메뉴 건너뛰기




Volumn 24, Issue 2, 2013, Pages 103-117

Towards in silico identification of the human ether-a-go-go-related gene channel blockers: Discriminative vs. generative classification models

Author keywords

classification models for hERG inhibitors; discriminative models; generative models; generative topographic maps; human ether a go go related gene; quantitative structure activity relationships; support vector machines

Indexed keywords

GENES; MAPS; SUPPORT VECTOR MACHINES;

EID: 84872419971     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936X.2012.742135     Document Type: Article
Times cited : (14)

References (52)
  • 1
    • 0038471102 scopus 로고    scopus 로고
    • The impact of drug-induced QT interval prolongation on drug discovery and development
    • Fermini, B and Fossa, A. 2003. The impact of drug-induced QT interval prolongation on drug discovery and development. Nature Rev. Drug Discov., 2: 439-447.
    • (2003) Nature Rev. Drug Discov. , vol.2 , pp. 439-447
    • Fermini, B.1    Fossa, A.2
  • 2
    • 0034244378 scopus 로고    scopus 로고
    • The potential for QT prolongation and proarrhythmia by non-antiarrhythmic drugs: Clinical and regulatory implications. Report on a policy conference of the European Society of Cardiology
    • Haverkamp, W. 2000. The potential for QT prolongation and proarrhythmia by non-antiarrhythmic drugs: Clinical and regulatory implications. Report on a policy conference of the European Society of Cardiology. Eur. Heart J., 21: 1216-1231.
    • (2000) Eur. Heart J. , vol.21 , pp. 1216-1231
    • Haverkamp, W.1
  • 3
    • 14544268139 scopus 로고    scopus 로고
    • QT prolongation through hERG K+ channel blockade: Current knowledge and strategies for the early prediction during drug development
    • Recanatini, M, Poluzzi, E, Masetti, M, Cavalli, A and De Ponti, F. 2005. QT prolongation through hERG K+ channel blockade: Current knowledge and strategies for the early prediction during drug development. Med. Res. Rev, 25: 133-166.
    • (2005) Med. Res. Rev , vol.25 , pp. 133-166
    • Recanatini, M.1    Poluzzi, E.2    Masetti, M.3    Cavalli, A.4    de Ponti, F.5
  • 5
    • 39749088786 scopus 로고    scopus 로고
    • HERG Classification model based on a combination of support vector machine method and GRIND descriptors
    • Li, Q, Jorgensen, FS, Oprea, T, Brunak, S and Taboreau, O. 2008. HERG Classification model based on a combination of support vector machine method and GRIND descriptors. Mol. Pharmaceutics, 5: 117-127.
    • (2008) Mol. Pharmaceutics , vol.5 , pp. 117-127
    • Li, Q.1    Jorgensen, F.S.2    Oprea, T.3    Brunak, S.4    Taboreau, O.5
  • 6
    • 65249092596 scopus 로고    scopus 로고
    • Similarity-based classifier using topomers to provide a knowledge base for hERG channel inhibition
    • Nisius, B and Goller, A. 2009. Similarity-based classifier using topomers to provide a knowledge base for hERG channel inhibition. J. Chem. Inf. Model., 49: 247-256.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 247-256
    • Nisius, B.1    Goller, A.2
  • 7
    • 19544393375 scopus 로고    scopus 로고
    • A discriminant model constructed by the support vector maachine method for hERG potassium channel inhibitors
    • Tobita, M, Nishikawa, T and Nagashima, R. 2005. A discriminant model constructed by the support vector maachine method for hERG potassium channel inhibitors. Bioorg. Med. Chem. Lett., 15: 2886-2890.
    • (2005) Bioorg. Med. Chem. Lett. , vol.15 , pp. 2886-2890
    • Tobita, M.1    Nishikawa, T.2    Nagashima, R.3
  • 8
    • 2442700335 scopus 로고    scopus 로고
    • Prediction of torsade-causing potential of drugs by support vector machine approach
