메뉴 건너뛰기




Volumn 1844, Issue 1 PART B, 2014, Pages 207-213

Prediction of drug target groups based on chemical-chemical similarities and chemical-chemical/protein connections

Author keywords

Chemical chemical connection; Chemical chemical similarity; Chemical protein connection; Drug target interaction network; Jackknife test

Indexed keywords

CELL ANTIGEN; CELL NUCLEUS RECEPTOR; CYTOKINE; CYTOKINE RECEPTOR; ENZYME; G PROTEIN COUPLED RECEPTOR; ION CHANNEL; PROTEIN; PROTEIN KINASE; SULINDAC;

EID: 84890123436     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.05.021     Document Type: Article
Times cited : (20)

References (39)
  • 1
    • 0037264608 scopus 로고    scopus 로고
    • Target selection in drug discovery
    • DOI 10.1038/nrd986
    • J. Knowles, and G. Gromo Target selection in drug discovery Nat. Rev. Drug Discov. 2 2003 63 69 (Pubitemid 37361625)
    • (2003) Nature Reviews Drug Discovery , vol.2 , Issue.1 , pp. 63-69
    • Knowles, J.1    Gromo, G.2
  • 3
    • 27544507236 scopus 로고    scopus 로고
    • A probabilistic model for mining implicit 'chemical compound-gene' relations from literature
    • S. Zhu, Y. Okuno, G. Tsujimoto, and H. Mamitsuka A probabilistic model for mining implicit 'chemical compound-gene' relations from literature Bioinformatics 21 2005 ii245 ii251
    • (2005) Bioinformatics , vol.21
    • Zhu, S.1    Okuno, Y.2    Tsujimoto, G.3    Mamitsuka, H.4
  • 5
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • M. Rarey, B. Kramer, T. Lengauer, and G. Klebe A fast flexible docking method using an incremental construction algorithm J. Mol. Biol. 261 1996 470 489 (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 6
    • 47249146126 scopus 로고    scopus 로고
    • Drug target identification using side-effect similarity
    • DOI 10.1126/science.1158140
    • M. Campillos, M. Kuhn, A.C. Gavin, L.J. Jensen, and P. Bork Drug target identification using side-effect similarity Science 321 2008 263 266 (Pubitemid 351989100)
    • (2008) Science , vol.321 , Issue.5886 , pp. 263-266
    • Campillos, M.1    Kuhn, M.2    Gavin, A.-C.3    Jensen, L.J.4    Bork, P.5
  • 7
    • 84875359061 scopus 로고    scopus 로고
    • 3D MI-DRAGON: New model for the reconstruction of US FDA drug-target network and theoretical-experimental studies of inhibitors of rasagiline derivatives for AChE
    • F. Prado-Prado, X. Garcia-Mera, M. Escobar, N. Alonso, O. Caamano, M. Yanez, and H. Gonzalez-Diaz 3D MI-DRAGON: new model for the reconstruction of US FDA drug-target network and theoretical-experimental studies of inhibitors of rasagiline derivatives for AChE Curr. Top. Med. Chem. 12 2012 1843 1865
    • (2012) Curr. Top. Med. Chem. , vol.12 , pp. 1843-1865
    • Prado-Prado, F.1    Garcia-Mera, X.2    Escobar, M.3    Alonso, N.4    Caamano, O.5    Yanez, M.6    Gonzalez-Diaz, H.7
  • 8
    • 84857196333 scopus 로고    scopus 로고
    • LIBP-Pred: Web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria
    • H. González-Díaz, C.R. Munteanu, L. Postelnicu, F. Prado-Prado, M. Gestal, and A. Pazos LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria Mol. Biosyst. 8 2012 851 862
    • (2012) Mol. Biosyst. , vol.8 , pp. 851-862
    • González-Díaz, H.1    Munteanu, C.R.2    Postelnicu, L.3    Prado-Prado, F.4    Gestal, M.5    Pazos, A.6
  • 9
    • 84863695210 scopus 로고    scopus 로고
    • Prediction of drug-target interactions and drug repositioning via network-based inference
    • F. Cheng, C. Liu, J. Jiang, W. Lu, W. Li, G. Liu, W. Zhou, J. Huang, and Y. Tang Prediction of drug-target interactions and drug repositioning via network-based inference PLoS Comput. Biol. 8 2012 e1002503
    • (2012) PLoS Comput. Biol. , vol.8 , pp. 1002503
    • Cheng, F.1    Liu, C.2    Jiang, J.3    Lu, W.4    Li, W.5    Liu, G.6    Zhou, W.7    Huang, J.8    Tang, Y.9
  • 10
    • 78650184476 scopus 로고    scopus 로고
    • Using compound similarity and functional domain composition for prediction of drug-target interaction networks
