, D.3    Poroikov, V.4
  • 11
    • 0035237681 scopus 로고    scopus 로고
    • Top 200 medicines: Can new actions be discovered through computer-aided prediction?
    • Poroikov, V.; Akimov, D.; Shabelnikova, E.; Filimonov, D. Top 200 Medicines: Can New Actions Be Discovered through Computer-Aided Prediction? SAR QSAR Environ. Res. 2001, 12, 327-344.
    • (2001) SAR QSAR Environ. Res. , vol.12 , pp. 327-344
    • Poroikov, V.1    Akimov, D.2    Shabelnikova, E.3    Filimonov, D.4
  • 13
    • 84858921870 scopus 로고    scopus 로고
    • accessedDec2005
    • Elsevier MDL Home Page, http://www.mdli.com (accessed Dec 2005).
    • Elsevier MDL Home Page
  • 14
    • 84858925812 scopus 로고    scopus 로고
    • accessed Dec 2005
    • Inpharmatica Index, http://www.inpharmatica.co.uk (accessed Dec 2005).
  • 15
    • 84858923872 scopus 로고    scopus 로고
    • accessedDec2005
    • Jubilant Biosys. http://jubilantbiosys.com (accessed Dec 2005).
  • 16
    • 84858922661 scopus 로고    scopus 로고
    • accessed Dec 2005
    • GVK Bio. http://www.gvkbio.com (accessed Dec 2005).
  • 17
    • 84858918246 scopus 로고    scopus 로고
    • accessed Dec 2005
    • Chembank - Initiative for Chemical Genetics. http://chembank.broad. harvard.edu (accessed Dec 2005).
    • Initiative for Chemical Genetics
  • 20
    • 10244222365 scopus 로고    scopus 로고
    • Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
    • Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of Topological Descriptors for Similarity-Based Virtual Screening Using Multiple Bioactive Reference Structures. Org. Biomol. Chem. 2004, 2, 3256-3266.
    • (2004) Org. Biomol. Chem. , vol.2 , pp. 3256-3266
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 21
    • 10844249112 scopus 로고    scopus 로고
    • Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D)
    • Bender, A.; Mussa, H. Y.; Gill, G. S.; Glen, R. C. Molecular Surface Point Environments for Virtual Screening and the Elucidation of Binding Patterns (MOLPRINT 3D). J. Med. Chem. 2004, 47, 6569-6583.
    • (2004) J. Med. Chem. , vol.47 , pp. 6569-6583
    • Bender, A.1    Mussa, H.Y.2    Gill, G.S.3    Glen, R.C.4
  • 22
    • 0041353959 scopus 로고    scopus 로고
    • Chemical genomic profiling of biological networks using graph theory and combinations of small molecule perturbations
    • Haggarty, S. J.; Clemons, P. A.; Schreiber, S. L. Chemical Genomic Profiling of Biological Networks Using Graph Theory and Combinations of Small Molecule Perturbations. J. Am. Chem. Soc. 2003, 125, 10543-10545.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 10543-10545
    • Haggarty, S.J.1    Clemons, P.A.2    Schreiber, S.L.3
  • 23
    • 9744222830 scopus 로고    scopus 로고
    • A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes
    • Jenkins, J. L.; Glick, M.; Davies, J. W. A 3D Similarity Method for Scaffold Hopping from Known Drugs or Natural Ligands to New Chemotypes. J. Med. Chem. 2004, 47, 6144-6159.
    • (2004) J. Med. Chem. , vol.47 , pp. 6144-6159
    • Jenkins, J.L.1    Glick, M.2    Davies, J.W.3
  • 24
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based scaffold hopping method and its application to a bacterial protein-protein interaction
    • Rush, T. S., III; Grant, J. A.; Mosyak, L.; Nicholls, A. A Shape-Based Scaffold Hopping Method and Its Application to a Bacterial Protein-Protein Interaction. J. Med. Chem. 2005, 48, 1489-1495.
    • (2005) J. Med. Chem. , vol.48 , pp. 1489-1495
    • Rush III, T.S.1    Grant, J.A.2    Mosyak, L.3    Nicholls, A.4
  • 25
    • 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
  • 26
    • 4544350863 scopus 로고    scopus 로고
    • Enrichment of extremely noisy high-throughput screening data using a naive bayes classifier
    • Glick, M.; Klon, A. E.; Acklin, P.; Davies, J. W. Enrichment of Extremely Noisy High-Throughput Screening Data Using a Naive Bayes Classifier. J. Biomol. Screening 2004, 9, 32-36.
