메뉴 건너뛰기




Volumn 24, Issue 19, 2008, Pages 2149-2156

Protein-ligand interaction prediction: An improved chemogenomics approach

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; G PROTEIN COUPLED RECEPTOR; ION CHANNEL;

EID: 52749085437     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn409     Document Type: Article
Times cited : (328)

References (55)
  • 1
    • 5844297152 scopus 로고
    • Theory of reproducing kernels
    • Aronszajn,N. (1950) Theory of reproducing kernels. Trans. Am. Math. Soc., 68, 337-404.
    • (1950) Trans. Am. Math. Soc , vol.68 , pp. 337-404
    • Aronszajn, N.1
  • 2
    • 0037248869 scopus 로고    scopus 로고
    • Prints and its automatic supplement, preprints
    • Attwood,T.K. et al. (2003) Prints and its automatic supplement, preprints. Nucleic Acids Res., 31, 400-402.
    • (2003) Nucleic Acids Res , vol.31 , pp. 400-402
    • Attwood, T.K.1
  • 3
    • 34250813174 scopus 로고    scopus 로고
    • One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties
    • Azencott,C.-A. et al. (2007) One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties. J. Chem. Inf. Model, 47, 965-974.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 965-974
    • Azencott, C.-A.1
  • 4
    • 0036827077 scopus 로고    scopus 로고
    • Property-based design of GPCR-targeted library
    • Balakin,K.V. et al. (2002) Property-based design of GPCR-targeted library. J. Chem. Inf. Comput. Sci., 42, 1332-1342.
    • (2002) J. Chem. Inf. Comput. Sci , vol.42 , pp. 1332-1342
    • Balakin, K.V.1
  • 5
    • 0034801665 scopus 로고    scopus 로고
    • G protein-coupled receptor drug discovery: Implications from the crystal structure of rhodopsin
    • Ballesteros,J. and Palczewski,K. (2001) G protein-coupled receptor drug discovery: Implications from the crystal structure of rhodopsin. Curr. Opin. Drug Discov. Devel., 4, 561-574.
    • (2001) Curr. Opin. Drug Discov. Devel , vol.4 , pp. 561-574
    • Ballesteros, J.1    Palczewski, K.2
  • 6
    • 26944463088 scopus 로고    scopus 로고
    • Virtual screen for ligands of orphan g protein-coupled receptors
    • Bock,J.R. and Gough,D.A. (2005) Virtual screen for ligands of orphan g protein-coupled receptors. J. Chem. Inf. Model, 45, 1402-1414.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1402-1414
    • Bock, J.R.1    Gough, D.A.2
  • 7
    • 33745771638 scopus 로고    scopus 로고
    • Protein function prediction via graph kernels
    • Borgwardt,K. et al. (2005) Protein function prediction via graph kernels. Bioinformatics, 21(Suppl. 1), i47-i56.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Borgwardt, K.1
  • 10
    • 0036606241 scopus 로고    scopus 로고
    • Predicting ADME properties in silico: Methods and models
    • Butina,D. et al. (2002) Predicting ADME properties in silico: methods and models. Drug Discov. Today, 7(Suppl. 11), S83-S88.
    • (2002) Drug Discov. Today , vol.7 , Issue.SUPPL. 11
    • Butina, D.1
  • 11
    • 0345548661 scopus 로고    scopus 로고
    • Comparison of support vector machine and artificial neural network systems for drug/nondrug classification
    • Byvatov,E. et al. (2003) Comparison of support vector machine and artificial neural network systems for drug/nondrug classification. J. Chem. Inf. Comput. Sci., 43, 1882-1889.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 1882-1889
    • Byvatov, E.1
  • 12
    • 23244459989 scopus 로고    scopus 로고
    • The context-tree kernel for strings
    • Cuturi,M. and Vert,J.-P. (2005) The context-tree kernel for strings. Neural Netw., 18, 1111-1123.
    • (2005) Neural Netw , vol.18 , pp. 1111-1123
    • Cuturi, M.1    Vert, J.-P.2
  • 13
    • 9644283060 scopus 로고    scopus 로고
    • Predicting enzyme class from protein structure without alignments
    • Dobson,P. and Doig,A. (2005) Predicting enzyme class from protein structure without alignments. J. Mol. Biol., 345, 187-199.
