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Volumn 3, Issue 1, 2011, Pages 22-30

Chemical-protein interactome and its application in off-target identification

Author keywords

adverse drug reaction; chemical protein interactome; drug repositioning; off system; off target

Indexed keywords

DRUG; PROTEIN;

EID: 84862833676     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-011-0051-8     Document Type: Article
Times cited : (28)

References (59)
  • 5
    • 13444262395 scopus 로고    scopus 로고
    • The European Bioinformatics Institute's data resources: towards systems biology
    • Brooksbank, C., Cameron, G., Thornton, J. 2005. The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res 33, D46-53.
    • (2005) Nucleic Acids Res , vol.33
    • Brooksbank, C.1    Cameron, G.2    Thornton, J.3
  • 7
    • 47249146126 scopus 로고    scopus 로고
    • Drug target identification using side-effect similarity
    • Campillos, M., Kuhn, M., Gavin, A. C., Jensen, L. J., Bork, P. 2008. Drug target identification using side-effect similarity. Science 321, 263-266.
    • (2008) Science , vol.321 , pp. 263-266
    • Campillos, M.1    Kuhn, M.2    Gavin, A.C.3    Jensen, L.J.4    Bork, P.5
  • 8
    • 38049136610 scopus 로고    scopus 로고
    • Improved human disease candidate gene prioritization using mouse phenotype
    • Chen, J., Xu, H., Aronow, B. J., Jegga, A. G. 2007. Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics 8, 392.
    • (2007) BMC Bioinformatics , vol.8 , pp. 392
    • Chen, J.1    Xu, H.2    Aronow, B.J.3    Jegga, A.G.4
  • 9
    • 62849126285 scopus 로고    scopus 로고
    • Disease candidate gene identification and prioritization using protein interaction networks
    • Chen, J., Aronow, B. J., Jegga, A. G. 2009a. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics 10, 73.
    • (2009) BMC Bioinformatics , vol.10 , pp. 73
    • Chen, J.1    Aronow, B.J.2    Jegga, A.G.3
  • 10
    • 67849130563 scopus 로고    scopus 로고
    • ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
    • Chen, J., Bardes, E. E., Aronow, B. J., Jegga, A. G. 2009b. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 37, W305-311.
    • (2009) Nucleic Acids Res , vol.37
    • Chen, J.1    Bardes, E.E.2    Aronow, B.J.3    Jegga, A.G.4
  • 12
    • 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., Zhi, D. G. 2001. Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule. Proteins 43, 217-226.
    • (2001) Proteins , vol.43 , pp. 217-226
    • Chen, Y.Z.1    Zhi, D.G.2
  • 14
    • 77957857557 scopus 로고    scopus 로고
    • Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements
    • de Franchi, E., Schalon, C., Messa, M., Onofri, F., Benfenati, F., Rognan, D. 2010. Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements. PLoS ONE 5.
    • (2010) PLoS ONE , vol.5
    • de Franchi, E.1    Schalon, C.2    Messa, M.3    Onofri, F.4    Benfenati, F.5    Rognan, D.6
  • 19
    • 0030827973 scopus 로고    scopus 로고
    • Specific binding of aminoglycosides to a human rRNA construct based on a DNA polymorphism which causes aminoglycoside-induced deafness
    • Hamasaki, K., Rando, R. R. 1997. Specific binding of aminoglycosides to a human rRNA construct based on a DNA polymorphism which causes aminoglycoside-induced deafness. Biochemistry 36, 12323-12328.
    • (1997) Biochemistry , vol.36 , pp. 12323-12328
    • Hamasaki, K.1    Rando, R.R.2
  • 20
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins, A. L. 2008. Network pharmacology: The next paradigm in drug discovery. Nat Chem Biol 4, 682-690.
    • (2008) Nat Chem Biol , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 21
    • 70349310091 scopus 로고    scopus 로고
    • Parallel functional activity profiling reveals valvulopathogens are potent 5-hydroxytryptamine(2B) receptor agonists: implications for drug safety assessment