    • (2004) J. Biomol. Screening , vol.9 , pp. 32-36
    • Glick, M.1    Klon, A.E.2    Acklin, P.3    Davies, J.W.4
  • 27
    • 26944503021 scopus 로고    scopus 로고
    • Using extended-connectivity fingerprints with laplacian-modified bayesian analysis in high-throughput screening follow-up
    • Rogers, D.; Brown, R. D.; Hahn, M. Using Extended-Connectivity Fingerprints with Laplacian-Modified Bayesian Analysis in High-Throughput Screening Follow-Up. J. Biomol. Screening 2005, 10, 682-686.
    • (2005) J. Biomol. Screening , vol.10 , pp. 682-686
    • Rogers, D.1    Brown, R.D.2    Hahn, M.3
  • 28
    • 33244482848 scopus 로고    scopus 로고
    • Enrichment of high-throughput screening data with increasing levels of noise using support vector machines, recursive partitioning, and laplacian-modified naive bayesian classifiers
    • Glick, M.; Jenkins, J. L.; Nettles, J. H.; Hitchings, H.; Davies, J. W. Enrichment of High-Throughput Screening Data with Increasing Levels of Noise Using Support Vector Machines, Recursive Partitioning, and Laplacian-Modified Naive Bayesian Classifiers. J. Chem. Inf. Model 2006, 46, 193-200.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 193-200
    • Glick, M.1    Jenkins, J.L.2    Nettles, J.H.3    Hitchings, H.4    Davies, J.W.5
  • 29
    • 2442716437 scopus 로고    scopus 로고
    • Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results
    • Klon, A. E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J. W. Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results. J. Med. Chem. 2004, 47, 2743-2749.
    • (2004) J. Med. Chem. , vol.47 , pp. 2743-2749
    • Klon, A.E.1    Glick, M.2    Thoma, M.3    Acklin, P.4    Davies, J.W.5
  • 30
    • 0000293407 scopus 로고
    • The generation of a unique machine description for chemical structures - A technique developed at chemical abstracts service
    • Morgan, H. L. The Generation of a Unique Machine Description for Chemical Structures - A Technique Developed at Chemical Abstracts Service. J. Chem. Doc. 1965, 5, 107-113.
    • (1965) J. Chem. Doc. , vol.5 , pp. 107-113
    • Morgan, H.L.1
  • 31
    • 33646249968 scopus 로고    scopus 로고
    • New methods for ligand-based virtual screening: Use of data fusion and machine learning to enhance the effectiveness of similarity searching
    • in press
    • Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching. J. Chem. Inf. Model. 2006, in press.
    • (2006) J. Chem. Inf. Model.
    • Hert, J.1    Willett, P.2    Wilton, D.J.3    Acklin, P.4    Azzaoui, K.5    Jacoby, E.6    Schuffenhauer, A.7
  • 32
    • 0029894013 scopus 로고    scopus 로고
    • The properties of known drugs. 1. molecular frameworks
    • Bemis, G. W.; Murcko, M. A. The Properties of Known Drugs. 1. Molecular Frameworks. J. Med. Chem. 1996, 39, 2887-2893.
    • (1996) J. Med. Chem. , vol.39 , pp. 2887-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 33
    • 0033000990 scopus 로고    scopus 로고
    • Histone acetylases and deacetylases in cell proliferation
    • Kouzarides, T. Histone Acetylases and Deacetylases in Cell Proliferation. Curr. Opin. Genet. Dev. 1999, 9, 40-48.
    • (1999) Curr. Opin. Genet. Dev. , vol.9 , pp. 40-48
    • Kouzarides, T.1
  • 34
    • 0024996768 scopus 로고
    • Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A
    • Yoshida, M.; Kijima, M.; Akita, M.; Beppu, T. Potent and Specific Inhibition of Mammalian Histone Deacetylase both in Vivo and in Vitro by Trichostatin A. J. Biol. Chem. 1990, 265, 17174-17179.
