메뉴 건너뛰기




Volumn 51, Issue 1, 2011, Pages 15-24

Cross-target view to feature selection: Identification of molecular interaction features in ligand-target space

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL EFFICIENCY; DIMENSIONALITY REDUCTION; LIGANDS; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE; PREDICTIVE ANALYTICS;

EID: 79952595140     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci1001394     Document Type: Article
Times cited : (21)

References (49)
  • 1
    • 34548319109 scopus 로고    scopus 로고
    • Chemogenomic approaches to drug discovery: Similar receptors bind similar ligands
    • DOI 10.1038/sj.bjp.0707308, PII 0707308
    • Klabunde, T. Chemogenomic approaches to drug discovery: similar receptors bind similar ligands. Br. J. Pharmacol. 2007, 152, 5-7. (Pubitemid 47339899)
    • (2007) British Journal of Pharmacology , vol.152 , Issue.1 , pp. 5-7
    • Klabunde, T.1
  • 2
    • 34548317031 scopus 로고    scopus 로고
    • Chemogenomic approaches to rational drug design
    • DOI 10.1038/sj.bjp.0707307, PII 0707307
    • Rognan, D. Chemogenomic approaches to rational drug design. Br. J. Pharmacol. 2007, 152, 38-52. (Pubitemid 47339898)
    • (2007) British Journal of Pharmacology , vol.152 , Issue.1 , pp. 38-52
    • Rognan, D.1
  • 3
    • 43949145741 scopus 로고    scopus 로고
    • Computational analysis of ligand relationships within target families
    • Bajorath, J. Computational analysis of ligand relationships within target families. Curr. Opin. Chem. Biol. 2008, 12, 352-358.
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 352-358
    • Bajorath, J.1
  • 4
    • 26944463088 scopus 로고    scopus 로고
    • Virtual screen for ligands of orphan G protein-coupled receptors
    • DOI 10.1021/ci050006d
    • Bock, J. R.; Gough, D. A. Virtual screen for ligands of orphan G protein-coupled receptors. J. Chem. Inf. Model 2005, 45, 1402-1414. (Pubitemid 41476023)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.5 , pp. 1402-1414
    • Bock, J.R.1    Gough, D.A.2
  • 5
    • 33646251586 scopus 로고    scopus 로고
    • Collaborative filtering on a family of biological targets
    • Erhan, D.; L'Heureux, P.-J.; Yue, S. Y.; Bengio, Y. Collaborative filtering on a family of biological targets. J. Chem. Inf. Model. 2006, 46, 626-635.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 626-635
    • Erhan, D.1    L'Heureux, P.-J.2    Yue, S.Y.3    Bengio, Y.4
  • 6
    • 33745561205 scopus 로고    scopus 로고
    • An introduction to variable and feature selection
    • Guyon, I.; Elisseeff, A. An introduction to variable and feature selection. J. Mach. Learn. Res. 2003, 3, 1157-1182.
    • (2003) J. Mach. Learn. Res. , vol.3 , pp. 1157-1182
    • Guyon, I.1    Elisseeff, A.2
  • 7
    • 8544221141 scopus 로고    scopus 로고
    • Towards optimal descriptor subset selection with support vector machines in classification and regression
    • DOI 10.1002/qsar.200410011
    • Fröhlich, H.; Wegner, J. K.; Zell, A. Towards optimal descriptor subset selection with support vector machines in classification and regression. QSAR Comb. Sci. 2004, 23, 311-318. (Pubitemid 39490409)
    • (2004) QSAR and Combinatorial Science , vol.23 , Issue.5 , pp. 311-318
    • Frohlich, H.1    Wegner, J.K.2    Zell, A.3
  • 8
    • 2942702317 scopus 로고    scopus 로고
    • SVM-based feature selection for characterization of focused com-pound collections
    • Byvatov, E.; Schneider, G. SVM-based feature selection for characterization of focused com-pound collections. J. Chem. Inf. Comput. Sci. 2004, 44, 993-999.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 993-999
    • Byvatov, E.1    Schneider, G.2
  • 9
    • 5444272497 scopus 로고    scopus 로고
    • Effect of molecular de-scriptor feature selection in support vector machine classification of pharmacokinetic and toxicological properties of chemical agents
    • Xue, Y.; Li, Z. R.; Yap, C. W.; Sun, L. Z.; Chen, X.; Chen, Y. Z. Effect of molecular de-scriptor feature selection in support vector machine classification of pharmacokinetic and toxicological properties of chemical agents. J. Chem. Inf. Comput. Sci. 2004, 44, 1630-1638.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 1630-1638
    • Xue, Y.1    Li, Z.R.2    Yap, C.W.3    Sun, L.Z.4    Chen, X.5    Chen, Y.Z.6
  • 11
    • 4544371135 scopus 로고    scopus 로고
    • Dimensionality reduction for supervised learning with reproducing kernel Hilbert spaces
    • Fukumizu, K.; Bach, F. R.; Jordan, M. I. Dimensionality reduction for supervised learning with reproducing kernel Hilbert spaces. J. Mach. Learn. Res. 2004, 5, 73-99.
