메뉴 건너뛰기




Volumn 20, Issue 1, 2014, Pages 23-36

Network pharmacology strategies toward multi-target anticancer therapies: From computational models to experimental design principles

Author keywords

Anticancer therapies; Computational models; Experimental design; Network pharmacology

Indexed keywords

ANTINEOPLASTIC AGENT; LIGAND;

EID: 84907033076     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/13816128113199990470     Document Type: Article
Times cited : (110)

References (178)
  • 2
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • [2] Hopkins AL. Network pharmacology: The next paradigm in drug discovery. Nat Chem Biol 2008; 4: 682-90.
    • (2008) Nat Chem Biol , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 3
    • 33847377573 scopus 로고    scopus 로고
    • A robustness-based approach to systems-oriented drug design
    • [3] Kitano H. A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 2007; 6: 202-10.
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 202-210
    • Kitano, H.1
  • 4
    • 84855882587 scopus 로고    scopus 로고
    • Novel computational approaches to polypharmacology as a means to define responses to individual drugs
    • [4] Xie L, Xie L, Kinnings SL, Bourne PE. Novel computational approaches to polypharmacology as a means to define responses to individual drugs. Annu Rev Pharmacol Toxicol 2012; 52: 361-79.
    • (2012) Annu Rev Pharmacol Toxicol , vol.52 , pp. 361-379
    • Xie, L.1    Xie, L.2    Kinnings, S.L.3    Bourne, P.E.4
  • 5
    • 67650488269 scopus 로고    scopus 로고
    • Synergistic drug combinations tend to improve therapeutically relevant selectivity
    • [5] Lehár J, Krueger AS, Avery W, et al. Synergistic drug combinations tend to improve therapeutically relevant selectivity. Nat Biotechnol 2009; 27: 659-66.
    • (2009) Nat Biotechnol , vol.27 , pp. 659-666
    • Lehár, J.1    Krueger, A.S.2    Avery, W.3
  • 6
    • 84865254848 scopus 로고    scopus 로고
    • Mechanisms of acquired resistance to targeted cancer therapies
    • [6] Lackner MR, Wilson TR, Settleman J. Mechanisms of acquired resistance to targeted cancer therapies. Future Oncol 2012; 8: 999-1014.
    • (2012) Future Oncol , vol.8 , pp. 999-1014
    • Lackner, M.R.1    Wilson, T.R.2    Settleman, J.3
  • 7
    • 34447506266 scopus 로고    scopus 로고
    • Rational design of cancer-drug combinations
    • [7] Ramaswamy S. Rational design of cancer-drug combinations. N Engl J Med 2007; 357: 299-300.
    • (2007) N Engl J Med , vol.357 , pp. 299-300
    • Ramaswamy, S.1
  • 8
    • 79953283356 scopus 로고    scopus 로고
    • Genetic interactions in cancer progression and treatment
    • [8] Ashworth A, Lord CJ, Reis-Filho JS. Genetic interactions in cancer progression and treatment. Cell 2011; 145: 30-8.
    • (2011) Cell , vol.145 , pp. 30-38
    • Ashworth, A.1    Lord, C.J.2    Reis-Filho, J.S.3
  • 9
    • 79952635505 scopus 로고    scopus 로고
    • Principles and strategies for developing network models in cancer
    • [9] Pe’er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell 2011; 144: 864-73.
    • (2011) Cell , vol.144 , pp. 864-873
    • Pe’Er, D.1    Hacohen, N.2
  • 10
    • 33748798478 scopus 로고    scopus 로고
    • Graph-based methods for analysing networks in cell biology
    • [10] Aittokallio T, Schwikowski B. Graph-based methods for analysing networks in cell biology. Brief Bioinform 2006; 7: 243-55.
    • (2006) Brief Bioinform , vol.7 , pp. 243-255
    • Aittokallio, T.1    Schwikowski, B.2
  • 11
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • [11] Vidal M, Cusick ME, Barabási A-L. Interactome networks and human disease. Cell 2011; 144: 986-98.
    • (2011) Cell , vol.144 , pp. 986-998
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.-L.3
  • 12
    • 70249134919 scopus 로고    scopus 로고
    • Molecular networks as sensors and drivers of common human diseases
    • [12] Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature 2009; 461: 218-23.
    • (2009) Nature , vol.461 , pp. 218-223
    • Schadt, E.E.1
  • 16
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell’s functional organization
    • [16] Barabási A-L, Oltvai ZN. Network biology: Understanding the cell’s functional organization. Nat Rev Genet 2004; 5: 101-13.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabási, A.-L.1    Oltvai, Z.N.2
  • 17
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: A network-based approach to human disease
    • [17] Barabási A-L, Gulbahce N, Loscalzo J. Network medicine: A network-based approach to human disease. Nat Rev Genet 2011; 12: 56-68.
    • (2011) Nat Rev Genet , vol.12 , pp. 56-68
    • Barabási, A.-L.1    Gulbahce, N.2    Loscalzo, J.3
  • 19
    • 67349276056 scopus 로고    scopus 로고
    • A network medicine approach to human disease
    • [19] Zanzoni A, Soler-López M, Aloy P. A network medicine approach to human disease. FEBS Lett 2009; 583: 1759-65.
    • (2009) FEBS Lett , vol.583 , pp. 1759-1765
    • Zanzoni, A.1    Soler-López, M.2    Aloy, P.3
  • 20
    • 41149167511 scopus 로고    scopus 로고
    • Network medicine
    • [20] Pawson T, Linding R. Network medicine. FEBS Lett 2008; 582: 1266-70.
    • (2008) FEBS Lett , vol.582 , pp. 1266-1270
    • Pawson, T.1    Linding, R.2
  • 21
    • 84866122803 scopus 로고    scopus 로고
    • Navigating cancer network attractors for tumor-specific therapy
    • [21] Creixell P, Schoof EM, Erler JT, Linding R. Navigating cancer network attractors for tumor-specific therapy. Nat Biotechnol 2012; 30: 842-8.
    • (2012) Nat Biotechnol , vol.30 , pp. 842-848
    • Creixell, P.1    Schoof, E.M.2    Erler, J.T.3    Linding, R.4
  • 22
    • 84889002223 scopus 로고    scopus 로고
    • Network-based drug discovery by integrating systems biology and computational technologies
    • [22] Leung EL, Cao Z-W, Jiang Z-H, Zhou H, Liu L. Network-based drug discovery by integrating systems biology and computational technologies. Brief Bioinform 2012; doi: 10.1093/bib/bbs043.
    • (2012) Brief Bioinform
    • Leung, E.L.1    Cao, Z.-W.2    Jiang, Z.-H.3    Zhou, H.4    Liu, L.5
  • 23
    • 77649182705 scopus 로고    scopus 로고
    • Unveiling the role of network and systems biology in drug discovery
    • [23] Pujol A, Mosca R, Farrés J, Aloy P. Unveiling the role of network and systems biology in drug discovery. Trends Pharmacol Sci 2010; 31: 115-23.
    • (2010) Trends Pharmacol Sci , vol.31 , pp. 115-123
    • Pujol, A.1    Mosca, R.2    Farrés, J.3    Aloy, P.4
  • 24
    • 70350690962 scopus 로고    scopus 로고
    • Systems pharmacology and genome medicine: A future perspective
    • [24] Wist AD, Berger SI, Iyengar R. Systems pharmacology and genome medicine: A future perspective. Genome Med 2009; 1: 11.
    • (2009) Genome Med , vol.1
    • Wist, A.D.1    Berger, S.I.2    Iyengar, R.3
  • 25
    • 77953811662 scopus 로고    scopus 로고
    • Network systems biology for drug discovery
    • [25] Arrell DK, Terzic A. Network systems biology for drug discovery. Clin Pharmacol Ther 2010; 88: 120-5.