    • (1990) J. Biol. Chem. , vol.265 , pp. 17174-17179
    • Yoshida, M.1    Kijima, M.2    Akita, M.3    Beppu, T.4
  • 35
    • 2942532642 scopus 로고    scopus 로고
    • Trichostatin a-like hydroxamate histone deacetylase inhibitors as therapeutic agents: Toxicological point of view
    • Vanhaecke, T.; Papeleu, P.; Elaut, G.; Rogiers, V. Trichostatin A-Like Hydroxamate Histone Deacetylase Inhibitors as Therapeutic Agents: Toxicological Point of View. Curr. Med. Chem. 2004, 11, 1629-1643.
    • (2004) Curr. Med. Chem. , vol.11 , pp. 1629-1643
    • Vanhaecke, T.1    Papeleu, P.2    Elaut, G.3    Rogiers, V.4
  • 36
    • 0035024737 scopus 로고    scopus 로고
    • Histone deacetylase: A target for antiproliferative and antiprotozoal agents
    • Meinke, P. T.; Liberator, P. Histone Deacetylase: A Target for Antiproliferative and Antiprotozoal Agents. Curr. Med. Chem. 2001, 8, 211-235.
    • (2001) Curr. Med. Chem. , vol.8 , pp. 211-235
    • Meinke, P.T.1    Liberator, P.2
  • 38
    • 0022333546 scopus 로고
    • Synthesis, toxicity, and therapeutic efficacy of 4-amino-N-(2′- aminophenyl)-benzamide: A new compound preferentially active in slowly gowing tumors
    • Berger, M. R.; Bicshoff, H.; Fritschi, E.; Henne, T.; Herrmann, M.; Pool, B. L.; Satzinger, G.; Schmal, D.; Weiershausen, U. Synthesis, Toxicity, and Therapeutic Efficacy of 4-Amino-N-(2′-aminophenyl)-benzamide: A New Compound Preferentially Active in Slowly Gowing Tumors. Cancer Treat. Rep. 1985, 69, 1415-1424.
    • (1985) Cancer Treat. Rep. , vol.69 , pp. 1415-1424
    • Berger, M.R.1    Bicshoff, H.2    Fritschi, E.3    Henne, T.4    Herrmann, M.5    Pool, B.L.6    Satzinger, G.7    Schmal, D.8    Weiershausen, U.9
  • 40
    • 2442535179 scopus 로고    scopus 로고
    • Tachykinin NK2 receptor antagonists for the treatment of irritable bowel syndrome
    • Lecci, A.; Capriati, A.; Maggi, C. A. Tachykinin NK2 Receptor Antagonists for the Treatment of Irritable Bowel Syndrome. Br. J. Pharmacol. 2004, 141, 1249-1263.
    • (2004) Br. J. Pharmacol. , vol.141 , pp. 1249-1263
    • Lecci, A.1    Capriati, A.2    Maggi, C.A.3
  • 42
  • 43
    • 27644566447 scopus 로고    scopus 로고
    • Biologic therapy for inflammatory bowel disease
    • Ardizzone, S.; Porro, G. B. Biologic Therapy for Inflammatory Bowel Disease. Drugs 2005, 65, 2253-2286.
    • (2005) Drugs , vol.65 , pp. 2253-2286
    • Ardizzone, S.1    Porro, G.B.2
  • 44
    • 14844363404 scopus 로고    scopus 로고
    • Aliskiren, a novel orally effective renin inhibitor, provides dose-dependent antihypertensive efficacy and placebo-like tolerability in hypertensive patients
    • Gradman, A. H.; Schmieder, R. E.; Lins, R. L.; Nussberger, J.; Chiang, Y.; Bedigian, M. P. Aliskiren, a Novel Orally Effective Renin Inhibitor, Provides Dose-Dependent Antihypertensive Efficacy and Placebo-Like Tolerability in Hypertensive Patients. Circulation 2005, 111, 1012-1018.
