메뉴 건너뛰기




Volumn 28, Issue 6, 2014, Pages 597-618

Computational chemogenomics: Is it more than inductive transfer?

Author keywords

Chemogenomics; Inductive transfer; Machine learning; Proteochemometrics; QSAR

Indexed keywords

COMPUTATIONAL CHEMISTRY; DATA MINING; KNOWLEDGE MANAGEMENT; LEARNING SYSTEMS; LIGANDS; MOLECULAR GRAPHICS; MOLECULES;

EID: 84902801801     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9743-1     Document Type: Article
Times cited : (25)

References (51)
  • 1
    • 64149107285 scopus 로고    scopus 로고
    • A new approach to collaborative filtering: Operator estimation with spectral regularization
    • Abernethy J, Bach F, Evgeniou T, Vert JP (2009) A new approach to collaborative filtering: operator estimation with spectral regularization. J Mach Learn Res 10:803-826
    • (2009) J Mach Learn Res , vol.10 , pp. 803-826
    • Abernethy, J.1    Bach, F.2    Evgeniou, T.3    Vert, J.P.4
  • 2
    • 55149088329 scopus 로고    scopus 로고
    • Convex multi-task feature learning
    • Argyriou A, Evgeniou T, Pontil M (2008) Convex multi-task feature learning. Mach Learn 73(3):243-272
    • (2008) Mach Learn , vol.73 , Issue.3 , pp. 243-272
    • Argyriou, A.1    Evgeniou, T.2    Pontil, M.3
  • 3
    • 0042034151 scopus 로고    scopus 로고
    • A new method to estimate ligandreceptor energetics
    • Bock JR, Gough DA (2002) A new method to estimate ligandreceptor energetics. Mol Cell Proteomics 1(11):904-910
    • (2002) Mol Cell Proteomics , vol.1 , Issue.11 , pp. 904-910
    • Bock, J.R.1    Gough, D.A.2
  • 4
    • 26944463088 scopus 로고    scopus 로고
    • Virtual screen for ligands of orphan G protein-coupled receptors
    • DOI 10.1021/ci050006d
    • Bock JR, Gough DA (2005) Virtual screen for ligands of orphan G protein-coupled receptors. J Chem Inf Model 45(5):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
    • 41549123745 scopus 로고    scopus 로고
    • Fuzzy tricentric pharmacophore fingerprints. 2. Application of topological fuzzy pharmacophore triplets in quantitative structure-activity relationships
    • DOI 10.1021/ci7003237
    • Bonachera F, Horvath D (2008) Fuzzy tricentric pharmacophore fingerprints. 2. Application of topological fuzzy pharmacophore triplets in quantitative structure-activity relationships. J Chem Inf Model 48(2):409-425 (Pubitemid 351473043)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.2 , pp. 409-425
    • Bonachera, F.1    Horvath, D.2
  • 6
    • 33845791138 scopus 로고    scopus 로고
    • Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes
    • DOI 10.1021/ci6002416
    • Bonachera F, Parent B, Barbosa F, Froloff N, Horvath D (2006) Fuzzy tricentric pharmacophore fingerprints. 1-topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes. J Chem Inf Model 46:2457-2477 (Pubitemid 46008118)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2457-2477
    • Bonachera, F.1    Parent, B.2    Barbosa, F.3    Froloff, N.4    Horvath, D.5
  • 7
    • 84894542859 scopus 로고    scopus 로고
    • Compound-protein interaction prediction within chemogenomics: Theoretical concepts, practical usage, and future directions
    • Brown J, Nijima S, Okuno Y (2013) Compound-protein interaction prediction within chemogenomics: theoretical concepts, practical usage, and future directions. Mol Inf 32:906-921
    • (2013) Mol Inf , vol.32 , pp. 906-921
    • Brown, J.1    Nijima, S.2    Okuno, Y.3
  • 8
    • 84863012821 scopus 로고    scopus 로고
    • Systems biology and systems chemistry: New directions for drug discovery
    • Brown J, Okuno Y (2012) Systems biology and systems chemistry: new directions for drug discovery. Chem Biol 19(1):23-28
    • (2012) Chem Biol , vol.19 , Issue.1 , pp. 23-28
    • Brown, J.1    Okuno, Y.2
  • 9
    • 0031189914 scopus 로고    scopus 로고
    • Multitask learning
    • Caruana R (1997) Multitask learning. Mach Learn 28(1):41-75
