메뉴 건너뛰기




Volumn 55, Issue 7, 2015, Pages 1483-1494

Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach

Author keywords

[No Author keywords available]

Indexed keywords

DIGITAL STORAGE; FORECASTING; PROTEINS; SINGULAR VALUE DECOMPOSITION;

EID: 84938067400     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00030     Document Type: Article
Times cited : (36)

References (45)
  • 2
    • 84871595040 scopus 로고    scopus 로고
    • Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces
    • Yamanishi, Y.; Pauwels, E.; Kotera, M. Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces J. Chem. Inf. Model. 2012, 52, 3284-3292 10.1021/ci2005548
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 3284-3292
    • Yamanishi, Y.1    Pauwels, E.2    Kotera, M.3
  • 3
    • 79955969387 scopus 로고    scopus 로고
    • Predicting Drug Side-Effect Profiles: A Chemical Fragment-Based Approach
    • Pauwels, E.; Stoven, V.; Yamanishi, Y. Predicting Drug Side-Effect Profiles: A Chemical Fragment-Based Approach BMC Bioinf. 2011, 12, 169 10.1186/1471-2105-12-169
    • (2011) BMC Bioinf. , vol.12 , pp. 169
    • Pauwels, E.1    Stoven, V.2    Yamanishi, Y.3
  • 4
    • 84866460840 scopus 로고    scopus 로고
    • Relating Drug-Protein Interaction Network with Drug Side Effects
    • Mizutani, S.; Pauwels, E.; Stoven, V.; Goto, S.; Yamanishi, Y. Relating Drug-Protein Interaction Network with Drug Side Effects Bioinformatics 2012, 28, i522-i528 10.1093/bioinformatics/bts383
    • (2012) Bioinformatics , vol.28 , pp. i522-i528
    • Mizutani, S.1    Pauwels, E.2    Stoven, V.3    Goto, S.4    Yamanishi, Y.5
  • 5
    • 84863548955 scopus 로고    scopus 로고
    • Large-Scale Prediction of Adverse Drug Reactions Using Chemical, Biological, and Phenotypic Properties of Drugs
    • Liu, M.; Wu, Y.; Chen, Y.; Sun, J.; Zhao, Z.; Chen, X. W.; Matheny, M. E.; Xu, H. Large-Scale Prediction of Adverse Drug Reactions Using Chemical, Biological, and Phenotypic Properties of Drugs J. Am. Med. Inform Assoc 2012, 19, e28-35 10.1136/amiajnl-2011-000699
    • (2012) J. Am. Med. Inform Assoc , vol.19 , pp. e28-e35
    • Liu, M.1    Wu, Y.2    Chen, Y.3    Sun, J.4    Zhao, Z.5    Chen, X.W.6    Matheny, M.E.7    Xu, H.8
  • 6
    • 79952394490 scopus 로고    scopus 로고
    • An Algorithmic Framework for Predicting Side Effects of Drugs
    • Atias, N.; Sharan, R. An Algorithmic Framework for Predicting Side Effects of Drugs J. Comput. Biol. 2011, 18, 207-218 10.1089/cmb.2010.0255
    • (2011) J. Comput. Biol. , vol.18 , pp. 207-218
    • Atias, N.1    Sharan, R.2
  • 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. Drug Target Identification Using Side-Effect Similarity Science 2008, 321, 263-266 10.1126/science.1158140
    • (2008) Science , vol.321 , pp. 263-266
    • Campillos, M.1    Kuhn, M.2    Gavin, A.C.3    Jensen, L.J.4    Bork, P.5
  • 9
    • 78049445175 scopus 로고    scopus 로고
    • Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model
    • Chang, R. L.; Xie, L.; Xie, L.; Bourne, P. E.; Palsson, B. O. Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model PLoS Comput. Biol. 2010, 6, e1000938 10.1371/journal.pcbi.1000938
    • (2010) PLoS Comput. Biol. , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.O.5
  • 10
    • 79953100964 scopus 로고    scopus 로고
    • Structure-Based Systems Biology for Analyzing Off-Target Binding
    • Xie, L.; Xie, L.; Bourne, P. E. Structure-Based Systems Biology for Analyzing Off-Target Binding Curr. Opin. Struct. Biol. 2011, 21, 189-199 10.1016/j.sbi.2011.01.004