    • (2010) Clin Pharmacol Ther , vol.88 , pp. 120-125
    • Arrell, D.K.1    Terzic, A.2
  • 26
    • 77954052283 scopus 로고    scopus 로고
    • Systems approaches to polypharmacology and drug discovery
    • [26] Boran ADW, Iyengar R. Systems approaches to polypharmacology and drug discovery. Curr Opin Drug Discov Devel 2010; 13: 297-309.
    • (2010) Curr Opin Drug Discov Devel , vol.13 , pp. 297-309
    • Boran, A.1    Iyengar, R.2
  • 27
    • 70349847876 scopus 로고    scopus 로고
    • Network analyses in systems pharmacology
    • [27] Berger SI, Iyengar R. Network analyses in systems pharmacology. Bioinformatics 2009; 25: 2466-72.
    • (2009) Bioinformatics , vol.25 , pp. 2466-2472
    • Berger, S.I.1    Iyengar, R.2
  • 28
    • 84855906454 scopus 로고    scopus 로고
    • Systems pharmacology: Network analysis to identify multiscale mechanisms of drug action
    • [28] Zhao S, Iyengar R. Systems pharmacology: Network analysis to identify multiscale mechanisms of drug action. Annu Rev Pharmacol Toxicol 2012; 52: 505-21.
    • (2012) Annu Rev Pharmacol Toxicol , vol.52 , pp. 505-521
    • Zhao, S.1    Iyengar, R.2
  • 30
    • 84862795414 scopus 로고    scopus 로고
    • Structure-Based Virtual Screening for Drug Discovery: A Problem-Centric Review
    • [30] Cheng T, Li Q, Zhou Z, Wang Y, Bryant SH. Structure-Based Virtual Screening for Drug Discovery: A Problem-Centric Review. AAPS J 2012; 14: 133-41.
    • (2012) AAPS J , vol.14 , pp. 133-141
    • Cheng, T.1    Li, Q.2    Zhou, Z.3    Wang, Y.4    Bryant, S.H.5
  • 31
    • 84860851412 scopus 로고    scopus 로고
    • Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks
    • [31] Lee MJ, Ye AS, Gardino AK, et al. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 2012; 149: 780-94.
    • (2012) Cell , vol.149 , pp. 780-794
    • Lee, M.J.1    Ye, A.S.2    Gardino, A.K.3
  • 32
    • 84876148983 scopus 로고    scopus 로고
    • Dynamic networks in systems medicine
    • [32] Capobianco E. Dynamic networks in systems medicine. Front Genet 2012; 3: 185.
    • (2012) Front Genet , vol.3
    • Capobianco, E.1
  • 33
    • 84860214990 scopus 로고    scopus 로고
    • Intra-tumour heterogeneity: A looking glass for cancer?
    • [33] Marusyk A, Almendro V, Polyak K. Intra-tumour heterogeneity: A looking glass for cancer? Nat Rev Cancer 2012; 12: 323-34.
    • (2012) Nat Rev Cancer , vol.12 , pp. 323-334
    • Marusyk, A.1    Almendro, V.2    Polyak, K.3
  • 34
    • 84862757952 scopus 로고    scopus 로고
    • Evolutionary dynamics of carcinogenesis and why targeted therapy does not work
    • [34] Gillies RJ, Verduzco D, Gatenby RA. Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat Rev Cancer 2012; 12: 487-93.
    • (2012) Nat Rev Cancer , vol.12 , pp. 487-493
    • Gillies, R.J.1    Verduzco, D.2    Gatenby, R.A.3
  • 35
    • 33947587274 scopus 로고    scopus 로고
    • Simulation and prediction of in vivo drug metabolism in human populations from in vitro data
    • [35] Rostami-Hodjegan A, Tucker GT. Simulation and prediction of in vivo drug metabolism in human populations from in vitro data. Nat Rev Drug Discov 2007; 6: 140-8.
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 140-148
    • Rostami-Hodjegan, A.1    Tucker, G.T.2
  • 36
    • 84865271285 scopus 로고    scopus 로고
    • Quantitative in vitro to in vivo extrapolation of cell-based toxicity assay results
    • [36] Yoon M, Campbell JL, Andersen ME, Clewell HJ. Quantitative in vitro to in vivo extrapolation of cell-based toxicity assay results. Crit Rev Toxicol 2012; 42: 633-52.
    • (2012) Crit Rev Toxicol , vol.42 , pp. 633-652
    • Yoon, M.1    Campbell, J.L.2    Ersen, M.E.3    Clewell, H.J.4
  • 37
    • 77957696701 scopus 로고    scopus 로고
    • A quantitative framework and strategies for management and evaluation of metabolic drug-drug interactions in oncology drug development: New molecular entities as object drugs
    • [37] Venkatakrishnan K, Pickard MD, Von Moltke LL. A quantitative framework and strategies for management and evaluation of metabolic drug-drug interactions in oncology drug development: New molecular entities as object drugs. Clin Pharmacokinet 2010; 49: 703-27.
    • (2010) Clin Pharmacokinet , vol.49 , pp. 703-727
    • Venkatakrishnan, K.1    Pickard, M.D.2    Von Moltke, L.L.3
  • 38
    • 33746622984 scopus 로고    scopus 로고
    • Strategies for optimizing combinations of molecularly targeted anticancer agents
    • [38] Dancey JE, Chen HX. Strategies for optimizing combinations of molecularly targeted anticancer agents. Nat Rev Drug Discov 2006; 5: 649-59.
    • (2006) Nat Rev Drug Discov , vol.5 , pp. 649-659
    • Dancey, J.E.1    Chen, H.X.2
  • 39
    • 33845762340 scopus 로고    scopus 로고
    • Multi-target therapeutics: When the whole is greater than the sum of the parts
    • [39] Zimmermann GR, Lehár J, Keith CT. Multi-target therapeutics: When the whole is greater than the sum of the parts. Drug Discov Today 2007; 12: 34-42.
    • (2007) Drug Discov Today , vol.12 , pp. 34-42
    • Zimmermann, G.R.1    Lehár, J.2    Keith, C.T.3
  • 40
    • 59349083179 scopus 로고    scopus 로고
    • Mechanisms of drug combinations: Interaction and network perspectives
    • [40] Jia J, Zhu F, Ma X, Cao ZW, Li YX, Chen YZ. Mechanisms of drug combinations: Interaction and network perspectives. Nat Rev Drug Discov 2009; 8: 111-28.
    • (2009) Nat Rev Drug Discov , vol.8 , pp. 111-128
    • Jia, J.1    Zhu, F.2    Ma, X.3    Cao, Z.W.4    Li, Y.X.5    Chen, Y.Z.6
  • 41
    • 84863651163 scopus 로고    scopus 로고
    • Combinatorial drug therapy for cancer in the post-genomic era
    • [41] Al-Lazikani B, Banerji U, Workman P. Combinatorial drug therapy for cancer in the post-genomic era. Nat Biotechnol 2012; 30: 679-92.
    • (2012) Nat Biotechnol , vol.30 , pp. 679-692
    • Al-Lazikani, B.1    Banerji, U.2    Workman, P.3
  • 42
    • 81055140589 scopus 로고    scopus 로고
    • From in silico target prediction to multi-target drug design: Current databases, methods and applications
    • [42] Koutsoukas A, Simms B, Kirchmair J, et al. From in silico target prediction to multi-target drug design: Current databases, methods and applications. J of Proteomics 2011; 74: 2554-74.
    • (2011) J of Proteomics , vol.74 , pp. 2554-2574
    • Koutsoukas, A.1    Simms, B.2    Kirchmair, J.3
  • 44
    • 84855874154 scopus 로고    scopus 로고
    • Chemical genetics-based target identification in drug discovery
    • [44] Cong F, Cheung AK, Huang S-MA. Chemical genetics-based target identification in drug discovery. Annu Rev Pharmacol Toxicol 2012; 52: 57-78.