    • (1997) Mach Learn , vol.28 , Issue.1 , pp. 41-75
    • Caruana, R.1
  • 10
    • 79955702502 scopus 로고    scopus 로고
    • LIBSVM: A library for support vector machines
    • Chang CC, Lin CJ (2011) LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol 2(27):1-27
    • (2011) ACM Trans Intell Syst Technol , vol.2 , Issue.27 , pp. 1-27
    • Chang, C.C.1    Lin, C.J.2
  • 11
    • 0029031962 scopus 로고
    • Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogs
    • Collantes E, Dunn W (1995) Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogs. J Med Chem 38(14):2705-2713
    • (1995) J Med Chem , vol.38 , Issue.14 , pp. 2705-2713
    • Collantes, E.1    Dunn, W.2
  • 13
    • 22944479010 scopus 로고    scopus 로고
    • A physicogenetic method to assign ligand-binding relationships between 7TM receptors
    • DOI 10.1016/j.bmcl.2005.05.102, PII S0960894X05007043, G-Protein Coupled Receptors in Drug Discovery
    • Frimurer T, Ulven T, Elling C, Gerlach LO, Kostenis E, Hogberg T (2005) A physicogenetic method to assign ligand-binding relationships between 7TM receptors. Bioorg Med Chem Lett 15:3707-3712 (Pubitemid 41043167)
    • (2005) Bioorganic and Medicinal Chemistry Letters , vol.15 , Issue.16 , pp. 3707-3712
    • Frimurer, T.M.1    Ulven, T.2    Elling, C.E.3    Gerlach, L.-O.4    Kostenis, E.5    Hogberg, T.6
  • 16
    • 0003732572 scopus 로고    scopus 로고
    • Regression modeling strategies: With applications to linear models, logistic regression, and survival analysis
    • Springer, Berlin
    • Harrell F (2001) Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis. Graduate texts in mathematics. Springer, Berlin
    • (2001) Graduate Texts in Mathematics
    • Harrell, F.1
  • 17
    • 34250796895 scopus 로고    scopus 로고
    • Stochastic versus stepwise strategies for quantitative structure-activity relationship generation-how much effort may the mining for successful QSAR models take?
    • DOI 10.1021/ci600476r
    • Horvath D, Bonachera F, Solov'ev V, Gaudin C, Varnek A (2007) Stochastic versus stepwise strategies for quantitative structure-activity relationship generation - how much effort may the mining for successful QSAR models take? J Chem Inf Model 47:927-939 (Pubitemid 46973707)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.3 , pp. 927-939
    • Horvath, D.1    Bonachera, F.2    Solov'ev, V.3    Gaudin, C.4    Varnek, A.5
  • 18
    • 84880520518 scopus 로고    scopus 로고
    • Do not hesitate to use tversky - And other hints for successful active analogue searches with feature count descriptors
    • Horvath D, Marcou G, Varnek A (2013) Do not hesitate to use tversky - and other hints for successful active analogue searches with feature count descriptors. J Chem Inf Model 53(7):1543-1562
    • (2013) J Chem Inf Model , vol.53 , Issue.7 , pp. 1543-1562
    • Horvath, D.1    Marcou, G.2    Varnek, A.3
  • 21
    • 52749098733 scopus 로고    scopus 로고
    • Virtual screening of GPCRS: An in silico chemogenomics approach
    • Jacob L, Hoffmann B, Stoven V, Vert JP (2008) Virtual screening of GPCRS: an in silico chemogenomics approach. BMC Bioinform 9(1):363
    • (2008) BMC Bioinform , vol.9 , Issue.1 , pp. 363
    • Jacob, L.1    Hoffmann, B.2    Stoven, V.3    Vert, J.P.4
  • 22
    • 52749085437 scopus 로고    scopus 로고
    • Protein-ligand interaction prediction: An improved chemogenomics approach
    • Jacob L, Vert JP (2008) Protein-ligand interaction prediction: an improved chemogenomics approach. Bioinformatics 24(19):2149-2156
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2149-2156
    • Jacob, L.1    Vert, J.P.2
  • 23
    • 54249099193 scopus 로고    scopus 로고
    • Generalized proteochemometric model of multiple cytochrome p450 enzymes and their inhibitors
    • Kontijevskis A, Komorowski J, Wikberg JES (2008) Generalized proteochemometric model of multiple cytochrome p450 enzymes and their inhibitors. J Chem Inf Model 48(9):1840-1850