    • (2005) J. Mol. Biol , vol.345 , pp. 187-199
    • Dobson, P.1    Doig, A.2
  • 14
    • 33646251586 scopus 로고    scopus 로고
    • Collaborative filtering on a family of biological targets
    • Erhan,D. et al. (2006) Collaborative filtering on a family of biological targets. J. Chem. Inf. Model, 46, 626-635.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 626-635
    • Erhan, D.1
  • 15
    • 21844456299 scopus 로고    scopus 로고
    • Learning multiple tasks with kernel methods
    • Evgeniou,T. et al. (2005) Learning multiple tasks with kernel methods. J. Mach. Learn. Res., 6, 615-637.
    • (2005) J. Mach. Learn. Res , vol.6 , pp. 615-637
    • Evgeniou, T.1
  • 16
    • 22944479010 scopus 로고    scopus 로고
    • A physicogenetic method to assign ligand-binding relationships between 7tm receptors
    • Frimurer,T.M. et al. (2005) A physicogenetic method to assign ligand-binding relationships between 7tm receptors. Bioorg. Med. Chem. Lett., 15, 3707-3712.
    • (2005) Bioorg. Med. Chem. Lett , vol.15 , pp. 3707-3712
    • Frimurer, T.M.1
  • 17
    • 9444266406 scopus 로고    scopus 로고
    • On graph kernels: Hardness results and efficient alternatives
    • Schölkopf,B. and Warmuth,M, eds Proceedings of the Sixteenth Annual Conference on Computational Learning Theory and the Seventh Annual Workshop on Kernel Machines. of, Springer, Heidelberg, pp
    • Gärtner,T. et al. (2003) On graph kernels: Hardness results and efficient alternatives. In Schölkopf,B. and Warmuth,M. (eds) Proceedings of the Sixteenth Annual Conference on Computational Learning Theory and the Seventh Annual Workshop on Kernel Machines. Vol. 2777 of Lecture Notes in Computer Science. Springer, Heidelberg, pp. 129-143.
    • (2003) Lecture Notes in Computer Science , vol.2777 , pp. 129-143
    • Gärtner, T.1
  • 18
    • 10244231694 scopus 로고    scopus 로고
    • Gasteiger,J. and Engel,T, eds, Wiley
    • Gasteiger,J. and Engel,T. (eds) (2003) Chemoinformatics: A Textbook Wiley.
    • (2003) Chemoinformatics: A Textbook
  • 19
    • 0034464742 scopus 로고    scopus 로고
    • Uncovering molecular mechanisms involved in activation of g protein-coupled receptors
    • Gether,U. (2000) Uncovering molecular mechanisms involved in activation of g protein-coupled receptors. Endocr. Rev., 21, 90-113.
    • (2000) Endocr. Rev , vol.21 , pp. 90-113
    • Gether, U.1
  • 20
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithm and a guide to scoring functions
    • Halperin,I. et al. (2002) Principles of docking: An overview of search algorithm and a guide to scoring functions. Proteins, 47 409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1
  • 23
    • 0003410183 scopus 로고
    • International Union of Biochemistry and Molecular Biology , Academic Press, California, USA
    • International Union of Biochemistry and Molecular Biology (1992) Enzyme Nomenclature 1992. Academic Press, California, USA.
    • (1992) Enzyme Nomenclature 1992
  • 24
    • 34848824629 scopus 로고    scopus 로고
    • Ivanciuc,O. (2007) Applications of support vector machines in chemistry. In Lipkowitz,K.B. and Cundari,T.R. (eds) Reviews in Computational Chemistry. 23. Wiley-VCH, Weiheim, pp. 291-400.
    • Ivanciuc,O. (2007) Applications of support vector machines in chemistry. In Lipkowitz,K.B. and Cundari,T.R. (eds) Reviews in Computational Chemistry. Vol. 23. Wiley-VCH, Weiheim, pp. 291-400.
  • 25
    • 0034048878 scopus 로고    scopus 로고
    • A discriminative framework for detecting remote protein homologies
    • Jaakkola,T. et al. (2000) A discriminative framework for detecting remote protein homologies. J. Comput. Biol., 7, 95-114.
    • (2000) J. Comput. Biol , vol.7 , pp. 95-114
    • Jaakkola, T.1
  • 26
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles. with few known binders
    • Jacob,L. and Vert,J.-P. (2008) Efficient peptide-MHC-I binding prediction for alleles. with few known binders. Bioinformatics, 24, 358-366.