    • (2012) Annu Rev Pharmacol Toxicol , vol.52 , pp. 57-78
    • Cong, F.1    Cheung, A.K.2    Huang, S.M.A.3
  • 45
    • 82355165009 scopus 로고    scopus 로고
    • Identifying cellular targets of small-molecule probes and drugs with biochemical enrichment and SILAC
    • [45] Ong S-E, Li X, Schenone M, Schreiber SL, Carr SA. Identifying cellular targets of small-molecule probes and drugs with biochemical enrichment and SILAC. Methods Mol Biol 2012; 803: 129-40.
    • (2012) Methods Mol Biol , vol.803 , pp. 129-140
    • Ong, S.-E.1    Li, X.2    Schenone, M.3    Schreiber, S.L.4    Carr, S.A.5
  • 47
    • 79952171625 scopus 로고    scopus 로고
    • Probing the links between in vitro potency, ADMET and physicochemical parameters
    • [47] Gleeson MP, Hersey A, Montanari D, Overington J. Probing the links between in vitro potency, ADMET and physicochemical parameters. Nat Rev Drug Discov 2011; 10: 197-208.
    • (2011) Nat Rev Drug Discov , vol.10 , pp. 197-208
    • Gleeson, M.P.1    Hersey, A.2    Montanari, D.3    Overington, J.4
  • 48
    • 77955629600 scopus 로고    scopus 로고
    • Identifying the cellular targets of bioactive small molecules with activity-based probes
    • [48] Li X, Hu Y. Identifying the cellular targets of bioactive small molecules with activity-based probes. Curr Med Chem 2010; 17: 3030-44.
    • (2010) Curr Med Chem , vol.17 , pp. 3030-3044
    • Li, X.1    Hu, Y.2
  • 49
    • 13444292249 scopus 로고    scopus 로고
    • Using genome-wide transcriptional profiling to elucidate small-molecule mechanism
    • [49] Butcher RA, Schreiber SL. Using genome-wide transcriptional profiling to elucidate small-molecule mechanism. Curr Opin Chem Biol 2005; 9: 25-30.
    • (2005) Curr Opin Chem Biol , vol.9 , pp. 25-30
    • Butcher, R.A.1    Schreiber, S.L.2
  • 50
    • 84856392676 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics in preclinical drug discovery
    • [50] Schirle M, Bantscheff M, Kuster B. Mass spectrometry-based proteomics in preclinical drug discovery. Chem Biol 2012; 19: 72-84.
    • (2012) Chem Biol , vol.19 , pp. 72-84
    • Schirle, M.1    Bantscheff, M.2    Kuster, B.3
  • 51
    • 77956651201 scopus 로고    scopus 로고
    • Biochemical network-based drugtarget prediction
    • [51] Klipp E, Wade RC, Kummer U. Biochemical network-based drugtarget prediction. Curr Opin Biotechnol 2010; 21: 511-6.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 511-516
    • Klipp, E.1    Wade, R.C.2    Kummer, U.3
  • 52
    • 0342645323 scopus 로고    scopus 로고
    • Use of structure_activity data to compare structure-based clustering methods and descriptors for use in compound selection
    • [52] Brown RD, Martin YC. Use of structure_activity data to compare structure-based clustering methods and descriptors for use in compound selection. J Chem Inf Comput Sci 1996; 36: 572-84.
    • (1996) J Chem Inf Comput Sci , vol.36 , pp. 572-584
    • Brown, R.D.1    Martin, Y.C.2
  • 53
    • 76749120557 scopus 로고    scopus 로고
    • Interpretable correlation descriptors for quantitative structure-activity relationships
    • [53] Spowage BM, Bruce CL, Hirst JD. Interpretable correlation descriptors for quantitative structure-activity relationships. J Cheminform 2009; 1: 22.
    • (2009) J Cheminform , vol.1
    • Spowage, B.M.1    Bruce, C.L.2    Hirst, J.D.3
  • 55
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • [55] Pearson WR. Empirical statistical estimates for sequence similarity searches. J Mol Biol 1998; 276: 71-84.
    • (1998) J Mol Biol , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 56
    • 84863889195 scopus 로고    scopus 로고
    • Identifying mechanismof-action targets for drugs and probes
    • [56] Gregori-Puigjané E, Setola V, Hert J, et al. Identifying mechanismof-action targets for drugs and probes. Proc Natl Acad Sci USA 2012; 109: 11178-83.
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 11178-11183
    • Gregori-Puigjané, E.1    Setola, V.2    Hert, J.3
  • 58
    • 84878771632 scopus 로고    scopus 로고
    • WOMBAT and WOMBATPK: Bioactivity databases for lead and drug discovery
    • In: Schreiber SL, Kapoor P, Wess G, Eds., New York: Wiley-VCH
    • [58] Olah M, Rad R, Ostopovici L, et al. WOMBAT and WOMBATPK: Bioactivity databases for lead and drug discovery. In: Schreiber SL, Kapoor P, Wess G, Eds. In chemical biology: From small molecules to systems biology and drug design. New York: Wiley-VCH; 2007; pp. 760-86.
    • (2007) Chemical Biology: From Small Molecules to Systems Biology and Drug Design , pp. 760-786
    • Olah, M.1    Rad, R.2    Ostopovici, L.3
  • 60
    • 34548304745 scopus 로고    scopus 로고
    • In silico pharmacology for drug discovery: Methods for virtual ligand screening and profiling
    • [60] Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: Methods for virtual ligand screening and profiling. Br. J Pharmacol 2007; 152: 9-20.
    • (2007) Br. J Pharmacol , vol.152 , pp. 9-20
    • Ekins, S.1    Mestres, J.2    Testa, B.3
  • 61
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: A web-accessible database of experimentally determined proteinligand binding affinities
    • [61] Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. BindingDB: A web-accessible database of experimentally determined proteinligand binding affinities. Nucleic Acids Res 2007; 35: D198-201.
    • (2007) Nucleic Acids Res , vol.35 , pp. 198-201
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 62
    • 42449107423 scopus 로고    scopus 로고
    • The synergy between combinatorial chemistry and highthroughput screening
    • [62] Diller DJ. The synergy between combinatorial chemistry and highthroughput screening. Curr Opin Drug Discov Devel 2008; 11: 346-55.
    • (2008) Curr Opin Drug Discov Devel , vol.11 , pp. 346-355
    • Diller, D.J.1
  • 64
    • 84856389159 scopus 로고    scopus 로고
    • Structural biology and drug discovery of difficult targets: The limits of ligandability
    • [64] Surade S, Blundell TL. Structural biology and drug discovery of difficult targets: The limits of ligandability. Chem Biol 2012; 19: 42-50.
    • (2012) Chem Biol , vol.19 , pp. 42-50
    • Surade, S.1    Blundell, T.L.2
  • 65
    • 0346799108 scopus 로고    scopus 로고
    • Prediction of protein function from protein sequence and structure
    • [65] Whisstock JC, Lesk AM. Prediction of protein function from protein sequence and structure. Q Rev Biophys 2003; 36: 307-40.
    • (2003) Q Rev Biophys , vol.36 , pp. 307-340
    • Whisstock, J.C.1    Lesk, A.M.2
  • 66
    • 45149124684 scopus 로고    scopus 로고
    • Molecular drug targets and structure based drug design: A holistic approach
    • [66] Singh S, Malik BK, Sharma DK. Molecular drug targets and structure based drug design: A holistic approach. Bioinformation 2006; 1: 314-20.