    • (2004) J. Mach. Learn. Res. , vol.5 , pp. 73-99
    • Fukumizu, K.1    Bach, F.R.2    Jordan, M.I.3
  • 12
    • 68649121147 scopus 로고    scopus 로고
    • Kernel dimensionality reduction in regression
    • Fukumizu, K.; Bach, F. R.; Jordan, M. I. Kernel dimensionality reduction in regression. Ann. Stat. 2009, 37, 1871-1905.
    • (2009) Ann. Stat. , vol.37 , pp. 1871-1905
    • Fukumizu, K.1    Bach, F.R.2    Jordan, M.I.3
  • 14
    • 33645422011 scopus 로고    scopus 로고
    • Are target-familyprivileged substructures truly privileged
    • Schnur, D. M.; Hermsmeier, M. A.; Tebben, A. J. Are target- familyprivileged substructures truly privileged. J. Med. Chem. 2006, 49, 2000-2009.
    • (2006) J. Med. Chem. , vol.49 , pp. 2000-2009
    • Schnur, D.M.1    Hermsmeier, M.A.2    Tebben, A.J.3
  • 15
    • 5344268130 scopus 로고    scopus 로고
    • Annotating and mining the ligand-target chemogenomics knowledge space
    • DOI 10.1016/S1741-8364(04)02408-4, PII S1741836404024084
    • Schuffenhauer, A.; Jacoby, E. Annotating and mining the ligandtarget chemogenomics knowledge space. Drug Discovery Today 2004, 2, 190-200. (Pubitemid 39349125)
    • (2004) Drug Discovery Today: BIOSILICO , vol.2 , Issue.5 , pp. 190-200
    • Schuffenhauer, A.1    Jacoby, E.2
  • 16
    • 38349114038 scopus 로고    scopus 로고
    • Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor
    • Faulon, J.-L.; Misra, M.; Martin, S.; Sale, K.; Sapra, R. Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. Bioinformatics 2008, 24, 225-233.
    • (2008) Bioinformatics , vol.24 , pp. 225-233
    • Faulon, J.-L.1    Misra, M.2    Martin, S.3    Sale, K.4    Sapra, R.5
  • 17
    • 52749085437 scopus 로고    scopus 로고
    • Protein-ligand interaction prediction: An improved chemogenomics ap-proach
    • Jacob, L.; Vert, J.-P. Protein-ligand interaction prediction: an improved chemogenomics ap-proach. Bioinformatics 2008, 24, 2149-2156.
    • (2008) Bioinformatics , vol.24 , pp. 2149-2156
    • Jacob, L.1    Vert, J.-P.2
  • 18
    • 34548128437 scopus 로고    scopus 로고
    • Statistical prediction of protein - Chemical interactions based on chemical structure and mass spectrometry data
    • DOI 10.1093/bioinformatics/btm266
    • Nagamine, N.; Sakakibara, Y. Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data. Bioinformatics 2007, 23, 2004-2012. (Pubitemid 47299842)
    • (2007) Bioinformatics , vol.23 , Issue.15 , pp. 2004-2012
    • Nagamine, N.1    Sakakibara, Y.2
  • 20
    • 70350495651 scopus 로고    scopus 로고
    • Ligand prediction for orphan targets using support vector machines and various target-ligand kernels is dominated by nearest neighbor effects
    • Wassermann, A. M.; Geppert, H.; Bajorath, J. Ligand prediction for orphan targets using support vector machines and various target-ligand kernels is dominated by nearest neighbor effects. J. Chem. Inf. Model 2009, 49, 2155-2167.
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 2155-2167
    • Wassermann, A.M.1    Geppert, H.2    Bajorath, J.3
  • 21
    • 66149131771 scopus 로고    scopus 로고
    • Development and validation of a novel proteinligand fingerprint to mine chemogenomic space: Application to G protein-coupled receptors and their ligands
    • Weill, N.; Rognan, D. Development and validation of a novel proteinligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands. J. Chem. Inf. Model 2009, 49, 1049-62.