    • Huang, X. P., Setola, V., Yadav, P. N., Allen, J. A., Rogan, S. C., Hanson, B. J., Revankar, C., Robers, M., Doucette, C., Roth, B. L. 2009. Parallel functional activity profiling reveals valvulopathogens are potent 5-hydroxytryptamine(2B) receptor agonists: implications for drug safety assessment. Mol Pharmacol 76, 710-722.
    • (2009) Mol Pharmacol , vol.76 , pp. 710-722
    • Huang, X.P.1    Setola, V.2    Yadav, P.N.3    Allen, J.A.4    Rogan, S.C.5    Hanson, B.J.6    Revankar, C.7    Robers, M.8    Doucette, C.9    Roth, B.L.10
  • 24
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - a free database of commercially available compounds for virtual screening
    • Irwin, J. J., Shoichet, B. K. 2005. ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model 45, 177-182.
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 25
    • 37649007431 scopus 로고    scopus 로고
    • Selective estrogen-receptor modulators and antihormonal resistance in breast cancer
    • Jordan, V. C., O'Malley, B. W. 2007. Selective estrogen-receptor modulators and antihormonal resistance in breast cancer. J Clin Oncol 25, 5815-5824.
    • (2007) J Clin Oncol , vol.25 , pp. 5815-5824
    • Jordan, V.C.1    O'Malley, B.W.2
  • 28
    • 68249144628 scopus 로고    scopus 로고
    • Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis
    • Kinnings, S. L., Liu, N., Buchmeier, N., Tonge, P. J., Xie, L., Bourne, P. E. 2009. Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comput Biol 5, e1000423.
    • (2009) PLoS Comput Biol , vol.5
    • Kinnings, S.L.1    Liu, N.2    Buchmeier, N.3    Tonge, P.J.4    Xie, L.5    Bourne, P.E.6
  • 29
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • Kitchen, D. B., Decornez, H., Furr, J. R., Bajorath, J. 2004. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat Rev Drug Discov 3, 935-949.
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 30
    • 41149096945 scopus 로고    scopus 로고
    • Large-scale prediction of drug-target relationships
    • Kuhn, M., Campillos, M., Gonzalez, P., Jensen, L. J., Bork, P. 2008. Large-scale prediction of drug-target relationships. FEBS Lett 582, 1283-1290.
    • (2008) FEBS Lett , vol.582 , pp. 1283-1290
    • Kuhn, M.1    Campillos, M.2    Gonzalez, P.3    Jensen, L.J.4    Bork, P.5
  • 32
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I. D. 1992. Structure-based strategies for drug design and discovery. Science 257, 1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 34
    • 68249111344 scopus 로고    scopus 로고
    • Building diseasespecific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts
    • Li, J., Zhu, X., Chen, J. Y. 2009. Building diseasespecific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol 5, e1000450.
    • (2009) PLoS Comput Biol , vol.5
    • Li, J.1    Zhu, X.2    Chen, J.Y.3
  • 35
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu, T., Lin, Y., Wen, X., Jorissen, R. N., Gilson, M. K. 2007. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35, D198-201.
    • (2007) Nucleic Acids Res , vol.35
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 37
    • 59849106371 scopus 로고    scopus 로고
    • Protein promiscuity and its implications for biotechnology
    • Nobeli, I., Favia, A. D., Thornton, J. M. 2009. Protein promiscuity and its implications for biotechnology. Nat Biotechnol 27, 157-167.
    • (2009) Nat Biotechnol , vol.27 , pp. 157-167
    • Nobeli, I.1    Favia, A.D.2    Thornton, J.M.3
  • 41
    • 70249086620 scopus 로고    scopus 로고
    • hERG-related drug toxicity and models for predicting hERG liability and QT prolongation