    • (2006) Bioinformation , vol.1 , pp. 314-320
    • Singh, S.1    Malik, B.K.2    Sharma, D.K.3
  • 67
    • 24744435534 scopus 로고    scopus 로고
    • Kernel methods for predicting proteinprotein interactions
    • [67] Ben-Hur A, Noble WS. Kernel methods for predicting proteinprotein interactions. Bioinformatics 2005; 21: I38-46.
    • (2005) Bioinformatics , vol.21 , pp. 38-46
    • Ben-Hur, A.1    Noble, W.S.2
  • 68
    • 84866459051 scopus 로고    scopus 로고
    • Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization
    • [68] Gönen M. Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization. Bioinformatics 2012; 28: 2304-10.
    • (2012) Bioinformatics , vol.28 , pp. 2304-2310
    • Gönen, M.1
  • 69
    • 36349010717 scopus 로고    scopus 로고
    • Prediction of potential drug targets based on simple sequence properties
    • [69] Li Q, Lai L. Prediction of potential drug targets based on simple sequence properties. BMC Bioinformatics 2007; 8: 353.
    • (2007) BMC Bioinformatics , vol.8
    • Li, Q.1    Lai, L.2
  • 70
    • 46249090791 scopus 로고    scopus 로고
    • Prediction of drug-target interaction networks from the integration of chemical and genomic spaces
    • [70] Yamanishi Y, Araki M, Gutteridge A, Honda W, Kanehisa M. Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 2008; 24: I232-40.
    • (2008) Bioinformatics , vol.24 , pp. 232-240
    • Yamanishi, Y.1    Araki, M.2    Gutteridge, A.3    Honda, W.4    Kanehisa, M.5
  • 72
    • 77950448057 scopus 로고    scopus 로고
    • Predicting drug-target interaction networks based on functional groups and biological features
    • [72] He Z, Zhang J, Shi XH, et al. Predicting drug-target interaction networks based on functional groups and biological features. PLoS One 2010; 5: E9603
    • (2010) Plos One , vol.5
    • He, Z.1    Zhang, J.2    Shi, X.H.3
  • 73
    • 33846155913 scopus 로고    scopus 로고
    • Structure-based maximal affinity model predicts small-molecule druggability
    • [73] Cheng AC, Coleman RG, Smyth KT, et al. Structure-based maximal affinity model predicts small-molecule druggability. Nat Biotechnol 2007; 25: 71-5.
    • (2007) Nat Biotechnol , vol.25 , pp. 71-75
    • Cheng, A.C.1    Coleman, R.G.2    Smyth, K.T.3
  • 74
    • 84856819274 scopus 로고    scopus 로고
    • Docking methods, ligand design, and validation data sets in the structural genomics era
    • Gu J, Bourne PE. Eds, 2nd ed. New York: Wiley-Blackwell
    • [74] Brooijmans N. Docking methods, ligand design, and validation data sets in the structural genomics era. In: Gu J, Bourne PE. Eds. Structural bioinformatics. 2nd ed. New York: Wiley-Blackwell 2009; pp. 635-63.
    • (2009) Structural Bioinformatics , pp. 635-663
    • Brooijmans, N.1
  • 75
    • 33749506205 scopus 로고    scopus 로고
    • Methods for the prediction of proteinligand binding sites for structure-based drug design and virtual ligand screening
    • [75] Laurie ATR, Jackson RM. Methods for the prediction of proteinligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci 2006; 7: 395-406.
    • (2006) Curr Protein Pept Sci , vol.7 , pp. 395-406
    • Laurie, A.1    Jackson, R.M.2
  • 76
    • 79953100964 scopus 로고    scopus 로고
    • Structure-based systems biology for analyzing off-target binding
    • [76] Xie L, Xie L, Bourne PE. Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol 2011; 21: 189-99.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 189-199
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 77
    • 33845876254 scopus 로고    scopus 로고
    • The Connectivity Map: A new tool for biomedical research
    • [77] Lamb J. The Connectivity Map: A new tool for biomedical research. Nat Rev Cancer 2007; 7: 54-60.
    • (2007) Nat Rev Cancer , vol.7 , pp. 54-60
    • Lamb, J.1
  • 78
    • 77957044703 scopus 로고    scopus 로고
    • Discovery of drug mode of action and drug repositioning from transcriptional responses
    • [78] Iorio F, Bosotti R, Scacheri E, et al. Discovery of drug mode of action and drug repositioning from transcriptional responses. Proc Natl Acad Sci USA 2010; 107: 14621-6.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 14621-14626
    • Iorio, F.1    Bosotti, R.2    Scacheri, E.3
  • 79
    • 78651339534 scopus 로고    scopus 로고
    • NCBI GEO: Archive for functional genomics data sets--10 years on
    • [79] Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: Archive for functional genomics data sets--10 years on. Nucleic Acids Res 2010; 39: D1005-10.
    • (2010) Nucleic Acids Res , vol.39 , pp. 1005-1010
    • Barrett, T.1    Troup, D.B.2    Wilhite, S.E.3
  • 80
    • 47049105891 scopus 로고    scopus 로고
    • Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data
    • [80] Hassane DC, Guzman ML, Corbett C, et al. Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood 2008; 111: 5654-62.
    • (2008) Blood , vol.111 , pp. 5654-5662
    • Hassane, D.C.1    Guzman, M.L.2    Corbett, C.3
  • 81
    • 40849130043 scopus 로고    scopus 로고
    • Proteomic methods for drug target discovery
    • [81] Sleno L, Emili A. Proteomic methods for drug target discovery. Curr Opin Chem Biol 2008; 12: 46-54.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 46-54
    • Sleno, L.1    Emili, A.2
  • 82
    • 80054903948 scopus 로고    scopus 로고
    • Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology
    • [82] Chen B, McConnell KJ, Wale N, Wild DJ, Gifford EM. Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology. Bioinformatics 2011; 27: 3044-9.
    • (2011) Bioinformatics , vol.27 , pp. 3044-3049
    • Chen, B.1    McConnell, K.J.2    Wale, N.3    Wild, D.J.4    Gifford, E.M.5
  • 83
    • 32344440237 scopus 로고    scopus 로고
    • Analysis of drug-induced effect patterns to link structure and side effects of medicines
    • [83] Fliri AF, Loging WT, Thadeio PF, Volkmann RA. Analysis of drug-induced effect patterns to link structure and side effects of medicines. Nat Chem Biol 2005; 1: 389-97.
    • (2005) Nat Chem Biol , vol.1 , pp. 389-397
    • Fliri, A.F.1    Loging, W.T.2    Thadeio, P.F.3    Volkmann, R.A.4
  • 84
    • 47249146126 scopus 로고    scopus 로고
    • Drug target identification using side-effect similarity
    • [84] Campillos M, Kuhn M, Gavin A-C, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science 2008; 321: 263-6.
    • (2008) Science , vol.321 , pp. 263-266
    • Campillos, M.1    Kuhn, M.2    Gavin, A.-C.3    Jensen, L.J.4    Bork, P.5
  • 86
    • 75149130051 scopus 로고    scopus 로고
    • Targeting the cancer kinome through polypharmacology
    • [86] Knight ZA, Lin H, Shokat KM. Targeting the cancer kinome through polypharmacology. Nat Rev Cancer 2010; 10: 130-7.
    • (2010) Nat Rev Cancer , vol.10 , pp. 130-137
    • Knight, Z.A.1    Lin, H.2    Shokat, K.M.3
  • 88
    • 84859313468 scopus 로고    scopus 로고
    • Quantitative models of signal transduction networks: How detailed should they be?
    • [88] Cirit M, Haugh JM. Quantitative models of signal transduction networks: How detailed should they be? Commun Integr Biol 2011; 4: 353-6.
