메뉴 건너뛰기




Volumn 3, Issue 4, 2006, Pages 413-421

In silico target fishing: Predicting biological targets from chemical structure

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; ALPHA TOCOPHEROL; BENZODIAZEPINE RECEPTOR; BENZODIAZEPINE RECEPTOR BLOCKING AGENT; CALMODULIN; COLLAGENASE; ESTROGEN RECEPTOR; LEUKOTRIENE B4 RECEPTOR; ORPHAN DRUG; PAMICOGREL; PROSTAGLANDIN SYNTHASE; PROSTAGLANDIN SYNTHASE INHIBITOR; PROTEIN KINASE C; TAMOXIFEN; TESTOSTERONE 17BETA DEHYDROGENASE;

EID: 33846518797     PISSN: 17406749     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ddtec.2006.12.008     Document Type: Review
Times cited : (154)

References (40)
  • 1
    • 17044373269 scopus 로고    scopus 로고
    • Finding the target after screening the phenotype
    • Hart C.P. Finding the target after screening the phenotype. Drug Discov. Today 10 (2005) 513-519
    • (2005) Drug Discov. Today , vol.10 , pp. 513-519
    • Hart, C.P.1
  • 2
    • 77956726346 scopus 로고    scopus 로고
    • Molecular similarity: advances in methods, applications, and validations in virtual screening and QSAR
    • Spellmeyer D.C. (Ed), Elsevier, Amsterdam
    • Bender A., et al. Molecular similarity: advances in methods, applications, and validations in virtual screening and QSAR. In: Spellmeyer D.C. (Ed). Annual Reports In Computational Chemistry Vol. 2 (2006), Elsevier, Amsterdam 141-168
    • (2006) Annual Reports In Computational Chemistry , vol.2 , pp. 141-168
    • Bender, A.1
  • 3
    • 33646270382 scopus 로고    scopus 로고
    • Training similarity measures for specific activities: application to reduced graphs
    • Birchall K., et al. Training similarity measures for specific activities: application to reduced graphs. J. Chem. Inf. Model. 46 (2006) 577-586
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 577-586
    • Birchall, K.1
  • 4
    • 33746883889 scopus 로고    scopus 로고
    • Mapping algorithms for molecular similarity analysis and ligand-based virtual screening: design of DynaMAD and comparison with MAD and DMC
    • Eckert H., et al. Mapping algorithms for molecular similarity analysis and ligand-based virtual screening: design of DynaMAD and comparison with MAD and DMC. J. Chem. Inf. Model. 46 (2006) 1623-1634
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1623-1634
    • Eckert, H.1
  • 5
    • 33750986884 scopus 로고    scopus 로고
    • 'Bayes affinity fingerprints' improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multi-target drugs a feasible concept?
    • Bender A., et al. 'Bayes affinity fingerprints' improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multi-target drugs a feasible concept?. J. Chem. Inf. Model 46 (2006) 2445-2456
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2445-2456
    • Bender, A.1
  • 6
    • 33646261627 scopus 로고    scopus 로고
    • A knowledge-based weighting approach to ligand-based virtual screening
    • Stiefl N., and Zaliani A. A knowledge-based weighting approach to ligand-based virtual screening. J. Chem. Inf. Model 46 (2006) 587-596
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 587-596
    • Stiefl, N.1    Zaliani, A.2
  • 7
    • 33646730764 scopus 로고    scopus 로고
    • Robust ligand-based modeling of the biological targets of known drugs
    • Cleves A.E., and Jain A.N. Robust ligand-based modeling of the biological targets of known drugs. J. Med. Chem. 49 (2006) 2921-2938
    • (2006) J. Med. Chem. , vol.49 , pp. 2921-2938
    • Cleves, A.E.1    Jain, A.N.2
  • 8
    • 33750994920 scopus 로고    scopus 로고
    • Bridging chemical and biological space: 'target fishing' using 2D and 3D molecular descriptors
    • Nettles J.N., et al. Bridging chemical and biological space: 'target fishing' using 2D and 3D molecular descriptors. J. Med. Chem. 49 (2006) 6802-6810
    • (2006) J. Med. Chem. , vol.49 , pp. 6802-6810
    • Nettles, J.N.1
  • 9
    • 0038170311 scopus 로고    scopus 로고