    • (2008) J Chem Inf Model , vol.48 , Issue.9 , pp. 1840-1850
    • Kontijevskis, A.1    Komorowski, J.2    Wikberg, J.E.S.3
  • 26
    • 0035895752 scopus 로고    scopus 로고
    • Development of proteo-chemometrics: A novel technology for the analysis of drug-receptor interactions
    • DOI 10.1016/S0304-4165(00)00187-2, PII S0304416500001872
    • Lapinsh M, Prusis P, Gutcaits A, Lundstedt T, Wikberg J (2001) Development of proteo-chemometrics: a novel technology for the analysis of drug-receptor interactions. Biochim Biophys Acta 1525:180-190 (Pubitemid 32149991)
    • (2001) Biochimica et Biophysica Acta - General Subjects , vol.1525 , Issue.1-2 , pp. 180-190
    • Lapinsh, M.1    Prusis, P.2    Gutcaits, A.3    Lundstedt, T.4    Wikberg, J.E.S.5
  • 27
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • DOI 10.1093/bioinformatics/btg431
    • Leslie CS, Eskin E, Cohen A, Weston J, Noble WS (2004) Mismatch string kernels for discriminative protein classification. Bioinformatics 20(4):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
  • 28
    • 65449147106 scopus 로고    scopus 로고
    • A novel method for protein-ligand binding affinity prediction and the related descriptors exploration
    • Li S, Xi L, Wang C, Li J, Lei B, Liu H, Yao X (2009) A novel method for protein-ligand binding affinity prediction and the related descriptors exploration. J Comput Chem 30(6):900-909
    • (2009) J Comput Chem , vol.30 , Issue.6 , pp. 900-909
    • Li, S.1    Xi, L.2    Wang, C.3    Li, J.4    Lei, B.5    Liu, H.6    Yao, X.7
  • 29
    • 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 ZR, Lin HH, Han LY, Jiang L, Chen X, Chen YZ (2006) PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucl Acids Res 34(Suppl. 2):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
  • 31
    • 84902830074 scopus 로고    scopus 로고
    • The embedding problem
    • Borwein P, Borwein J (eds) Combinatorial methods. Springer, New York
    • Mikhalev AA, Shpilrain V, Yu JT (2004) The embedding problem. In: Borwein P, Borwein J (eds) Combinatorial methods. CMS books in mathematics. Springer, New York, pp 108-128
    • (2004) CMS Books in Mathematics , pp. 108-128
    • Mikhalev, A.A.1    Shpilrain, V.2    Yu, J.T.3
  • 33
    • 79959928391 scopus 로고    scopus 로고
    • Update of PROFEAT: A web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • Rao HB, Zhu F, Yang GB, Li ZR, Chen YZ (2011) Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucl Acids Res 39(Suppl. 2):W385-W390
    • (2011) Nucl Acids Res , vol.39 , Issue.SUPPL. 2
    • Rao, H.B.1    Zhu, F.2    Yang, G.B.3    Li, Z.R.4    Chen, Y.Z.5
  • 34
    • 84880848367 scopus 로고    scopus 로고
    • Inferring multi-target QSAR models with taxonomy-based multitask learning
    • Rosenbaum L, Dorr A, Bauer MR, Boeckler FM, Zell A (2013) Inferring multi-target QSAR models with taxonomy-based multitask learning. J Cheminform 5:1-20
    • (2013) J Cheminform , vol.5 , pp. 1-20
    • Rosenbaum, L.1    Dorr, A.2    Bauer, M.R.3    Boeckler, F.M.4    Zell, A.5
  • 35
    • 84900640204 scopus 로고    scopus 로고
    • Quantitative structure-property relationship modeling: A valuable support in high-throughput screening quality control
    • Ruggiu F, Gizzi P, Galzi JL, Hibert M, Haiech J, Baskin I, Horvath D, Marcou G, Varnek A (2014) Quantitative structure-property relationship modeling: a valuable support in high-throughput screening quality control. Anal Chem 86(5):2510-2520
    • (2014) Anal Chem , vol.86 , Issue.5 , pp. 2510-2520
    • Ruggiu, F.1    Gizzi, P.2    Galzi, J.L.3    Hibert, M.4    Haiech, J.5    Baskin, I.6    Horvath, D.7    Marcou, G.8    Varnek, A.9
  • 36
    • 79958834912 scopus 로고    scopus 로고
    • Isida property-labelled fragment descriptors
    • Ruggiu F, Marcou G, Varnek A, Horvath D (2010) Isida property-labelled fragment descriptors. Mol Inform 29(12):855-868