    • (2011) Commun Integr Biol , vol.4 , pp. 353-356
    • Cirit, M.1    Haugh, J.M.2
  • 90
    • 31444453554 scopus 로고    scopus 로고
    • Computational modelling of ErbB family phosphorylation dynamics in response to transforming growth factor alpha and heregulin indicates spatial compartmentation of phosphatase activity
    • [90] Hendriks BS, Cook J, Burke JM, Beusmans JM, Lauffenburger DA, De Graaf D. Computational modelling of ErbB family phosphorylation dynamics in response to transforming growth factor alpha and heregulin indicates spatial compartmentation of phosphatase activity. Syst Biol (Stevenage) 2006; 153: 22-33.
    • (2006) Syst Biol (Stevenage) , vol.153 , pp. 22-33
    • Hendriks, B.S.1    Cook, J.2    Burke, J.M.3    Beusmans, J.M.4    Lauffenburger, D.A.5    De Graaf, D.6
  • 92
    • 62549162241 scopus 로고    scopus 로고
    • Modeling ERBB receptorregulated G1/S transition to find novel targets for de novo trastuzumab resistance
    • [92] Sahin O, Fröhlich H, Löbke C, et al. Modeling ERBB receptorregulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst Biol 2009; 3: 1.
    • (2009) BMC Syst Biol , vol.3
    • Sahin, O.1    Fröhlich, H.2    Löbke, C.3
  • 93
    • 84857704502 scopus 로고    scopus 로고
    • Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions
    • [93] Morris MK, Shriver Z, Sasisekharan R, Lauffenburger DA. Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions. Biotechnol J 2012; 7: 374-86.
    • (2012) Biotechnol J , vol.7 , pp. 374-386
    • Morris, M.K.1    Shriver, Z.2    Sasisekharan, R.3    Lauffenburger, D.A.4
  • 94
    • 0842288337 scopus 로고    scopus 로고
    • Inferring Cellular Networks Using Probabilistic Graphical Models
    • [94] Friedman N. Inferring Cellular Networks Using Probabilistic Graphical Models. Science. 2004; 303: 799-805.
    • (2004) Science , vol.303 , pp. 799-805
    • Friedman, N.1
  • 95
    • 84866343535 scopus 로고    scopus 로고
    • Mathematical and statistical modeling in cancer systems biology
    • [95] Blair RH, Trichler DL, Gaille DP. Mathematical and statistical modeling in cancer systems biology. Front Physiol 2012; 3: 227.
    • (2012) Front Physiol , vol.3
    • Blair, R.H.1    Trichler, D.L.2    Gaille, D.P.3
  • 97
    • 79960431407 scopus 로고    scopus 로고
    • Drug metabolite profiling and identification by high-resolution mass spectrometry
    • [97] Zhu M, Zhang H, Humphreys WG. Drug metabolite profiling and identification by high-resolution mass spectrometry. J Biol Chem 2011; 286: 25419-25.
    • (2011) J Biol Chem , vol.286 , pp. 25419-25425
    • Zhu, M.1    Zhang, H.2    Humphreys, W.G.3
  • 98
    • 84863230581 scopus 로고    scopus 로고
    • Metabolic network modeling and simulation for drug targeting and discovery
    • [98] Kim HU, Sohn SB, Lee SY. Metabolic network modeling and simulation for drug targeting and discovery. Biotechnol J 2012; 7: 330-42.
    • (2012) Biotechnol J , vol.7 , pp. 330-342
    • Kim, H.U.1    Sohn, S.B.2    Lee, S.Y.3
  • 99
    • 33846910173 scopus 로고    scopus 로고
    • Global reconstruction of the human metabolic network based on genomic and bibliomic data
    • [99] Duarte NC, Becker SA, Jamshidi N, et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 2007; 104: 1777-82.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 1777-1782
    • Duarte, N.C.1    Becker, S.A.2    Jamshidi, N.3
  • 100
    • 77954791900 scopus 로고    scopus 로고
    • Compartmentalization of the Edinburgh Human Metabolic Network
    • [100] Hao T, Ma H-W, Zhao X-M, Goryanin I. Compartmentalization of the Edinburgh Human Metabolic Network. BMC Bioinformatics 2010; 11: 393.
    • (2010) BMC Bioinformatics , vol.11
    • Hao, T.1    Ma, H.-W.2    Zhao, X.-M.3    Goryanin, I.4
  • 103
    • 80053980945 scopus 로고    scopus 로고
    • Critical assessment of human metabolic pathway databases: A stepping stone for future integration
    • [103] Stobbe MD, Houten SM, Jansen GA, Van Kampen AH, Moerland PD. Critical assessment of human metabolic pathway databases: A stepping stone for future integration. BMC Syst Biol 2011; 5: 165.
    • (2011) BMC Syst Biol , vol.5
    • Stobbe, M.D.1    Houten, S.M.2    Jansen, G.A.3    Van Kampen, A.H.4    Moerland, P.D.5
  • 104
    • 84863662483 scopus 로고    scopus 로고
    • Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    • [104] Agren R, Bordel S, Mardinoglu A, Pornputtapong N, Nookaew I, Nielsen J. Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 2012; 8: E1002518.
    • (2012) Plos Comput Biol , vol.8
    • Agren, R.1    Bordel, S.2    Mardinoglu, A.3    Pornputtapong, N.4    Nookaew, I.5    Nielsen, J.6
  • 105
    • 78650034777 scopus 로고    scopus 로고
    • Towards a knowledgebased Human Protein Atlas
    • [105] Uhlen M, Oksvold P, Fagerberg L, et al. Towards a knowledgebased Human Protein Atlas. Nat Biotechnol 2010; 28: 1248-50.
    • (2010) Nat Biotechnol , vol.28 , pp. 1248-1250
    • Uhlen, M.1    Oksvold, P.2    Fagerberg, L.3
  • 106
    • 84870933131 scopus 로고    scopus 로고
    • Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
    • [106] Wang Y, Eddy JA, Price ND. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst Biol 2012; 6: 153.
    • (2012) BMC Syst Biol , vol.6
    • Wang, Y.1    Eddy, J.A.2    Price, N.D.3
  • 107
    • 34548577156 scopus 로고    scopus 로고
    • Constraint-based functional similarity of metabolic genes: Going beyond network topology
    • [107] Rokhlenko O, Shlomi T, Sharan R, Ruppin E, Pinter RY. Constraint-based functional similarity of metabolic genes: Going beyond network topology. Bioinformatics 2007; 23: 2139-46.
    • (2007) Bioinformatics , vol.23 , pp. 2139-2146
    • Rokhlenko, O.1    Shlomi, T.2    Sharan, R.3    Ruppin, E.4    Pinter, R.Y.5
  • 108
    • 67449096729 scopus 로고    scopus 로고
    • Flux balance analysis of biological systems: Applications and challenges
    • [108] Raman K, Chandra N. Flux balance analysis of biological systems: Applications and challenges. Brief Bioinform 2009; 10: 435-49.
    • (2009) Brief Bioinform , vol.10 , pp. 435-449
    • Raman, K.1    Chandra, N.2
  • 109
    • 77957556494 scopus 로고    scopus 로고
    • Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines
    • [109] Li L, Zhou X, Ching WK, Wang P. Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines. BMC Bioinformatics 2010; 11: 501.
    • (2010) BMC Bioinformatics , vol.11 , pp. 501
    • Li, L.1    Zhou, X.2    Ching, W.K.3    Wang, P.4
  • 111
    • 79957936421 scopus 로고    scopus 로고
    • Role of systems pharmacology in understanding drug adverse events
    • [111] Berger SI, Iyengar R. Role of systems pharmacology in understanding drug adverse events. Wiley Interdiscip Rev Syst Biol Med 2011; 3: 129-35.