    • (2008) Bioinformatics , vol.24 , pp. 358-366
    • Jacob, L.1    Vert, J.-P.2
  • 27
    • 52749098733 scopus 로고    scopus 로고
    • Virtual screening of GPCRs: An in silico chemogenomics approach
    • in press
    • Jacob,L. et al. (2008) Virtual screening of GPCRs: An in silico chemogenomics approach. BMC Bioinformatics (in press).
    • (2008) BMC Bioinformatics
    • Jacob, L.1
  • 28
    • 51349117226 scopus 로고    scopus 로고
    • Chemical Genomics: Small Molecule Probes to Study Cellular Function
    • Jaroch,S.E. and Weinmann,H, eds, Springer, Berlin
    • Jaroch,S.E. and Weinmann,H. (eds) (2006) Chemical Genomics: Small Molecule Probes to Study Cellular Function. Ernst Schering Research Foundation Workshop. Springer, Berlin.
    • (2006) Ernst Schering Research Foundation Workshop
  • 29
    • 0036081062 scopus 로고    scopus 로고
    • The KEGG databases at GenomeNet
    • Kanehisa,M. et al. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res., 30, 42-46.
    • (2002) Nucleic Acids Res , vol.30 , pp. 42-46
    • Kanehisa, M.1
  • 30
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome, Database issue, D277-D280
    • Kanehisa,M. et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res., 32(Database issue), D277-D280.
    • (2004) Nucleic Acids Res , vol.32
    • Kanehisa, M.1
  • 32
    • 33750317385 scopus 로고    scopus 로고
    • Kernels for graphs
    • Schölkopf,B. et al, eds, MIT Press, pp
    • Kashima,H. et al. (2004) Kernels for graphs. In Schölkopf,B. et al. (eds) Kernel Methods in Computational Biology. MIT Press, pp. 155-170.
    • (2004) Kernel Methods in Computational Biology , pp. 155-170
    • Kashima, H.1
  • 33
    • 67650731066 scopus 로고    scopus 로고
    • Chemogenomics approaches to ligand design
    • Ch. 7, Wiley-VCH, Great Britain, pp
    • Klabunde,T. (2006) Chemogenomics approaches to ligand design. In Ligand Design for G Protein-coupled Receptors. Ch. 7, Wiley-VCH, Great Britain, pp. 115-135.
    • (2006) Ligand Design for G Protein-coupled Receptors , pp. 115-135
    • Klabunde, T.1
  • 34
    • 34548319109 scopus 로고    scopus 로고
    • Chemogenomic approaches to drug discovery: Similar receptors bind similar ligands
    • Klabunde,T. (2007) Chemogenomic approaches to drug discovery: Similar receptors bind similar ligands. Br. J. Pharmacol., 152, 5-7.
    • (2007) Br. J. Pharmacol , vol.152 , pp. 5-7
    • Klabunde, T.1
  • 35
    • 26944485524 scopus 로고    scopus 로고
    • An automated system for the analysis of g protein-coupled receptor transmembrane binding pockets: Alignment, receptor-based pharmacophores, and their application
    • Kratochwil,N.A. et al. (2005) An automated system for the analysis of g protein-coupled receptor transmembrane binding pockets: Alignment, receptor-based pharmacophores, and their application. J. Chem. Inf. Model, 45, 1324-1336.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 1324-1336
    • Kratochwil, N.A.1
  • 36
    • 22544448378 scopus 로고    scopus 로고
    • Profile-based string kernels for remote homology detection and motif extraction
    • Kuang,R. et al. (2005) Profile-based string kernels for remote homology detection and motif extraction. J. Bioinform. Comput. Biol. 3, 527-550.
    • (2005) J. Bioinform. Comput. Biol , vol.3 , pp. 527-550
    • Kuang, R.1
  • 37
    • 17844408611 scopus 로고    scopus 로고
    • Chemo-Genomics in Drug Discovery: A Medicinal Chemistry Perspective
    • Kubinyi,H. et al, eds, Wiley-VCH, New York
    • Kubinyi,H. et al. (eds) (2004) Chemo-Genomics in Drug Discovery: A Medicinal Chemistry Perspective. Methods and Principles in Medicinal Chemistry. Wiley-VCH, New York.
    • (2004) Methods and Principles in Medicinal Chemistry
  • 38
    • 8844263749 scopus 로고    scopus 로고
    • A statistical framework for genomic data fusion
    • Lanckriet,G.R.G. et al. (2004) A statistical framework for genomic data fusion. Bioinformatics, 20, 2626-2635.