    • (2005) Circulation , vol.111 , pp. 1012-1018
    • Gradman, A.H.1    Schmieder, R.E.2    Lins, R.L.3    Nussberger, J.4    Chiang, Y.5    Bedigian, M.P.6
  • 45
    • 14044271546 scopus 로고    scopus 로고
    • Aliskiren, a novel, orally effective renin inhibitor, lowers blood pressure in marmosets and spontaneously hypertensive rats
    • Wood, J. M.; Schnell, C. R.; Cumin, F.; Menard, J.; Webb, R. L. Aliskiren, a Novel, Orally Effective Renin Inhibitor, Lowers Blood Pressure in Marmosets and Spontaneously Hypertensive Rats. J. Hypertens. 2005, 23, 417-426.
    • (2005) J. Hypertens. , vol.23 , pp. 417-426
    • Wood, J.M.1    Schnell, C.R.2    Cumin, F.3    Menard, J.4    Webb, R.L.5
  • 46
    • 22144448151 scopus 로고    scopus 로고
    • Metamizol acts as an ATP sensitive potassium channel opener to inhibit the contracting response induced by angiotensin II but not to norepinephrine in rat thoracic aorta smooth muscle
    • Valenzuela, F.; Garcia-Saiso S.; Lemini, C.; Ramirez-Solares, R.; Vidria, H.; Mendoza-Fernandez, V. Metamizol Acts as an ATP Sensitive Potassium Channel Opener to Inhibit the Contracting Response Induced by Angiotensin II but not to Norepinephrine in Rat Thoracic Aorta Smooth Muscle. Vasc. Pharmacol. 2005, 43, 120-127.
    • (2005) Vasc. Pharmacol. , vol.43 , pp. 120-127
    • Valenzuela, F.1    Garcia-Saiso, S.2    Lemini, C.3    Ramirez-Solares, R.4    Vidria, H.5    Mendoza-Fernandez, V.6
  • 47
    • 0035976575 scopus 로고    scopus 로고
    • Prostaglandins and leukotrienes: Advances in eicosanoid biology
    • Funk, C. D. Prostaglandins and Leukotrienes: Advances in Eicosanoid Biology. Science 2001, 294, 1871-1875.
    • (2001) Science , vol.294 , pp. 1871-1875
    • Funk, C.D.1
  • 48
    • 19944370429 scopus 로고    scopus 로고
    • The selective cyclooxygenase-2 inhibitor celecoxib modulates the forma tion of vasoconstrictor eicosanoids and activates PPARgamma. influence of albumin
    • Lopez-Parra, M.; Claria, J.; Titos, E.; Planaguma, A.; Parrizas, M.; Masferrer, J. L.; Jimenez, W.; Arroyo, V.; Rivera, F.; Rodes, J. The Selective Cyclooxygenase-2 Inhibitor Celecoxib Modulates the Forma tion of Vasoconstrictor Eicosanoids and Activates PPARgamma. Influence of Albumin. J. Hepatol. 2005, 42, 75-81.
    • (2005) J. Hepatol. , vol.42 , pp. 75-81
    • Lopez-Parra, M.1    Claria, J.2    Titos, E.3    Planaguma, A.4    Parrizas, M.5    Masferrer, J.L.6    Jimenez, W.7    Arroyo, V.8    Rivera, F.9    Rodes, J.10
  • 49
    • 0033523672 scopus 로고    scopus 로고
    • "Scaffold-hopping" by topological pharmacophore search: A contribution to virtual screening
    • Schneider, G.; Neidhart, W.; Giller, T.; Schmid, G. "Scaffold- hopping" by Topological Pharmacophore Search: A Contribution to Virtual Screening. Angew. Chem., Int. Ed. 1999, 38, 2894-2896.
    • (1999) Angew. Chem., Int. Ed. , vol.38 , pp. 2894-2896
    • Schneider, G.1    Neidhart, W.2    Giller, T.3    Schmid, G.4
  • 50
    • 24144468145 scopus 로고    scopus 로고
    • Post-high-throughput screening analysis: An empirical compound prioritization scheme
    • Oprea, T. I.; Bologa, C. G.; Edwards, B. S.; Prossnitz, E. R.; Sklar, L. A. Post-High-Throughput Screening Analysis: An Empirical Compound Prioritization Scheme. J. Biomol. Screening 2005, 10, 419-426.
    • (2005) J. Biomol. Screening , vol.10 , pp. 419-426
    • Oprea, T.I.1    Bologa, C.G.2    Edwards, B.S.3    Prossnitz, E.R.4    Sklar, L.A.5


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