    • (2011) Wiley Interdiscip Rev Syst Biol Med , vol.3 , pp. 129-135
    • Berger, S.I.1    Iyengar, R.2
  • 112
    • 84868101830 scopus 로고    scopus 로고
    • Neighbor communities in drug combination networks characterize synergistic effect
    • [112] Zou J, Ji P, Zhao YL, et al. Neighbor communities in drug combination networks characterize synergistic effect. Mol Biosyst 2012; 8: 3185-96.
    • (2012) Mol Biosyst , vol.8 , pp. 3185-3196
    • Zou, J.1    Ji, P.2    Zhao, Y.L.3
  • 113
  • 114
    • 84861807752 scopus 로고    scopus 로고
    • The relationship between rational drug design and drug side effects
    • [114] Wang J, Li Z, Qiu C, Wang D, Cui Q. The relationship between rational drug design and drug side effects. Brief Bioinform 2012; 13: 377-82.
    • (2012) Brief Bioinform , vol.13 , pp. 377-382
    • Wang, J.1    Li, Z.2    Qiu, C.3    Wang, D.4    Cui, Q.5
  • 115
    • 67049100457 scopus 로고    scopus 로고
    • Drug discovery using chemical systems biology: Identification of the protein-ligand binding network to explain the side effects of CETP Inhibitors
    • [115] Xie L, Li J, Xie L, Bourne PE. Drug discovery using chemical systems biology: Identification of the protein-ligand binding network to explain the side effects of CETP Inhibitors. PLoS Comput Biol 2009; 5: E1000387.
    • (2009) Plos Comput Biol , vol.5
    • Xie, L.1    Li, J.2    Xie, L.3    Bourne, P.E.4
  • 116
    • 84862510972 scopus 로고    scopus 로고
    • Large-scale prediction and testing of drug activity on side-effect targets
    • [116] Lounkine E, Keiser MJ, Whitebread S, et al. Large-scale prediction and testing of drug activity on side-effect targets. Nature 2012; 486: 361-7.
    • (2012) Nature , vol.486 , pp. 361-367
    • Lounkine, E.1    Keiser, M.J.2    Whitebread, S.3
  • 117
    • 71949111724 scopus 로고    scopus 로고
    • Detecting drug targets with minimum side effects in metabolic networks
    • [117] Li Z, Wang R-S, Zhang X-S, Chen L. Detecting drug targets with minimum side effects in metabolic networks. IET Syst Biol 2009; 3: 523-33.
    • (2009) IET Syst Biol , vol.3 , pp. 523-533
    • Li, Z.1    Wang, R.-S.2    Zhang, X.-S.3    Chen, L.4
  • 118
    • 84865425410 scopus 로고    scopus 로고
    • Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
    • [118] Facchetti G, Zampieri M, Altafini C. Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer. BMC Syst Biol 2012; 6: 115.
    • (2012) BMC Syst Biol , vol.6
    • Facchetti, G.1    Zampieri, M.2    Altafini, C.3
  • 119
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • [119] Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol 2010; 6: E1000938.
    • (2010) Plos Comput Biol , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.5
  • 120
    • 84862535137 scopus 로고    scopus 로고
    • Drug discovery: Computer model predicts side effects
    • [120] Kolaja K. Drug discovery: Computer model predicts side effects. Nature 2012; 486: 326-7.
    • (2012) Nature , vol.486 , pp. 326-327
    • Kolaja, K.1
  • 121
    • 82255196220 scopus 로고    scopus 로고
    • Integrative genomics strategies to elucidate the complexity of drug response
    • [121] Kasarskis A, Yang X, Schadt E. Integrative genomics strategies to elucidate the complexity of drug response. Pharmacogenomics 2011; 12: 1695-715.
    • (2011) Pharmacogenomics , vol.12 , pp. 1695-1715
    • Kasarskis, A.1    Yang, X.2    Schadt, E.3
  • 122
    • 84869396522 scopus 로고    scopus 로고
    • Pharmacogenomics in clinical practice and drug development
    • [122] Harper AR, Topol EJ. Pharmacogenomics in clinical practice and drug development. Nat Biotechnol 2012; 30: 1117-24.
    • (2012) Nat Biotechnol , vol.30 , pp. 1117-1124
    • Harper, A.R.1    Topol, E.J.2
  • 123
    • 79952394490 scopus 로고    scopus 로고
    • An algorithmic framework for predicting side effects of drugs
    • [123] Atias N, Sharan R. An algorithmic framework for predicting side effects of drugs. J Comput Biol 2011; 18: 207-18.
    • (2011) J Comput Biol , vol.18 , pp. 207-218
    • Atias, N.1    Sharan, R.2
  • 125
    • 84872733056 scopus 로고    scopus 로고
    • Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures
    • [125] Huang L-C, Wu X, Chen JY. Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures. Proteomics 2013; 13: 313-24.
    • (2013) Proteomics , vol.13 , pp. 313-324
    • Huang, L.-C.1    Wu, X.2    Chen, J.Y.3
  • 126
  • 127
    • 84864231551 scopus 로고    scopus 로고
    • INDI: A computational framework for inferring drug interactions and their associated recommendations
    • [127] Gottlieb A, Stein GY, Oron Y, Ruppin E, Sharan R. INDI: A computational framework for inferring drug interactions and their associated recommendations. Mol Syst Biol 2012; 8: 592.
    • (2012) Mol Syst Biol , vol.8
    • Gottlieb, A.1    Stein, G.Y.2    Oron, Y.3    Ruppin, E.4    Sharan, R.5
  • 128
    • 84862192766 scopus 로고    scopus 로고
    • ChEMBL: A large-scale bioactivity database for drug discovery
    • [128] Gaulton A, Bellis LJ, Bento AP, et al. ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Res 2012; 40: D1100-07.
    • (2012) Nucleic Acids Res , vol.40 , pp. 1100-1107
    • Gaulton, A.1    Bellis, L.J.2    Bento, A.P.3
  • 129
    • 84860492047 scopus 로고    scopus 로고
    • CanSAR: An integrated cancer public translational research and drug discovery resource
    • [129] Halling-Brown MD, Bulusu KC, Patel M, Tym JE, Al-Lazikani B. canSAR: An integrated cancer public translational research and drug discovery resource. Nucleic Acids Res 2011; 40: D947-56.
    • (2011) Nucleic Acids Res , vol.40 , pp. 947-956
    • Halling-Brown, M.D.1    Bulusu, K.C.2    Patel, M.3    Tym, J.E.4    Al-Lazikani, B.5
  • 130
    • 38549151817 scopus 로고    scopus 로고
    • DrugBank: A knowledgebase for drugs, drug actions and drug targets
    • [130] Wishart DS, Knox C, Guo AC, et al. DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008; 36: D901-06.
    • (2008) Nucleic Acids Res , vol.36 , pp. 901-906
    • Wishart, D.S.1    Knox, C.2    Guo, A.C.3
  • 131
    • 84859267371 scopus 로고    scopus 로고
    • Therapeutic target database update 2012: A resource for facilitating target-oriented drug discovery
    • [131] Zhu F, Shi Z, Qin C, et al. Therapeutic target database update 2012: A resource for facilitating target-oriented drug discovery. Nucleic Acids Res 2012; 40: D1128-36.
    • (2012) Nucleic Acids Res , vol.40 , pp. 1128-1136
    • Zhu, F.1    Shi, Z.2    Qin, C.3
  • 132
    • 84857840354 scopus 로고    scopus 로고
    • SuperTarget goes quantitative: Update on drug-target interactions
    • [132] Hecker N, Ahmed J, Von Eichborn J, et al. SuperTarget goes quantitative: Update on drug-target interactions. Nucleic Acids Res 2012; 40: D1113-17.