    • L. Chen, Z.S. He, T. Huang, and Y.D. Cai Using compound similarity and functional domain composition for prediction of drug-target interaction networks Med. Chem. 6 2010 388 395
    • (2010) Med. Chem. , vol.6 , pp. 388-395
    • Chen, L.1    He, Z.S.2    Huang, T.3    Cai, Y.D.4
  • 11
    • 84855263818 scopus 로고    scopus 로고
    • Predicting biological functions of compounds based on chemical-chemical interactions
    • L.L. Hu, C. Chen, T. Huang, Y.D. Cai, and K.C. Chou Predicting biological functions of compounds based on chemical-chemical interactions PLoS One 6 2011 e29491
    • (2011) PLoS One , vol.6 , pp. 29491
    • Hu, L.L.1    Chen, C.2    Huang, T.3    Cai, Y.D.4    Chou, K.C.5
  • 12
    • 84866640436 scopus 로고    scopus 로고
    • Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins
    • Y.F. Gao, L. Chen, Y.D. Cai, K.Y. Feng, T. Huang, and Y. Jiang Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins PLoS One 7 2012 e45944
    • (2012) PLoS One , vol.7 , pp. 45944
    • Gao, Y.F.1    Chen, L.2    Cai, Y.D.3    Feng, K.Y.4    Huang, T.5    Jiang, Y.6
  • 13
    • 84859732713 scopus 로고    scopus 로고
    • Predicting anatomical therapeutic chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities
    • L. Chen, W.M. Zeng, Y.D. Cai, K.Y. Feng, and K.C. Chou Predicting anatomical therapeutic chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities PLoS One 7 2012 e35254
    • (2012) PLoS One , vol.7 , pp. 35254
    • Chen, L.1    Zeng, W.M.2    Cai, Y.D.3    Feng, K.Y.4    Chou, K.C.5
  • 14
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • M. Kanehisa, and S. Goto KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28 2000 27 30 (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 17
    • 77954074097 scopus 로고    scopus 로고
    • Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
    • L. Chen, K.Y. Feng, Y.D. Cai, K.C. Chou, and H.P. Li Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition BMC Bioinforma. 11 2010 293
    • (2010) BMC Bioinforma. , vol.11 , pp. 293
    • Chen, L.1    Feng, K.Y.2    Cai, Y.D.3    Chou, K.C.4    Li, H.P.5
  • 18
    • 77952351365 scopus 로고    scopus 로고
    • Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity
    • L. Chen, Z.L. Qian, K.Y. Fen, and Y.D. Cai Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarity J. Comput. Chem. 31 2010 1766 1776
    • (2010) J. Comput. Chem. , vol.31 , pp. 1766-1776
    • Chen, L.1    Qian, Z.L.2    Fen, K.Y.3    Cai, Y.D.4
  • 21
    • 46249090791 scopus 로고    scopus 로고
    • Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    • Y. Yamanishi, M. Araki, A. Gutteridge, W. Honda, and M. Kanehisa Prediction of drug-target interaction networks from the integration of chemical and genomic spaces Bioinformatics 24 2008 i232 i240
    • (2008) Bioinformatics , vol.24
    • Yamanishi, Y.1    Araki, M.2    Gutteridge, A.3    Honda, W.4    Kanehisa, M.5
  • 22
    • 0141843591 scopus 로고    scopus 로고
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    • DOI 10.1021/ja036030u
    • M. Hattori, Y. Okuno, S. Goto, and M. Kanehisa Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways J. Am. Chem. Soc. 125 2003 11853 11865 (Pubitemid 37175419)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.39 , pp. 11853-11865
    • Hattori, M.1    Okuno, Y.2    Goto, S.3    Kanehisa, M.4
  • 23
    • 0023965741 scopus 로고
    • Smiles, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • D. Weininger SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules J. Chem. Inf. Comput. Sci. 28 1988 31 36 (Pubitemid 18574254)
    • (1988) Journal of Chemical Information and Computer Sciences , vol.28 , Issue.1 , pp. 31-36
    • Weininger David1
  • 24
    • 84980090975 scopus 로고
    • The distribution of the flora in the alpine zone. 1
    • P. Jaccard The distribution of the flora in the alpine zone. 1 New Phytol. 11 1912 37 50
    • (1912) New Phytol. , vol.11 , pp. 37-50
    • Jaccard, P.1
  • 25