    • Similarity metrics for ligands reflecting the similarity of the target proteins
    • Schuffenhauer A., et al. Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci. 43 (2003) 391-405
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 391-405
    • Schuffenhauer, A.1
  • 10
    • 24944552075 scopus 로고    scopus 로고
    • High affinity targets of protein kinase inhibitors have similar residues at the positions energetically important for binding
    • Sheinerman F.B., et al. High affinity targets of protein kinase inhibitors have similar residues at the positions energetically important for binding. J. Mol. Biol. 352 (2005) 1134-1156
    • (2005) J. Mol. Biol. , vol.352 , pp. 1134-1156
    • Sheinerman, F.B.1
  • 11
    • 0037499669 scopus 로고    scopus 로고
    • How to acquire new biological activities in old compounds by computer prediction
    • Poroikov V.V., and Filimonov D.A. How to acquire new biological activities in old compounds by computer prediction. J. Comput. Aided Mol. Des. 16 (2002) 819-824
    • (2002) J. Comput. Aided Mol. Des. , vol.16 , pp. 819-824
    • Poroikov, V.V.1    Filimonov, D.A.2
  • 12
    • 0033737778 scopus 로고    scopus 로고
    • PASS: prediction of activity spectra for biologically active substances
    • Lagunin A., et al. PASS: prediction of activity spectra for biologically active substances. Bioinformatics 16 (2000) 747-748
    • (2000) Bioinformatics , vol.16 , pp. 747-748
    • Lagunin, A.1
  • 13
    • 2442652804 scopus 로고    scopus 로고
    • Design of new cognition enhancers: from computer prediction to synthesis and biological evaluation
    • Geronikaki A.A., et al. Design of new cognition enhancers: from computer prediction to synthesis and biological evaluation. J. Med. Chem. 47 (2004) 2870-2876
    • (2004) J. Med. Chem. , vol.47 , pp. 2870-2876
    • Geronikaki, A.A.1
  • 14
    • 2342565108 scopus 로고    scopus 로고
    • Prediction of biological targets using probabilistic neural networks and atom-type descriptors
    • Niwa T. Prediction of biological targets using probabilistic neural networks and atom-type descriptors. J. Med. Chem. 47 (2004) 2645-2650
    • (2004) J. Med. Chem. , vol.47 , pp. 2645-2650
    • Niwa, T.1
  • 15
    • 23844435134 scopus 로고    scopus 로고
    • WOMBAT: World of Molecular Bioactivity
    • Oprea T.I. (Ed), Wiley-VCH, New York
    • Olah M., et al. WOMBAT: World of Molecular Bioactivity. In: Oprea T.I. (Ed). Cheminformatics in Drug Discovery (2004), Wiley-VCH, New York
    • (2004) Cheminformatics in Drug Discovery
    • Olah, M.1
  • 16
    • 33745391215 scopus 로고    scopus 로고
    • Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases
    • Nidhi, et al. Prediction of biological targets for compounds using multiple-category Bayesian models trained on chemogenomics databases. J. Chem. Inf. Model. 46 (2006) 1124-1133
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1124-1133
    • Nidhi1
  • 17
    • 33746156959 scopus 로고    scopus 로고
    • Global mapping of pharmacological space
    • Paolini G.V., et al. Global mapping of pharmacological space. Nat. Biotechnol. 24 (2006) 805-815
    • (2006) Nat. Biotechnol. , vol.24 , pp. 805-815
    • Paolini, G.V.1
  • 18
    • 0028933247 scopus 로고
    • Peripheral benzodiazepine ligands inhibit aggregation and thromboxane synthesis induced by arachidonic acid in rabbit platelets in vitro
    • Choppin A., and Berry C.N. Peripheral benzodiazepine ligands inhibit aggregation and thromboxane synthesis induced by arachidonic acid in rabbit platelets in vitro. Thromb. Res. 78 (1995) 293-302
    • (1995) Thromb. Res. , vol.78 , pp. 293-302
    • Choppin, A.1    Berry, C.N.2
  • 19
    • 0029240364 scopus 로고
    • Predicting ligand binding to proteins by affinity fingerprinting
    • Kauvar L.M., et al. Predicting ligand binding to proteins by affinity fingerprinting. Chem. Biol. 2 (1995) 107-118
    • (1995) Chem. Biol. , vol.2 , pp. 107-118