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 189-199
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 12
    • 26944446576 scopus 로고    scopus 로고
    • Keynote Review: In Vitro Safety Pharmacology Profiling: An Essential Tool for Successful Drug Development
    • Whitebread, S.; Hamon, J.; Bojanic, D.; Urban, L. Keynote Review: In Vitro Safety Pharmacology Profiling: An Essential Tool for Successful Drug Development Drug Discovery Today 2005, 10, 1421-1433 10.1016/S1359-6446(05)03632-9
    • (2005) Drug Discovery Today , vol.10 , pp. 1421-1433
    • Whitebread, S.1    Hamon, J.2    Bojanic, D.3    Urban, L.4
  • 14
    • 33749234216 scopus 로고    scopus 로고
    • Drugs, Their Targets and the Nature and Number of Drug Targets
    • Imming, P.; Sinning, C.; Meyer, A. Drugs, Their Targets and the Nature and Number of Drug Targets Nat. Rev. Drug Discovery 2006, 5, 821-834 10.1038/nrd2132
    • (2006) Nat. Rev. Drug Discovery , vol.5 , pp. 821-834
    • Imming, P.1    Sinning, C.2    Meyer, A.3
  • 16
    • 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. Bindingdb: A Web-Accessible Database of Experimentally Determined Protein-Ligand Binding Affinities Nucleic Acids Res. 2007, 35, D198-201 10.1093/nar/gkl999
    • (2007) Nucleic Acids Res. , vol.35 , pp. D198-D201
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorissen, R.N.4    Gilson, M.K.5
  • 17
    • 32344440237 scopus 로고    scopus 로고
    • Analysis of Drug-Induced Effect Patterns to Link Structure and Side Effects of Medicines
    • Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Analysis of Drug-Induced Effect Patterns to Link Structure and Side Effects of Medicines Nat. Chem. Biol. 2005, 1, 389-397 10.1038/nchembio747
    • (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
  • 18
    • 27444447278 scopus 로고    scopus 로고
    • Biospectra Analysis: Model Proteome Characterizations for Linking Molecular Structure and Biological Response
    • Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Biospectra Analysis: Model Proteome Characterizations for Linking Molecular Structure and Biological Response J. Med. Chem. 2005, 48, 6918-6925 10.1021/jm050494g
    • (2005) J. Med. Chem. , vol.48 , pp. 6918-6925
    • Fliri, A.F.1    Loging, W.T.2    Thadeio, P.F.3    Volkmann, R.A.4
  • 19
    • 12244275244 scopus 로고    scopus 로고
    • Biological Spectra Analysis: Linking Biological Activity Profiles to Molecular Structure
    • Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Biological Spectra Analysis: Linking Biological Activity Profiles to Molecular Structure Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 261-266 10.1073/pnas.0407790101
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 261-266
    • Fliri, A.F.1    Loging, W.T.2    Thadeio, P.F.3    Volkmann, R.A.4
  • 21
    • 72149104630 scopus 로고    scopus 로고
    • Profiling Bioactivity of the Toxcast Chemical Library Using Biomap Primary Human Cell Systems
    • Houck, K. A.; Dix, D. J.; Judson, R. S.; Kavlock, R. J.; Yang, J.; Berg, E. L. Profiling Bioactivity of the Toxcast Chemical Library Using Biomap Primary Human Cell Systems J. Biomol. Screening 2009, 14, 1054-1066 10.1177/1087057109345525
    • (2009) J. Biomol. Screening , vol.14 , pp. 1054-1066
    • Houck, K.A.1    Dix, D.J.2    Judson, R.S.3    Kavlock, R.J.4    Yang, J.5    Berg, E.L.6
  • 23
    • 84864633122 scopus 로고    scopus 로고
    • Prediction of Activity Spectra for Substances