    • (2012) Nucleic Acids Res , vol.40 , pp. 1113-1117
    • Hecker, N.1    Ahmed, J.2    Von Eichborn, J.3
  • 133
    • 38549182474 scopus 로고    scopus 로고
    • SuperTarget and Matador: Resources for exploring drug-target relationships
    • [133] Günther S, Kuhn M, Dunkel M, et al. SuperTarget and Matador: Resources for exploring drug-target relationships. Nucleic Acids Res 2008; 36: D919-22.
    • (2008) Nucleic Acids Res , vol.36 , pp. 919-922
    • Günther, S.1    Kuhn, M.2    Dunkel, M.3
  • 134
    • 67849104638 scopus 로고    scopus 로고
    • Pub-Chem: A public information system for analyzing bioactivities of small molecules
    • [134] Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. Pub-Chem: A public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 2009; 37: W623-33.
    • (2009) Nucleic Acids Res , vol.37 , pp. 623-633
    • Wang, Y.1    Xiao, J.2    Suzek, T.O.3    Zhang, J.4    Wang, J.5    Bryant, S.H.6
  • 136
    • 78651296264 scopus 로고    scopus 로고
    • ChemProt: A disease chemical biology database
    • [136] Taboureau O, Nielsen SK, Audouze K, et al. ChemProt: A disease chemical biology database. Nucleic Acids Res 2011; 39: D367-72.
    • (2011) Nucleic Acids Res , vol.39 , pp. 367-372
    • Taboureau, O.1    Nielsen, S.K.2    Audouze, K.3
  • 137
    • 0037314783 scopus 로고    scopus 로고
    • An intuitive look at the relationship of Ki and IC50: A more general use for the dixon plot
    • [137] Burlingham BT, Widlanski TS. An intuitive look at the relationship of Ki and IC50: A more general use for the dixon plot. J Chem Educ 2003; 80: 214.
    • (2003) J Chem Educ , vol.80
    • Burlingham, B.T.1    Widlanski, T.S.2
  • 138
    • 20144387067 scopus 로고    scopus 로고
    • The MIPS mammalian protein-protein interaction database
    • [138] Pagel P, Kovac S, Oesterheld M, et al. The MIPS mammalian protein-protein interaction database. Bioinformatics 2005; 21: 832-4.
    • (2005) Bioinformatics , vol.21 , pp. 832-834
    • Pagel, P.1    Kovac, S.2    Oesterheld, M.3
  • 139
    • 79955667824 scopus 로고    scopus 로고
    • The biomolecular interaction network database in PSI-MI 2.5
    • baq037
    • [139] Isserlin R, El-Badrawi RA, Bader GD. The biomolecular interaction network database in PSI-MI 2.5. Database 2011; baq037.
    • (2011) Database
    • Isserlin, R.1    El-Badrawi, R.A.2    Bader, G.D.3
  • 140
    • 79952201691 scopus 로고    scopus 로고
    • PRIDE and “database on demand” as valuable tools for computational proteomics
    • [140] Vizcaíno JA, Reisinger F, Côté R, Martens L. PRIDE and “database on demand” as valuable tools for computational proteomics. Methods Mol Biol 2011; 696: 93-105.
    • (2011) Methods Mol Biol , vol.696 , pp. 93-105
    • Vizcaíno, J.A.1    Reisinger, F.2    Côté, R.3    Martens, L.4
  • 141
    • 75549087047 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2010
    • [141] Aranda B, Achuthan P, Alam-Faruque Y, et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010; 38: D525-31.
    • (2010) Nucleic Acids Res , vol.38 , pp. 525-531
    • Aranda, B.1    Achuthan, P.2    Alam-Faruque, Y.3
  • 142
    • 75549083295 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2009 update
    • [142] Ceol A, Aryamontri AC, Licata L, et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010; 38: D532-39.
    • (2010) Nucleic Acids Res , vol.38 , pp. 532-539
    • Ceol, A.1    Aryamontri, A.C.2    Licata, L.3
  • 145
    • 58149193222 scopus 로고    scopus 로고
    • Human protein reference database—2009 update
    • [145] Prasad TSK, Goel R, Kandasamy K, et al. Human protein reference database—2009 update. Nucleic Acids Res 2009; 37: D767-72.
    • (2009) Nucleic Acids Res , vol.37 , pp. 767-772
    • Prasad, T.1    Goel, R.2    Kandasamy, K.3
  • 149
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • [149] Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 2012; 40: D109-114.
    • (2012) Nucleic Acids Res , vol.40 , pp. 109-114
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 150
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
    • [150] Schellenberger J, Park J, Conrad T, Palsson B. BiGG: A biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 2010; 11: 213.
    • (2010) BMC Bioinformatics , vol.11
    • Schellenberger, J.1    Park, J.2    Conrad, T.3    Palsson, B.4
  • 151
    • 77953907294 scopus 로고    scopus 로고
    • Chem2Bio2RDF: A semantic framework for linking and data mining chemogenomic and systems chemical biology data
    • [151] Chen B, Dong X, Jiao D, et al. Chem2Bio2RDF: A semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics 2010; 11: 255.
    • (2010) BMC Bioinformatics , vol.11
    • Chen, B.1    Dong, X.2    Jiao, D.3
  • 153
    • 29144531173 scopus 로고    scopus 로고
    • The druggable genome: An update
    • [153] Russ AP, Lampel S. The druggable genome: An update. Drug Discov Today 2005; 10: 1607-10.
    • (2005) Drug Discov Today , vol.10 , pp. 1607-1610
    • Russ, A.P.1    Lampel, S.2
  • 154
    • 79960721268 scopus 로고    scopus 로고
    • Enhancing the accuracy of chemogenomic models with a three-dimensional binding site kernel
    • [154] Meslamani J, Rognan D. Enhancing the accuracy of chemogenomic models with a three-dimensional binding site kernel. J Chem Inf Model 2011; 51: 1593-603.
    • (2011) J Chem Inf Model , vol.51 , pp. 1593-1603
    • Meslamani, J.1    Rognan, D.2
  • 155
    • 79959744025 scopus 로고    scopus 로고
    • Do cancer proteins really interact strongly in the human protein-protein interaction network?
    • [155] Xia J, Sun J, Jia P, Zhao Z. Do cancer proteins really interact strongly in the human protein-protein interaction network? Comput Biol Chem 2011; 35: 121-5.
    • (2011) Comput Biol Chem , vol.35 , pp. 121-125
    • Xia, J.1    Sun, J.2    Jia, P.3    Zhao, Z.4
  • 156
    • 84877929778 scopus 로고    scopus 로고
    • A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset
    • [156] Joung JG, Kim SJ, Shin SY, Zhang BT. A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset. BMC Bioinformatics 2012; 13: S12.
    • (2012) BMC Bioinformatics , vol.13
    • Joung, J.G.1    Kim, S.J.2    Shin, S.Y.3    Zhang, B.T.4
  • 157
    • 47049105891 scopus 로고    scopus 로고
    • Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data
    • [157] Hassane DC, Guzman ML, Corbett C, et al. Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood 2008; 111: 5654-62.
    • (2008) Blood , vol.111 , pp. 5654-5662
    • Hassane, D.C.1    Guzman, M.L.2    Corbett, C.3
  • 158
    • 84864031633 scopus 로고    scopus 로고
    • Gene expression signatures associated with the in vitro resistance to two tyrosine kinase inhibitors, nilotinib and imatinib
    • [158] Kim TM, Ha SA, Kim HK, et al. Gene expression signatures associated with the in vitro resistance to two tyrosine kinase inhibitors, nilotinib and imatinib. Blood Cancer J 2011; 1: E32.
    • (2011) Blood Cancer J , vol.1
    • Kim, T.M.1    Ha, S.A.2    Kim, H.K.3
  • 159
    • 43049156566 scopus 로고    scopus 로고
    • Human metabolic network reconstruction and its impact on drug discovery and development
    • [159] Ma H, Goryanin I. Human metabolic network reconstruction and its impact on drug discovery and development. Drug Discov Today 2008; 13: 402-8.