    • Raschi, E., Ceccarini, L., De Ponti, F., Recanatini, M. 2009. hERG-related drug toxicity and models for predicting hERG liability and QT prolongation. Expert Opin Drug Metab Toxicol 5, 1005-1021.
    • (2009) Expert Opin Drug Metab Toxicol , vol.5 , pp. 1005-1021
    • Raschi, E.1    Ceccarini, L.2    De Ponti, F.3    Recanatini, M.4
  • 43
    • 23844449940 scopus 로고    scopus 로고
    • Computer-based de novo design of drug-like molecules
    • Schneider, G., Fechner, U. 2005. Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 4, 649-663.
    • (2005) Nat Rev Drug Discov , vol.4 , pp. 649-663
    • Schneider, G.1    Fechner, U.2
  • 47
    • 77449114835 scopus 로고    scopus 로고
    • Predicting drug side-effects by chemical systems biology
    • Tatonetti, N. P., Liu, T., Altman, R. B. 2009. Predicting drug side-effects by chemical systems biology. Genome Biol 10, 238.
    • (2009) Genome Biol , vol.10 , pp. 238
    • Tatonetti, N.P.1    Liu, T.2    Altman, R.B.3
  • 48
    • 6044267892 scopus 로고    scopus 로고
    • Failing the public health-rofecoxib, Merck, and the FDA
    • Topol, E. J. 2004. Failing the public health-rofecoxib, Merck, and the FDA. N Engl J Med 351, 1707-1709.
    • (2004) N Engl J Med , vol.351 , pp. 1707-1709
    • Topol, E.J.1
  • 49
    • 0346731233 scopus 로고    scopus 로고
    • Multiple active site corrections for docking and virtual screening
    • Vigers, G. P., Rizzi, J. P. 2004. Multiple active site corrections for docking and virtual screening. J Med Chem 47, 80-89.
    • (2004) J Med Chem , vol.47 , pp. 80-89
    • Vigers, G.P.1    Rizzi, J.P.2
  • 50
    • 77957954504 scopus 로고    scopus 로고
    • A structurebased approach for mapping adverse drug reactions to the perturbation of underlying biological pathways
    • Wallach, I., Jaitly, N., Lilien, R. 2010. A structurebased approach for mapping adverse drug reactions to the perturbation of underlying biological pathways. PLoS ONE 5, e12063.
    • (2010) PLoS ONE , vol.5
    • Wallach, I.1    Jaitly, N.2    Lilien, R.3
  • 53
    • 36949009488 scopus 로고    scopus 로고
    • In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
    • Xie, L., Wang, J., Bourne, P. E. 2007. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol 3, e217.
    • (2007) PLoS Comput Biol , vol.3
    • Xie, L.1    Wang, J.2    Bourne, P.E.3
  • 54
    • 46249090791 scopus 로고    scopus 로고
    • Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    • Yamanishi, Y., Araki, M., Gutteridge, A., Honda, W., Kanehisa, M. 2008. Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 24, i232-240.
    • (2008) Bioinformatics , vol.24
    • Yamanishi, Y.1    Araki, M.2    Gutteridge, A.3    Honda, W.4    Kanehisa, M.5
  • 55
    • 68249128647 scopus 로고    scopus 로고
    • Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome
    • Yang, L., Chen, J., He, L. 2009a. Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome. PLoS Comput Biol 5, e1000441.
    • (2009) PLoS Comput Biol , vol.5
    • Yang, L.1    Chen, J.2    He, L.3
  • 56
    • 67849110009 scopus 로고    scopus 로고
    • SePreSA: A server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome
    • Yang, L., Luo, H., Chen, J., Xing, Q., He, L. 2009b. SePreSA: A server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome. Nucleic Acids Res 37, W406-412.
    • (2009) Nucleic Acids Res , vol.37
    • Yang, L.1    Luo, H.2    Chen, J.3    Xing, Q.4    He, L.5
  • 57
    • 77949760141 scopus 로고    scopus 로고
    • Identifying unexpected therapeutic targets via chemical-protein interactome
    • Yang, L., Chen, J., Shi, L., Hudock, M., He, L. 2010a. Identifying unexpected therapeutic targets via chemical-protein interactome. PLoS ONE 5, e9568.
    • (2010) PLoS ONE , vol.5
    • Yang, L.1    Chen, J.2    Shi, L.3    Hudock, M.4    He, L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.