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • R. Sharan, I. Ulitsky, and R. Shamir Network-based prediction of protein function Mol. Syst. Biol. 3 2007 88
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 88
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 27
    • 77649178737 scopus 로고    scopus 로고
    • Prediction of protein functions based on function-function correlation relations
    • K.L. Ng, J.S. Ciou, and C.H. Huang Prediction of protein functions based on function-function correlation relations Comput. Biol. Med. 40 2010 300 305
    • (2010) Comput. Biol. Med. , vol.40 , pp. 300-305
    • Ng, K.L.1    Ciou, J.S.2    Huang, C.H.3
  • 28
    • 77949760141 scopus 로고    scopus 로고
    • Identifying unexpected therapeutic targets via chemical-protein interactome
    • L. Yang, J. Chen, L. Shi, M.P. Hudock, K. Wang, and L. He Identifying unexpected therapeutic targets via chemical-protein interactome PLoS One 5 3 2010 e9568
    • (2010) PLoS One , vol.5 , Issue.3 , pp. 9568
    • Yang, L.1    Chen, J.2    Shi, L.3    Hudock, M.P.4    Wang, K.5    He, L.6
  • 29
    • 68249128647 scopus 로고    scopus 로고
    • Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome
    • L. Yang, J. Chen, and L. He Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome PLoS Comput. Biol. 5 7 2009 e1000441
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.7 , pp. 1000441
    • Yang, L.1    Chen, J.2    He, L.3
  • 30
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • DOI 10.1023/A:1011115820450
    • T.J. Ewing, S. Makino, G.A. Skillman, and I.D. Kuntz DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases J. Comput. Aided Mol. Des. 15 2001 411 428 (Pubitemid 32452109)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.5 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 31
    • 64749100837 scopus 로고    scopus 로고
    • Predicting DNA-and RNA-binding proteins from sequences with kernel methods
    • X. Shao, Y. Tian, L. Wu, Y. Wang, L. Jing, and N. Deng Predicting DNA-and RNA-binding proteins from sequences with kernel methods J. Theor. Biol. 258 2009 289 293
    • (2009) J. Theor. Biol. , vol.258 , pp. 289-293
    • Shao, X.1    Tian, Y.2    Wu, L.3    Wang, Y.4    Jing, L.5    Deng, N.6
  • 32
    • 59649123088 scopus 로고    scopus 로고
    • Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition
    • D. Georgiou, T. Karakasidis, J. Nieto, and A. Torres Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition J. Theor. Biol. 257 2009 17 26
    • (2009) J. Theor. Biol. , vol.257 , pp. 17-26
    • Georgiou, D.1    Karakasidis, T.2    Nieto, J.3    Torres, A.4
  • 33
    • 33749585599 scopus 로고    scopus 로고
    • The steroid hormone biosynthesis pathway as a target for endocrine-disrupting chemicals
    • DOI 10.1093/toxsci/kfl051
    • J.T. Sanderson The steroid hormone biosynthesis pathway as a target for endocrine-disrupting chemicals Toxicol. Sci. 94 2006 3 21 (Pubitemid 44542325)
    • (2006) Toxicological Sciences , vol.94 , Issue.1 , pp. 3-21
    • Sanderson, J.T.1
  • 35
    • 84890121068 scopus 로고    scopus 로고
    • (accessed February, 2013)
    • http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi? cid=5280453&loc= ec-rcs (accessed February, 2013)
  • 36
    • 84890114789 scopus 로고    scopus 로고
    • (accessed February, 2013)
    • http://www.kegg.jp/dbget-bin/www-bget?dr:D00129 (accessed February, 2013)
  • 38
    • 0035246513 scopus 로고    scopus 로고
    • Cyclooxygenase inhibitors - Current status and future prospects
    • DOI 10.1016/S0223-5234(01)01197-7, PII S0223523401011977
    • G. Dannhardt, and W. Kiefer Cyclooxygenase inhibitors - current status and future prospects Eur. J. Med. Chem. 36 2001 109 126 (Pubitemid 32304514)
    • (2001) European Journal of Medicinal Chemistry , vol.36 , Issue.2 , pp. 109-126
    • Dannhardt, G.1    Kiefer, W.2
  • 39
    • 84890128613 scopus 로고    scopus 로고
    • (accessed February, 2013)
    • http://www.ncbi.nlm.nih.gov/mesh/68013467 (accessed February, 2013)


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.