    • (2008) Drug Discov Today , vol.13 , pp. 402-408
    • Ma, H.1    Goryanin, I.2
  • 160
    • 0038610570 scopus 로고    scopus 로고
    • Systematic discovery of multicomponent therapeutics
    • [160] Borisy AA, Elliott PJ, Hurst NW, et al. Systematic discovery of multicomponent therapeutics. Proc Natl Acad Sci USA 2003; 100: 7977-82.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 7977-7982
    • Borisy, A.A.1    Elliott, P.J.2    Hurst, N.W.3
  • 161
    • 58149166733 scopus 로고    scopus 로고
    • Search algorithms as a framework for the optimization of drug combinations
    • [161] Calzolari D, Bruschi S, Coquin L, et al. Search algorithms as a framework for the optimization of drug combinations. PLoS Comput Biol 2008; 4: E1000249.
    • (2008) Plos Comput Biol , vol.4
    • Calzolari, D.1    Bruschi, S.2    Coquin, L.3
  • 162
    • 70049113642 scopus 로고    scopus 로고
    • Optimal drug combinations and minimal hitting sets
    • [162] Vazquez A. Optimal drug combinations and minimal hitting sets. BMC Syst Biol 2009; 3: 81.
    • (2009) BMC Syst Biol , vol.3
    • Vazquez, A.1
  • 163
    • 81355127286 scopus 로고    scopus 로고
    • Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing
    • [163] Small BG, McColl BW, Allmendinger R, et al. Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing. Nat Chem Biol 2011; 7: 902-8.
    • (2011) Nat Chem Biol , vol.7 , pp. 902-908
    • Small, B.G.1    McColl, B.W.2    Allmendinger, R.3
  • 164
    • 42449099889 scopus 로고    scopus 로고
    • Closedloop control of cellular functions using combinatory drugs guided by a stochastic search algorithm
    • [164] Wong PK, Yu F, Shahangian A, Cheng G, Sun R, Ho CM. Closedloop control of cellular functions using combinatory drugs guided by a stochastic search algorithm. Proc Natl Acad Sci USA 2008; 105: 5105-10.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 5105-5110
    • Wong, P.K.1    Yu, F.2    Shahangian, A.3    Cheng, G.4    Sun, R.5    Ho, C.M.6
  • 165
    • 84857917830 scopus 로고    scopus 로고
    • Chemical-genomic profiling: Systematic analysis of the cellular targets of bioactive molecules
    • [165] Andrusiak K, Piotrowski JS, Boone C. Chemical-genomic profiling: Systematic analysis of the cellular targets of bioactive molecules. Bioorg Med Chem 2012; 20: 1952-60.
    • (2012) Bioorg Med Chem , vol.20 , pp. 1952-1960
    • Rusiak, K.1    Piotrowski, J.S.2    Boone, C.3
  • 166
    • 84869423899 scopus 로고    scopus 로고
    • Systematic identification of synergistic drug pairs targeting HIV
    • [166] Tan X, Hu L, Iii LJL, et al. Systematic identification of synergistic drug pairs targeting HIV. Nat Biotechnol 2012; 30: 1125-30.
    • (2012) Nat Biotechnol , vol.30 , pp. 1125-1130
    • Tan, X.1    Hu, L.2    Iii, L.3
  • 167
    • 33747367151 scopus 로고    scopus 로고
    • A strategy for extracting and analyzing large-scale quantitative epistatic interaction data
    • [167] Collins SR, Schuldiner M, Krogan NJ, Weissman JS. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol 2006; 7: R63.
    • (2006) Genome Biol , vol.7
    • Collins, S.R.1    Schuldiner, M.2    Krogan, N.J.3    Weissman, J.S.4
  • 168
    • 77955363536 scopus 로고    scopus 로고
    • Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices
    • [168] Eronen V-P, Lindén RO, Lindroos A, Kanerva M, Aittokallio T. Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices. PLoS ONE 2010; 5: E11611.
    • (2010) Plos ONE , vol.5
    • Eronen, V.-P.1    Lindén, R.O.2    Lindroos, A.3    Kanerva, M.4    Aittokallio, T.5
  • 170
    • 33847643207 scopus 로고    scopus 로고
    • Chemical combination effects predict connectivity in biological systems
    • [170] Lehár J, Zimmermann GR, Krueger AS, et al. Chemical combination effects predict connectivity in biological systems. Mol Syst Biol 2007; 3: 80.
    • (2007) Mol Syst Biol , vol.3
    • Lehár, J.1    Zimmermann, G.R.2    Krueger, A.S.3
  • 171
    • 80855124963 scopus 로고    scopus 로고
    • Systematic exploration of synergistic drug pairs
    • [171] Cokol M, Chua HN, Tasan M, et al. Systematic exploration of synergistic drug pairs. Mol Syst Biol 2011; 7: 544.
    • (2011) Mol Syst Biol , vol.7
    • Cokol, M.1    Chua, H.N.2    Tasan, M.3
  • 172
    • 79959199033 scopus 로고    scopus 로고
    • Network target for screening synergistic drug combinations with application to traditional Chinese medicine
    • [172] Li S, Zhang B, Zhang N. Network target for screening synergistic drug combinations with application to traditional Chinese medicine. BMC Syst Biol 2011; 5: S10.
    • (2011) BMC Syst Biol , vol.5
    • Li, S.1    Zhang, B.2    Zhang, N.3
  • 173
    • 77951134093 scopus 로고    scopus 로고
    • A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway
    • [173] Yan H, Zhang B, Li S, Zhao Q. A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway. BMC Syst Biol. 2010; 4: 50.
    • (2010) BMC Syst Biol , vol.4
    • Yan, H.1    Zhang, B.2    Li, S.3    Zhao, Q.4
  • 174
    • 77952538062 scopus 로고    scopus 로고
    • Analysis of compound synergy in high-throughput cellular screens by population-based lifetime modeling
    • [174] Peifer M, Weiss J, Sos ML, et al. Analysis of compound synergy in high-throughput cellular screens by population-based lifetime modeling. PLoS ONE 2010; 5: E8919.
    • (2010) Plos ONE , vol.5
    • Peifer, M.1    Weiss, J.2    Sos, M.L.3
  • 175
    • 0033539525 scopus 로고    scopus 로고
    • A model-based approach for assessing in vivo combination therapy interactions
    • [175] Lopez AM, Pegram MD, Slamon DJ, Landaw EM. A model-based approach for assessing in vivo combination therapy interactions. Proc Natl Acad Sci USA 1999; 96: 13023-8.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 13023-13028
    • Lopez, A.M.1    Pegram, M.D.2    Slamon, D.J.3    Landaw, E.M.4
  • 176
    • 51049117937 scopus 로고    scopus 로고
    • Models from experiments: Combinatorial drug perturbations of cancer cells
    • [176] Nelander S, Wang W, Nilsson B, et al. Models from experiments: Combinatorial drug perturbations of cancer cells. Mol Syst Biol 2008; 4: 216.
    • (2008) Mol Syst Biol , vol.4
    • Nelander, S.1    Wang, W.2    Nilsson, B.3
  • 177
    • 77956274693 scopus 로고    scopus 로고
    • Identification of optimal drug combinations targeting cellular networks: Integrating phospho-proteomics and computational network analysis
    • [177] Iadevaia S, Lu Y, Morales FC, Mills GB, Ram PT. Identification of optimal drug combinations targeting cellular networks: Integrating phospho-proteomics and computational network analysis. Cancer Res 2010; 70: 6704-14.
    • (2010) Cancer Res , vol.70 , pp. 6704-6714
    • Iadevaia, S.1    Lu, Y.2    Morales, F.C.3    Mills, G.B.4    Ram, P.T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.