    • Parasuraman, S. Prediction of Activity Spectra for Substances J. Pharmacol. Pharmacother. 2011, 2, 52-53 10.4103/0976-500X.77119
    • (2011) J. Pharmacol. Pharmacother. , vol.2 , pp. 52-53
    • Parasuraman, S.1
  • 24
    • 77958493840 scopus 로고    scopus 로고
    • A Novel Framework for Predicting in Vivo Toxicities from in Vitro Data Using Optimal Methods for Dense and Sparse Matrix Reordering and Logistic Regression
    • DiMaggio, P. A., Jr.; Subramani, A.; Judson, R. S.; Floudas, C. A. A Novel Framework for Predicting in Vivo Toxicities from in Vitro Data Using Optimal Methods for Dense and Sparse Matrix Reordering and Logistic Regression Toxicol. Sci. 2010, 118, 251-265 10.1093/toxsci/kfq233
    • (2010) Toxicol. Sci. , vol.118 , pp. 251-265
    • DiMaggio, P.A.1    Subramani, A.2    Judson, R.S.3    Floudas, C.A.4
  • 26
    • 80053906388 scopus 로고    scopus 로고
    • Chemical Structural Novelty: On-Targets and Off-Targets
    • Yera, E. R.; Cleves, A. E.; Jain, A. N. Chemical Structural Novelty: On-Targets and Off-Targets J. Med. Chem. 2011, 54, 6771-6785 10.1021/jm200666a
    • (2011) J. Med. Chem. , vol.54 , pp. 6771-6785
    • Yera, E.R.1    Cleves, A.E.2    Jain, A.N.3
  • 27
    • 44449139387 scopus 로고    scopus 로고
    • Detecting Evolutionary Relationships across Existing Fold Space, Using Sequence Order-Independent Profile-Profile Alignments
    • Xie, L.; Bourne, P. E. Detecting Evolutionary Relationships across Existing Fold Space, Using Sequence Order-Independent Profile-Profile Alignments Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 5441-5446 10.1073/pnas.0704422105
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 28
    • 66349119013 scopus 로고    scopus 로고
    • A Unified Statistical Model to Support Local Sequence Order Independent Similarity Searching for Ligand-Binding Sites and Its Application to Genome-Based Drug Discovery
    • Xie, L.; Bourne, P. E. A Unified Statistical Model to Support Local Sequence Order Independent Similarity Searching for Ligand-Binding Sites and Its Application to Genome-Based Drug Discovery Bioinformatics 2009, 25, i305-312 10.1093/bioinformatics/btp220
    • (2009) Bioinformatics , vol.25 , pp. i305-i312
    • Xie, L.1    Bourne, P.E.2
  • 29
    • 84855286318 scopus 로고    scopus 로고
    • Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding
    • Liu, T.; Altman, R. B. Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding PLoS Comput. Biol. 2011, 7, e1002326 10.1371/journal.pcbi.1002326
    • (2011) PLoS Comput. Biol. , vol.7
    • Liu, T.1    Altman, R.B.2
  • 30
    • 84880763942 scopus 로고    scopus 로고
    • Target Essentiality and Centrality Characterize Drug Side Effects
    • Wang, X.; Thijssen, B.; Yu, H. Target Essentiality and Centrality Characterize Drug Side Effects PLoS Comput. Biol. 2013, 9, e1003119 10.1371/journal.pcbi.1003119
    • (2013) PLoS Comput. Biol. , vol.9
    • Wang, X.1    Thijssen, B.2    Yu, H.3
  • 32
    • 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. Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome PLoS Comput. Biol. 2009, 5, e1000441 10.1371/journal.pcbi.1000441
    • (2009) PLoS Comput. Biol. , vol.5
    • Yang, L.1    Chen, J.2    He, L.3
  • 33
    • 77957954504 scopus 로고    scopus 로고
    • A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways
    • Wallach, I.; Jaitly, N.; Lilien, R. A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways PLoS One 2010, 5, e12063 10.1371/journal.pone.0012063
    • (2010) PLoS One , vol.5
    • Wallach, I.1    Jaitly, N.2    Lilien, R.3
  • 34
    • 0000107975 scopus 로고