    • Kauvar, L.M.1
  • 20
    • 0036668404 scopus 로고    scopus 로고
    • Chemoproteomics as a basis for post-genomic drug discovery
    • Beroza P., et al. Chemoproteomics as a basis for post-genomic drug discovery. Drug Discov. Today 7 (2002) 807-814
    • (2002) Drug Discov. Today , vol.7 , pp. 807-814
    • Beroza, P.1
  • 21
    • 0043031339 scopus 로고    scopus 로고
    • Predicting ADME properties and side effects: the BioPrint approach
    • Krejsa C.M., et al. Predicting ADME properties and side effects: the BioPrint approach. Curr. Opin. Drug Discov. Dev. 6 (2003) 470-480
    • (2003) Curr. Opin. Drug Discov. Dev. , vol.6 , pp. 470-480
    • Krejsa, C.M.1
  • 22
    • 12244275244 scopus 로고    scopus 로고
    • Biological spectra analysis: linking biological activity profiles to molecular structure
    • Fliri A.F., et al. Biological spectra analysis: linking biological activity profiles to molecular structure. Proc. Natl. Acad. Sci. U S A 102 (2005) 261-266
    • (2005) Proc. Natl. Acad. Sci. U S A , vol.102 , pp. 261-266
    • Fliri, A.F.1
  • 23
    • 17844396225 scopus 로고    scopus 로고
    • Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases
    • Covell D.G., et al. Linking tumor cell cytotoxicity to mechanism of drug action: an integrated analysis of gene expression, small-molecule screening and structural databases. Proteins 59 (2005) 403-433
    • (2005) Proteins , vol.59 , pp. 403-433
    • Covell, D.G.1
  • 24
    • 0037075063 scopus 로고    scopus 로고
    • Mining the National Cancer Institute's tumor-screening database: identification of compounds with similar cellular activities
    • Rabow A.A., et al. Mining the National Cancer Institute's tumor-screening database: identification of compounds with similar cellular activities. J. Med. Chem. 45 (2002) 818-840
    • (2002) J. Med. Chem. , vol.45 , pp. 818-840
    • Rabow, A.A.1
  • 25
    • 33746872563 scopus 로고    scopus 로고
    • Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects
    • Klekota J., et al. Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects. J. Chem. Inf. Model. 46 (2006) 1549-1562
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1549-1562
    • Klekota, J.1
  • 26
    • 17844400325 scopus 로고    scopus 로고
    • From targets to leads: the importance of advanced data analysis for decision support in drug discovery
    • Fischer H.P., and Heyse S. From targets to leads: the importance of advanced data analysis for decision support in drug discovery. Curr. Opin. Drug Discov. Dev. 8 (2005) 334-346
    • (2005) Curr. Opin. Drug Discov. Dev. , vol.8 , pp. 334-346
    • Fischer, H.P.1    Heyse, S.2
  • 27
    • 0037672857 scopus 로고    scopus 로고
    • Supertargeted chemistry: identifying relationships between molecular structures and their sub-cellular distribution
    • Rosania G.R. Supertargeted chemistry: identifying relationships between molecular structures and their sub-cellular distribution. Curr. Top. Med. Chem. 3 (2003) 659-685
    • (2003) Curr. Top. Med. Chem. , vol.3 , pp. 659-685
    • Rosania, G.R.1
  • 28
    • 0037262054 scopus 로고    scopus 로고
    • Ligand-protein docking: cancer research at the interface between biology and chemistry
    • Glen R.C., and Allen S.C. Ligand-protein docking: cancer research at the interface between biology and chemistry. Curr. Med. Chem. 10 (2003) 763-777
    • (2003) Curr. Med. Chem. , vol.10 , pp. 763-777
    • Glen, R.C.1    Allen, S.C.2
  • 29
    • 33749260698 scopus 로고    scopus 로고
    • A critical assessment of docking programs and scoring functions
    • Warren G.L., et al. A critical assessment of docking programs and scoring functions. J. Med. Chem. 49 (2006) 5912-5931
    • (2006) J. Med. Chem. , vol.49 , pp. 5912-5931
    • Warren, G.L.1
  • 30
    • 0035342428 scopus 로고    scopus 로고
    • Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