    • (2004) Bioinformatics , vol.20 , pp. 2626-2635
    • Lanckriet, G.R.G.1
  • 39
    • 0036358995 scopus 로고    scopus 로고
    • The spectrum kernel: A string kernel for SVM protein classification
    • Altman,R.B. et al, eds, World Scientific, Singapore, pp
    • Leslie,C. et al. (2002) The spectrum kernel: A string kernel for SVM protein classification. In Altman,R.B. et al. (eds) Proceedings of the Pacific Symposium on Biocomputing 2002. World Scientific, Singapore, pp. 564-575.
    • (2002) Proceedings of the Pacific Symposium on Biocomputing , pp. 564-575
    • Leslie, C.1
  • 40
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • Leslie,C.S. et al. (2004) Mismatch string kernels for discriminative protein classification. Bioinformatics, 20, 467-476.
    • (2004) Bioinformatics , vol.20 , pp. 467-476
    • Leslie, C.S.1
  • 41
    • 52949090429 scopus 로고    scopus 로고
    • Technical Report ccsd-00095488
    • HAL
    • Mahé,P. and Vert,J.-P. (2006) Graph kernels based on tree patterns for molecules. Technical Report ccsd-00095488, HAL.
    • (2006)
    • Mahé, P.1    Vert, J.-P.2
  • 42
    • 23844458045 scopus 로고    scopus 로고
    • Graph kernels for molecular structure-activity relationship analysis with support vector machines
    • Mahé,P. et al. (2005) Graph kernels for molecular structure-activity relationship analysis with support vector machines. J. Chem. Inf. Model, 45, 939-951.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 939-951
    • Mahé, P.1
  • 43
    • 33750294461 scopus 로고    scopus 로고
    • The pharmacophore kernel for virtual screening with support vector machines
    • Mahé,P. et al. (2006) The pharmacophore kernel for virtual screening with support vector machines. J. Chem. Inf. Model, 46 2003-2014.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 2003-2014
    • Mahé, P.1
  • 44
    • 0035498999 scopus 로고    scopus 로고
    • The impact of informatics and computational chemistry on synthesis and screening
    • Manly,C. et al. (2001) The impact of informatics and computational chemistry on synthesis and screening. Drug Discov. Today, 6, 1101-1110.
    • (2001) Drug Discov. Today , vol.6 , pp. 1101-1110
    • Manly, C.1
  • 45
    • 34249855107 scopus 로고    scopus 로고
    • A structural alignment kernel for protein structures
    • Qiu,J. et al. (2007) A structural alignment kernel for protein structures. Bioinformatics, 23, 1090-1098.
    • (2007) Bioinformatics , vol.23 , pp. 1090-1098
    • Qiu, J.1
  • 46
    • 23844480138 scopus 로고    scopus 로고
    • Graph kernels for chemical informatics
    • Ralaivola,L. et al. (2005) Graph kernels for chemical informatics. Neural Netw., 18, 1093-1110.
    • (2005) Neural Netw , vol.18 , pp. 1093-1110
    • Ralaivola, L.1
  • 47
    • 34548317031 scopus 로고    scopus 로고
    • Chemogenomic approaches to rational drug design
    • Rognan,D. (2007) Chemogenomic approaches to rational drug design. Br. J. Pharmacol., 152, 38-52.
    • (2007) Br. J. Pharmacol , vol.152 , pp. 38-52
    • Rognan, D.1
  • 52
    • 1642338802 scopus 로고    scopus 로고
    • Marginalized kernels for biological sequences
    • Tsuda,K. et al. (2002) Marginalized kernels for biological sequences. Bioinformatics, 18, S268-S275.
    • (2002) Bioinformatics , vol.18
    • Tsuda, K.1
  • 54
    • 11244331236 scopus 로고    scopus 로고
    • A tree kernel to analyze phylogenetic profiles
    • Vert,J.-P. (2002) A tree kernel to analyze phylogenetic profiles. Bioinformatics, 18, S276-S284.
    • (2002) Bioinformatics , vol.18
    • Vert, J.-P.1
  • 55
    • 10844256122 scopus 로고    scopus 로고
    • Local alignment kernels for biological sequences
    • Schölkopf,B. et al, eds, MIT Press, Cambridge, Massachussetts, pp
    • Vert,J.-P. et al. (2004) Local alignment kernels for biological sequences. In Schölkopf,B. et al. (eds) Kernel Methods in Computational Biology. MIT Press, Cambridge, Massachussetts, pp. 131-154.
    • (2004) Kernel Methods in Computational Biology , pp. 131-154
    • Vert, J.-P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.