    • (2010) Mol Inform , vol.29 , Issue.12 , pp. 855-868
    • Ruggiu, F.1    Marcou, G.2    Varnek, A.3    Horvath, D.4
  • 37
    • 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, Sjostrom M, Wold S (1998) New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. J Med Chem 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
  • 39
    • 4043137356 scopus 로고    scopus 로고
    • A tutorial on support vector regression
    • DOI 10.1023/B:STCO.0000035301.49549.88
    • Smola AJ, Schlkopf B (2004) A tutorial on support vector regression. Stat Comput 14(3):199-222 (Pubitemid 39063488)
    • (2004) Statistics and Computing , vol.14 , Issue.3 , pp. 199-222
    • Smola, A.J.1    Scholkopf, B.2
  • 41
    • 0036557849 scopus 로고    scopus 로고
    • Neural network studies. 4. Introduction to associative neural networks
    • Tetko IV (2002) Neural network studies. 4. Introduction to associative neural networks. J Chem Inf Comput Sci 42(3):717-728
    • (2002) J Chem Inf Comput Sci , vol.42 , Issue.3 , pp. 717-728
    • Tetko, I.V.1
  • 43
    • 79952520897 scopus 로고    scopus 로고
    • Proteochemometric modeling as a tool for designing selective compounds and extrapolating to novel targets
    • Van Westen G, Wegner J, Ijzerman A, Van Vlijmen H, Bender A (2011) Proteochemometric modeling as a tool for designing selective compounds and extrapolating to novel targets. Med Chem Commun 2:16-30
    • (2011) Med Chem Commun , vol.2 , pp. 16-30
    • Van Westen, G.1    Wegner, J.2    Ijzerman, A.3    Van Vlijmen, H.4    Bender, A.5
  • 44
    • 61949280507 scopus 로고    scopus 로고
    • Inductive transfer of knowledge: Application of multi-task learning and feature net approaches to model tissue-air partition coefficients
    • Varnek A, Gaudin C, Marcou G, Baskin I, Pandey AK, Tetko IV (2009) Inductive transfer of knowledge: application of multi-task learning and feature net approaches to model tissue-air partition coefficients. J Chem Inf Model 49(1):133-144
    • (2009) J Chem Inf Model , vol.49 , Issue.1 , pp. 133-144
    • Varnek, A.1    Gaudin, C.2    Marcou, G.3    Baskin, I.4    Pandey, A.K.5    Tetko, I.V.6
  • 46
    • 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 AM, Geppert H, Bajorath J (2009) Ligand prediction for orphan targets using support vector machines and various target-ligand kernels is dominated by nearest neighbor effects. J Chem Inf Model 49(10):2155-2167
    • (2009) J Chem Inf Model , vol.49 , Issue.10 , pp. 2155-2167
    • Wassermann, A.M.1    Geppert, H.2    Bajorath, J.3
  • 47
    • 66149131771 scopus 로고    scopus 로고
    • Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: Application to G protein-coupled receptors and their ligands
    • Weill N, Rognan D (2009) Development and validation of a novel protein-ligand fingerprint to mine chemogenomic space: application to G protein-coupled receptors and their ligands. J Chem Inf Model 49(4):1049-1062
    • (2009) J Chem Inf Model , vol.49 , Issue.4 , pp. 1049-1062
    • Weill, N.1    Rognan, D.2
  • 48
    • 75749155406 scopus 로고    scopus 로고
    • Alignment-free ultra-high-throughput comparison of druggable proteinligand binding sites
    • Weill N, Rognan D (2010) Alignment-free ultra-high-throughput comparison of druggable proteinligand binding sites. J Chem Inf Model 50(1):123-135 49.
    • (2010) J Chem Inf Model , vol.50 , Issue.1 , pp. 123-13549
    • Weill, N.1    Rognan, D.2
  • 50
    • 79952520897 scopus 로고    scopus 로고
    • Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets
    • van Westen GJP, Wegner JK, Ijzerman AP, van Vlijmen HWT, Bender A (2010) Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets. MedChemComm 2(1):16-30
    • (2010) MedChemComm , vol.2 , Issue.1 , pp. 16-30
    • Van Westen, G.J.P.1    Wegner, J.K.2    Ijzerman, A.P.3    Van Vlijmen, H.W.T.4    Bender, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.