    • Chen Y.Z., and Zhi D.G. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 43 (2001) 217-226
    • (2001) Proteins , vol.43 , pp. 217-226
    • Chen, Y.Z.1    Zhi, D.G.2
  • 31
    • 20444369842 scopus 로고    scopus 로고
    • Rapid computational identification of the targets of protein kinase inhibitors
    • Rockey W.M., and Elcock A.H. Rapid computational identification of the targets of protein kinase inhibitors. J. Med. Chem. 48 (2005) 4138-4152
    • (2005) J. Med. Chem. , vol.48 , pp. 4138-4152
    • Rockey, W.M.1    Elcock, A.H.2
  • 32
    • 1542286205 scopus 로고    scopus 로고
    • Recovering the true targets of specific ligands by virtual screening of the protein data bank
    • Paul N., et al. Recovering the true targets of specific ligands by virtual screening of the protein data bank. Proteins 54 (2004) 671-680
    • (2004) Proteins , vol.54 , pp. 671-680
    • Paul, N.1
  • 33
    • 0346962971 scopus 로고    scopus 로고
    • Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions
    • Deng Z., et al. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem. 47 (2004) 337-344
    • (2004) J. Med. Chem. , vol.47 , pp. 337-344
    • Deng, Z.1
  • 34
    • 24144468145 scopus 로고    scopus 로고
    • Post-high-throughput screening analysis: an empirical compound prioritization scheme
    • Oprea T.I., et al. Post-high-throughput screening analysis: an empirical compound prioritization scheme. J. Biomol. Screen. 10 (2005) 419-426
    • (2005) J. Biomol. Screen. , vol.10 , pp. 419-426
    • Oprea, T.I.1
  • 35
    • 1842532337 scopus 로고    scopus 로고
    • Chemogenomics: an emerging strategy for rapid target and drug discovery
    • Bredel M., and Jacoby E. Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet. 5 (2004) 262-275
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 262-275
    • Bredel, M.1    Jacoby, E.2
  • 36
    • 0033969620 scopus 로고    scopus 로고
    • Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition
    • Jain A.N. Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition. J. Comput. Aid. Mol. Des 14 (2000) 199-213
    • (2000) J. Comput. Aid. Mol. Des , vol.14 , pp. 199-213
    • Jain, A.N.1
  • 37
    • 1842790495 scopus 로고    scopus 로고
    • Calculating similarities between biological activities in the MDL drug data report database
    • Sheridan R.P., and Shpungin J. Calculating similarities between biological activities in the MDL drug data report database. J. Chem. Inf. Comput. Sci. 44 (2004) 727-740
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 727-740
    • Sheridan, R.P.1    Shpungin, J.2
  • 38
    • 33645409007 scopus 로고    scopus 로고
    • Assessment of in vitro and in vivo activities in the National Cancer Institute's anticancer screen with respect to chemical structure, target specificity, and mechanism of action
    • Huang R., et al. Assessment of in vitro and in vivo activities in the National Cancer Institute's anticancer screen with respect to chemical structure, target specificity, and mechanism of action. J. Med. Chem. 49 (2006) 1964-1979
    • (2006) J. Med. Chem. , vol.49 , pp. 1964-1979
    • Huang, R.1
  • 39
    • 27444447278 scopus 로고    scopus 로고
    • Biospectra analysis: model proteome characterizations for linking molecular structure and biological response
    • Fliri A.F., et al. Biospectra analysis: model proteome characterizations for linking molecular structure and biological response. J. Med. Chem. 48 (2005) 6918-6925
    • (2005) J. Med. Chem. , vol.48 , pp. 6918-6925
    • Fliri, A.F.1
  • 40
    • 33244457597 scopus 로고    scopus 로고
    • Evaluating chemical structure similarity as an indicator of cellular growth inhibition
    • Wallqvist A., et al. Evaluating chemical structure similarity as an indicator of cellular growth inhibition. J. Chem. Inf. Model. 46 (2006) 430-437
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 430-437
    • Wallqvist, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.