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Volumn 31, Issue 15, 2015, Pages 2523-2529

Global optimization-based inference of chemogenomic features from drug-target interactions

Author keywords

[No Author keywords available]

Indexed keywords

DRUG; PROTEIN; PROTEIN BINDING;

EID: 84943620492     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv181     Document Type: Article
Times cited : (30)

References (32)
  • 1
    • 9144257886 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Bateman, A. et al. (2004) The Pfam protein families database. Nucleic Acids. Res., 32, D138-D141.
    • (2004) Nucleic Acids. Res. , vol.32 , pp. D138-D141
    • Bateman, A.1
  • 2
    • 0029894013 scopus 로고    scopus 로고
    • The properties of know drugs.1. Molecular frameworks
    • Bemis, G. W. et al. (1996) The properties of know drugs.1. Molecular frameworks. J. Med. Chem., 39, 2887-2893.
    • (1996) J. Med. Chem. , vol.39 , pp. 2887-2893
    • Bemis, G.W.1
  • 3
    • 1842532337 scopus 로고    scopus 로고
    • Chemogenomics: An emerging strategy for rapid target and drug discovery
    • Bredel, M. and Jacoby, E. (2004) Chemogenomics: an emerging strategy for rapid target and drug discovery. Nat. Rev. Genet., 5, 262-275.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 262-275
    • Bredel, M.1    Jacoby, E.2
  • 4
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman, H. M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 5
    • 0021118508 scopus 로고
    • Principles that determine the structure of proteins
    • Chothia, C. (1984) Principles that determine the structure of proteins. Annu. Rev. Biohem., 53, 537-572.
    • (1984) Annu. Rev. Biohem. , vol.53 , pp. 537-572
    • Chothia, C.1
  • 6
    • 0036799752 scopus 로고    scopus 로고
    • Inferring domain-domain interactions from protein-protein interactions
    • Deng, M. et al. (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Res., 12, 1540-1548.
    • (2002) Genome Res. , vol.12 , pp. 1540-1548
    • Deng, M.1
  • 7
    • 84891820493 scopus 로고    scopus 로고
    • PDBsum additions
    • De Beer, T. A. et al. (2014) PDBsum additions. Nucleic Acids. Res., 42, D292-D296.
    • (2014) Nucleic Acids. Res. , vol.42 , pp. D292-D296
    • De Beer, T.A.1
  • 8
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm
    • Dempster, A. P. et al. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Series. B., 39, 1-38.
    • (1977) J. R. Stat. Soc. Series. B. , vol.39 , pp. 1-38
    • Dempster, A.P.1
  • 9
    • 84876496265 scopus 로고    scopus 로고
    • Analysis of chemical and biological features yields mechanistic insights into drug side effects
    • Duran-Frigola, M. and Aloy, P. (2013) Analysis of chemical and biological features yields mechanistic insights into drug side effects. Chem. Biol. 20, 594-603.
    • (2013) Chem. Biol , vol.20 , pp. 594-603
    • Duran-Frigola, M.1    Aloy, P.2
  • 10
    • 0018115641 scopus 로고
    • Assessing the accuracy of the maximum likelihood estimator: Observed versus expected Fisher information
    • Efron, B. et al. (1978) Assessing the accuracy of the maximum likelihood estimator: Observed versus expected Fisher information. Biometrika, 65, 457-483.
    • (1978) Biometrika , vol.65 , pp. 457-483
    • Efron, B.1
  • 11
    • 84873304969 scopus 로고    scopus 로고
    • PLI: A web-based tool for the comparison of protein-ligand interactions observed on PDB structures
    • Gallina, A. M. et al. (2013) PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures. Bioinformatics, 29, 395-397.
    • (2013) Bioinformatics , vol.29 , pp. 395-397
    • Gallina, A.M.1
  • 12