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 1049-1062
    • Weill, N.1    Rognan, D.2
  • 23
    • 34547830852 scopus 로고    scopus 로고
    • Gene selection via the BAHSIC family of algorithms
    • DOI 10.1093/bioinformatics/btm216
    • Song, L.; Bedo, J.; Borgwardt, K. M.; Gretton, A.; Smola, A. Gene selection via the BAHSIC family of algorithms. Bioinformatics 2007, 23, i490-i498. (Pubitemid 47244436)
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Song, L.1    Bedo, J.2    Borgwardt, K.M.3    Gretton, A.4    Smola, A.5
  • 24
    • 84945116550 scopus 로고
    • Sliced inverse regression for dimension reduction
    • Li, K.-C. Sliced inverse regression for dimension reduction. J. Am. Stat. Assoc. 1991, 86, 316-327.
    • (1991) J. Am. Stat. Assoc. , vol.86 , pp. 316-327
    • Li, K.-C.1
  • 25
    • 70350673962 scopus 로고    scopus 로고
    • Nonlinear dimension reduction with kernel sliced inverse regression
    • Yeh, Y.-R.; Huang, S.-Y.; Lee, Y.-J. Nonlinear dimension reduction with kernel sliced inverse regression. IEEE Trans. Knowledge Data Eng. 2009, 21, 1590-1603.
    • (2009) IEEE Trans. Knowledge Data Eng. , vol.21 , pp. 1590-1603
    • Yeh, Y.-R.1    Huang, S.-Y.2    Lee, Y.-J.3
  • 26
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • DOI 10.1023/A:1012487302797
    • Guyon, I.; Weston, J.; Barnhill, S.; Vapnik, V. Gene selection for cancer classification using support vector machines. Mach. Learn. 2002, 46, 389-422. (Pubitemid 34129977)
    • (2002) Machine Learning , vol.46 , Issue.1-3 , pp. 389-422
    • Guyon, I.1    Weston, J.2    Barnhill, S.3    Vapnik, V.4
  • 27
    • 0011812771 scopus 로고    scopus 로고
    • Kernel independent component analysis
    • Bach, F. R.; Jordan, M. I. Kernel independent component analysis. J. Mach. Learn. Res. 2002, 3, 1-48.
    • (2002) J. Mach. Learn. Res. , vol.3 , pp. 1-48
    • Bach, F.R.1    Jordan, M.I.2
  • 28
    • 0004236492 scopus 로고    scopus 로고
    • 3rd ed.; Johns Hopkins University Press: Baltimore
    • Golub, G. H.; Loan, C. F. V. Matrix Computations, 3rd ed.; Johns Hopkins University Press: Baltimore, 1996.
    • (1996) Matrix Computations
    • Golub, G.H.1    Loan, C.F.V.2
  • 29
    • 54249099193 scopus 로고    scopus 로고
    • Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors
    • Kontijevskis, A.; Komorowski, J.; Wikberg, J. E. S. Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors. J. Chem. Inf. Model 2008, 48, 1840-1850.
    • (2008) J. Chem. Inf. Model , vol.48 , pp. 1840-1850
    • Kontijevskis, A.1    Komorowski, J.2    Wikberg, J.E.S.3
  • 30
    • 66249085197 scopus 로고    scopus 로고
    • Proteochemometric modeling of drug resistance over the mu-tational space for multiple HIV protease variants and multiple protease inhibitors
    • Lapins, M.; Wikberg, J. E. S. Proteochemometric modeling of drug resistance over the mu-tational space for multiple HIV protease variants and multiple protease inhibitors. J. Chem. Inf. Model 2009, 49, 1202-1210.
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 1202-1210
    • Lapins, M.1    Wikberg, J.E.S.2
  • 32
    • 79952586544 scopus 로고    scopus 로고
    • Milano Chemometrics and QSAR Research Group: Milan
    • Dragon X, version 1.2; Milano Chemometrics and QSAR Research Group: Milan, 2007.
    • (2007) DragonX, version 1.2
  • 33
    • 79751531734 scopus 로고    scopus 로고
    • Chemical Computing Group Inc.: Montreal, Canada
    • MOE, version 2008.10; Chemical Computing Group Inc.: Montreal, Canada, 2008.
    • (2008) MOE, Version 2008.10
  • 34
    • 33747816816 scopus 로고    scopus 로고
    • PROFEAT: A web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • DOI 10.1093/nar/gkl305
    • Li, Z. R.; Lin, H. H.; Han, L. Y.; Jiang, L.; Chen, X.; Chen, Y. Z. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. 2006, 34, W32-W37. (Pubitemid 44529730)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS.