    • Relations between Two Sets of Variates
    • Hotelling, H. Relations between Two Sets of Variates Biometrika 1936, 28, 321 10.2307/2333955
    • (1936) Biometrika , vol.28 , pp. 321
    • Hotelling, H.1
  • 35
    • 10044285992 scopus 로고    scopus 로고
    • Canonical Correlation Analysis: An Overview with Application to Learning Methods
    • Hardoon, D. R.; Szedmak, S.; Shawe-Taylor, J. Canonical Correlation Analysis: An Overview with Application to Learning Methods Neural Comput 2004, 16, 2639-2664 10.1162/0899766042321814
    • (2004) Neural Comput , vol.16 , pp. 2639-2664
    • Hardoon, D.R.1    Szedmak, S.2    Shawe-Taylor, J.3
  • 36
    • 70149096300 scopus 로고    scopus 로고
    • A Penalized Matrix Decomposition, with Applications to Sparse Principal Components and Canonical Correlation Analysis
    • Witten, D. M.; Tibshirani, R.; Hastie, T. A Penalized Matrix Decomposition, with Applications to Sparse Principal Components and Canonical Correlation Analysis Biostatistics 2009, 10, 515-534 10.1093/biostatistics/kxp008
    • (2009) Biostatistics , vol.10 , pp. 515-534
    • Witten, D.M.1    Tibshirani, R.2    Hastie, T.3
  • 37
    • 76149120425 scopus 로고    scopus 로고
    • A Side Effect Resource to Capture Phenotypic Effects of Drugs
    • Kuhn, M.; Campillos, M.; Letunic, I.; Jensen, L. J.; Bork, P. A Side Effect Resource to Capture Phenotypic Effects of Drugs Mol. Syst. Biol. 2010, 6, 343 10.1038/msb.2009.98
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 343
    • Kuhn, M.1    Campillos, M.2    Letunic, I.3    Jensen, L.J.4    Bork, P.5
  • 38
    • 0024268931 scopus 로고
    • Point Mutations in the Human Vitamin D Receptor Gene Associated with Hypocalcemic Rickets
    • Hughes, M. R.; Malloy, P. J.; Kieback, D. G.; Kesterson, R. A.; Pike, J. W.; Feldman, D.; O'Malley, B. W. Point Mutations in the Human Vitamin D Receptor Gene Associated with Hypocalcemic Rickets Science 1988, 242, 1702-1705 10.1126/science.2849209
    • (1988) Science , vol.242 , pp. 1702-1705
    • Hughes, M.R.1    Malloy, P.J.2    Kieback, D.G.3    Kesterson, R.A.4    Pike, J.W.5    Feldman, D.6    O'Malley, B.W.7
  • 39
    • 33845732323 scopus 로고    scopus 로고
    • DNA Polymerase Beta Null Mouse Embryonic Fibroblasts Harbor a Homozygous Null Mutation in DNA Polymerase Iota
    • Sobol, R. W. DNA Polymerase Beta Null Mouse Embryonic Fibroblasts Harbor a Homozygous Null Mutation in DNA Polymerase Iota DNA Repair 2007, 6, 3-7 10.1016/j.dnarep.2006.08.005
    • (2007) DNA Repair , vol.6 , pp. 3-7
    • Sobol, R.W.1
  • 44
    • 84901296367 scopus 로고    scopus 로고
    • Identifying Druggable Targets by Protein Microenvironments Matching: Application to Transcription Factors
    • Liu, T.; Altman, R. B. Identifying Druggable Targets by Protein Microenvironments Matching: Application to Transcription Factors CPT: Pharmacometrics Syst. Pharmacol. 2014, 3, e93 10.1038/psp.2013.66
    • (2014) CPT: Pharmacometrics Syst. Pharmacol. , vol.3 , pp. e93
    • Liu, T.1    Altman, R.B.2
  • 45
    • 0031306229 scopus 로고    scopus 로고
    • Using the Radial Distributions of Physical Features to Compare Amino Acid Environments and Align Amino Acid Sequences
    • Wei, L.; Altman, R. B.; Chang, J. T. Using the Radial Distributions of Physical Features to Compare Amino Acid Environments and Align Amino Acid Sequences Pac Symp. Biocomput 1997, 465-476
    • Pac Symp. Biocomput 1997 , pp. 465-476
    • Wei, L.1    Altman, R.B.2    Chang, J.T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.