    • 84862192766 scopus 로고    scopus 로고
    • ChEMBL: A large-scale bioactivity database for drug discovery
    • Gaulton, A. et al. (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res., 40, D1100-D1107.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D1100-D1107
    • Gaulton, A.1
  • 13
    • 0021518209 scopus 로고
    • Stochastic relaxation, Gibbs distribution, and the Bayesian restoration of images
    • Geman, S. et al. (1984) Stochastic relaxation, Gibbs distribution, and the Bayesian restoration of images. IEEE Trans. Pattern Anal. Mach. Intell., 23, 97-115.
    • (1984) IEEE Trans. Pattern Anal. Mach. Intell. , vol.23 , pp. 97-115
    • Geman, S.1
  • 14
    • 14944383798 scopus 로고    scopus 로고
    • The evolving role of natural products in drug discovery, Nat
    • Koehn, F. E. and Carter G. T. (2005) The evolving role of natural products in drug discovery, Nat. Rev. Drug Discov., 4, 206-220.
    • (2005) Rev. Drug Discov. , vol.4 , pp. 206-220
    • Koehn, F.E.1    Carter, G.T.2
  • 15
    • 84877930051 scopus 로고    scopus 로고
    • Mapping small molecule binding data to structural domains
    • Kruger, F. A. et al. (2012) Mapping small molecule binding data to structural domains. BMC Bioinformatics, 13, S11.
    • (2012) BMC Bioinformatics , vol.13 , pp. S11
    • Kruger, F.A.1
  • 16
    • 84928981357 scopus 로고    scopus 로고
    • PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains
    • Kruger, F. A. et al. (2014) PPDMs-a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains. Bioinformatics, 31, 776-778.
    • (2014) Bioinformatics , vol.31 , pp. 776-778
    • Kruger, F.A.1
  • 17
    • 79151481489 scopus 로고    scopus 로고
    • Syntheses, antiproliferative activity and theoretical characterization of acitretin-type retinoids with changes in the lipophilic part
    • Magoulas, G. E. et al. (2011) Syntheses, antiproliferative activity and theoretical characterization of acitretin-type retinoids with changes in the lipophilic part. Eur. J. Med. Chem., 46, 721-737.
    • (2011) Eur. J. Med. Chem. , vol.46 , pp. 721-737
    • Magoulas, G.E.1
  • 18
    • 51349085387 scopus 로고    scopus 로고
    • Data completeness-the Achilles heel of drug-target networks, Nat
    • Mestres, J. et al. (2008) Data completeness-the Achilles heel of drug-target networks, Nat. Biotechnol., 26, 983-984.
    • (2008) Biotechnol. , vol.26 , pp. 983-984
    • Mestres, J.1
  • 19
    • 67849113794 scopus 로고    scopus 로고
    • The rise of fragment-based drug discovery, Nat
    • Murray, C. W. and Rees, D. C. (2009) The rise of fragment-based drug discovery, Nat. Chem., 1, 187-192.
    • (2009) Chem. , vol.1 , pp. 187-192
    • Murray, C.W.1    Rees, D.C.2
  • 20
    • 16544372480 scopus 로고    scopus 로고
    • Potentiated anticancer effects on hepatoma cells by the retinoid adapalene
    • Ocker, M. et al. (2004) Potentiated anticancer effects on hepatoma cells by the retinoid adapalene. Cancer Lett., 208, 51-58.
    • (2004) Cancer Lett. , vol.208 , pp. 51-58
    • Ocker, M.1
  • 21
    • 84898841252 scopus 로고    scopus 로고
    • PI3K-AKT signaling is a downstream effector of retinoid prevention of murine basal cell carcinogenesis
    • So, P. L. et al. (2014) PI3K-AKT signaling is a downstream effector of retinoid prevention of murine basal cell carcinogenesis. Cancer Prev. Res., 7, 407-417.
    • (2014) Cancer Prev. Res. , vol.7 , pp. 407-417
    • So, P.L.1
  • 22
    • 84877933286 scopus 로고    scopus 로고
    • Protein-ligand docking in the new millennium-a restrospective of 10 years in the field