    • Li, Z.R.1    Lin, H.H.2    Han, L.Y.3    Jiang, L.4    Chen, X.5    Chen, Y.Z.6
  • 35
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • DOI 10.1093/bioinformatics/btg431
    • Leslie, C. S.; Eskin, E.; Cohen, A.; Weston, J.; Noble, W. S. Mismatch string kernels for discriminative protein classification. Bioinformatics 2004, 20, 467-476. (Pubitemid 38344326)
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 467-476
    • Leslie, C.S.1    Eskin, E.2    Cohen, A.3    Weston, J.4    Noble, W.S.5
  • 36
    • 0032474777 scopus 로고    scopus 로고
    • New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids
    • DOI 10.1021/jm9700575
    • Sandberg, M.; Eriksson, L.; Jonsson, J.; Sjöström, M.; Wold, S. New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J. Med. Chem. 1998, 41, 2481-2491. (Pubitemid 28321898)
    • (1998) Journal of Medicinal Chemistry , vol.41 , Issue.14 , pp. 2481-2491
    • Sandberg, M.1    Eriksson, L.2    Jonsson, J.3    Sjostrom, M.4    Wold, S.5
  • 40
    • 33745216665 scopus 로고    scopus 로고
    • Designing better drugs: Predicting cytochrome P450 metabolism
    • de Groot, M. J. Designing better drugs: predicting cytochrome P450 metabolism. Drug Discovery Today 2006, 11, 601-606.
    • (2006) Drug Discovery Today , vol.11 , pp. 601-606
    • Groot, M.J.1
  • 41
    • 23444437988 scopus 로고    scopus 로고
    • A rapid computational filter for cytochrome P450 1A2 inhibition potential of compound libraries
    • DOI 10.1021/jm048959a
    • Chohan, K. K.; Paine, S. W.; Mistry, J.; Barton, P.; Davis, A. M. A rapid computational filter for cytochrome P450 1A2 inhibition potential of compound libraries. J. Med. Chem. 2005, 48, 5154-5161. (Pubitemid 41113903)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.16 , pp. 5154-5161
    • Chohan, K.K.1    Paine, S.W.2    Mistry, J.3    Barton, P.4    Davis, A.M.5
  • 42
    • 20544460560 scopus 로고    scopus 로고
    • Prediction of human cytochrome P450 inhibition using support vector machines
    • DOI 10.1002/qsar.200430925
    • Kriegl, J. M.; Arnhold, T.; Beck, B.; Fox, T. Prediction of human cytochrome P450 inhibition using support vector machines. QSAR Comb. Sci. 2005, 24, 491-502. (Pubitemid 40839677)
    • (2005) QSAR and Combinatorial Science , vol.24 , Issue.4 , pp. 491-502
    • Kriegl, J.M.1    Arnhold, T.2    Beck, B.3    Fox, T.4
  • 43
    • 33846923287 scopus 로고    scopus 로고
    • In silico prediction of cytochrome P450 2D6 and 3A4 inhibition using Gaussian Kernel weighted k-nearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors
    • DOI 10.1021/jm060333s
    • Jensen, B. F.; Vind, C.; Padkjær, S. B.; Brockhoff, P. B.; Refsgaard, H. H. F. In silico predic-tion of cytochrome P450 2D6 and 3A4 inhibition using Gaussian kernel weighted k-nearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors. J. Med. Chem. 2007, 50, 501-511. (Pubitemid 46239784)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.3 , pp. 501-511
    • Jensen, B.F.1    Vind, C.2    Padkjaer, S.B.3    Brockhoff, P.B.4    Refsgaard, H.H.F.5
  • 44
    • 0034950245 scopus 로고    scopus 로고
    • Development of a generalized, quantitative physicochemical model of CYP3A4 inhibition for use in early drug discovery
    • DOI 10.1023/A:1011085411050
    • Riley, R. J.; Parker, A. J.; Trigg, S.; Manners, C. N. Development of a generalized, quanti-tative physicochemical model of CYP3A4 inhibition for use in early drug discovery. Pharm. Res. 2001, 18, 652-655. (Pubitemid 32595794)
    • (2001) Pharmaceutical Research , vol.18 , Issue.5 , pp. 652-655
    • Riley, R.J.1    Parker, A.J.2    Trigg, S.3    Manners, C.N.4
  • 45
    • 77952772341 scopus 로고    scopus 로고
    • Extended-connectivity fingerprints
    • Rogers, D.; Hahn, M. Extended-connectivity fingerprints. J. Chem. Inf. Model 2010, 50, 742-754.
    • (2010) J. Chem. Inf. Model , vol.50 , pp. 742-754
    • Rogers, D.1    Hahn, M.2
  • 46
  • 48
    • 0037469148 scopus 로고    scopus 로고
    • A major role for a set of non-active site mutations in the development of HIV-1 protease drug resistance
    • DOI 10.1021/bi027019u
    • Muzammil, S.; Ross, P.; Freire, E. A major role for a set of nonactive site mutations in the development of HIV-1 protease drug resistance. Biochemistry 2003, 42, 631-638. (Pubitemid 36133287)
    • (2003) Biochemistry , vol.42 , Issue.3 , pp. 631-638
    • Muzammil, S.1    Ross, P.2    Freire, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.