    • Sousa, S. F. et al. (2013) Protein-ligand docking in the new millennium-a restrospective of 10 years in the field. Curr. Med. Chem., 20, 2296-2314.
    • (2013) Curr. Med. Chem. , vol.20 , pp. 2296-2314
    • Sousa, S.F.1
  • 23
    • 84866467225 scopus 로고    scopus 로고
    • Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers
    • Tabei, Y. et al. (2012) Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers. Bioinformatics, 28, i487-i494.
    • (2012) Bioinformatics , vol.28 , pp. i487-i494
    • Tabei, Y.1
  • 24
    • 79952031520 scopus 로고    scopus 로고
    • Mining significant substructure pairs for interpreting polypharmacology in drug-target network
    • Takigawa, I. et al. (2011) Mining significant substructure pairs for interpreting polypharmacology in drug-target network. PloS One, 6, e16999.
    • (2011) PloS One , vol.6 , pp. e16999
    • Takigawa, I.1
  • 25
    • 77953529620 scopus 로고    scopus 로고
    • Update of the national surgical adjuvant breast and bowel project study of tamoxifen and raloxifene (STAR) P-2 trial: Preventing breast cancer
    • Vogel, V. G. et al. (2010) Update of the national surgical adjuvant breast and bowel project study of tamoxifen and raloxifene (STAR) P-2 trial: preventing breast cancer. Cancer Prev. Res., 3, 696-706.
    • (2010) Cancer Prev. Res. , vol.3 , pp. 696-706
    • Vogel, V.G.1
  • 26
    • 67849104638 scopus 로고    scopus 로고
    • PubChem: A public information system for analyzing bioactivities of small molecules
    • Wang, Y. et al. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids. Res., 37, W623-W633.
    • (2009) Nucleic Acids. Res. , vol.37 , pp. W623-W633
    • Wang, Y.1
  • 27
    • 0028922586 scopus 로고
    • LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
    • Wallace, AC. et al. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng., 8, 127-134.
    • (1995) Protein Eng. , vol.8 , pp. 127-134
    • Wallace, A.C.1
  • 28
    • 38549151817 scopus 로고    scopus 로고
    • DrugBank: A knowledgebase for drugs, drug actions and drug targets
    • Wishart, D. S. et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids. Res., 36, D901-D906.
    • (2008) Nucleic Acids. Res. , vol.36 , pp. D901-D906
    • Wishart, D.S.1
  • 29
    • 79952345084 scopus 로고    scopus 로고
    • Analysis of multiple compound-protein interactions reveals novel bioactive molecules
    • Yabuuchi, H. et al. (2011) Analysis of multiple compound-protein interactions reveals novel bioactive molecules. Mol. Syst. Biol., 7, 472.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 472
    • Yabuuchi, H.1
  • 30
    • 79960262560 scopus 로고    scopus 로고
    • Extracting sets of chemical substructures and protein domains governing drug-target interactions
    • Yamanishi, Y. et al. (2011) Extracting sets of chemical substructures and protein domains governing drug-target interactions. J. Chem. Inf. Model., 51, 1183-1184.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1183-1184
    • Yamanishi, Y.1
  • 31
    • 84885655034 scopus 로고    scopus 로고
    • Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
    • Yang, J. et al. (2013) Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics, 29, 2588-2595.
    • (2013) Bioinformatics , vol.29 , pp. 2588-2595
    • Yang, J.1
  • 32
    • 77955628292 scopus 로고    scopus 로고
    • Network-based relating pharmacological and genomic spaces for drug target identification
    • Zhao, S. and Li, S. (2010) Network-based relating pharmacological and genomic spaces for drug target identification. Plos One, 5, e11764.
    • (2010) Plos One , vol.5 , pp. e11764
    • Zhao, S.1    Li, S.2


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