    • Yap, CW, Cai, CZ, Xue, Y and Chen, YZ. 2004. Prediction of torsade-causing potential of drugs by support vector machine approach. Toxicol. Sci., 79: 170-177.
    • (2004) Toxicol. Sci. , vol.79 , pp. 170-177
    • Yap, C.W.1    Cai, C.Z.2    Xue, Y.3    Chen, Y.Z.4
  • 9
    • 77954075802 scopus 로고    scopus 로고
    • Gaussian processes for classification: QSAR modeling of ADMET and target activity
    • Obrezanova, O and Segall, MD. 2010. Gaussian processes for classification: QSAR modeling of ADMET and target activity. J. Chem. Inf. Model., 50: 1053-1061.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1053-1061
    • Obrezanova, O.1    Segall, M.D.2
  • 10
    • 77951675415 scopus 로고    scopus 로고
    • Prospective validation of a comprehensive in silico HERG model and its applications to commercial compound and drug database
    • Doddareddy, M, Klaase, EC, Shugufta, Izerman, AP and Bender, AP. 2010. Prospective validation of a comprehensive in silico HERG model and its applications to commercial compound and drug database. ChemMedChem, 5: 716-729.
    • (2010) ChemMedChem , vol.5 , pp. 716-729
    • Doddareddy, M.1    Klaase, E.C.2    Shugufta3    Izerman, A.P.4    Bender, A.P.5
  • 11
    • 0036904104 scopus 로고    scopus 로고
    • A virtual screening method for prediction of the HERG potassium channel liability of compound libraries
    • Roche, O, Trube, G, Zuegge, J, Pflimlin, P, Alanine, A and Schneider, G. 2002. A virtual screening method for prediction of the HERG potassium channel liability of compound libraries. ChemBioChem, 3: 455-459.
    • (2002) ChemBioChem , vol.3 , pp. 455-459
    • Roche, O.1    Trube, G.2    Zuegge, J.3    Pflimlin, P.4    Alanine, A.5    Schneider, G.6
  • 12
    • 52649109749 scopus 로고    scopus 로고
    • Classification models for HERG inhibitors by counter-propagation neural networks
    • Thai, K-M and Ecker, GF. 2008. Classification models for HERG inhibitors by counter-propagation neural networks. ChemBiolDrugDes, 72: 279-289.
    • (2008) ChemBiolDrugDes , vol.72 , pp. 279-289
    • Thai, K.-M.1    Ecker, G.F.2
  • 13
    • 68349152323 scopus 로고    scopus 로고
    • Similarity-based SIBAR descriptors for classification of chemically diverse HERG blockers
    • Thai, K-M and Ecker, GF. 2009. Similarity-based SIBAR descriptors for classification of chemically diverse HERG blockers. Mol. Divers., 13: 321-336.
    • (2009) Mol. Divers. , vol.13 , pp. 321-336
    • Thai, K.-M.1    Ecker, G.F.2
  • 14
    • 78751633853 scopus 로고    scopus 로고
    • Prediction of the HERG potassium channel inhibition potential with use of artificial neural network
    • Polak, S, Wisniowska, B, Ahamadi, M and Mendyk, A. 2011. Prediction of the HERG potassium channel inhibition potential with use of artificial neural network. Appl. Soft Comput., 11: 2611-2617.
    • (2011) Appl. Soft Comput. , vol.11 , pp. 2611-2617
    • Polak, S.1    Wisniowska, B.2    Ahamadi, M.3    Mendyk, A.4
  • 15
    • 79151471075 scopus 로고    scopus 로고
    • Predicting HERG activities of compounds from their 3D structures: Development and evaluation of a global descriptors based QSAR model
    • Sinha, N and Sen, S. 2011. Predicting HERG activities of compounds from their 3D structures: Development and evaluation of a global descriptors based QSAR model. Eur. J. Med. Chem., 46: 618-630.
    • (2011) Eur. J. Med. Chem. , vol.46 , pp. 618-630
    • Sinha, N.1    Sen, S.2
  • 16
    • 33646487003 scopus 로고    scopus 로고
    • An accurate and interpretable bayesian classification model for predicting of HERG liability
    • Sun, H. 2006. An accurate and interpretable bayesian classification model for predicting of HERG liability. ChemMedChem, 1: 315-322.
    • (2006) ChemMedChem , vol.1 , pp. 315-322
    • Sun, H.1
  • 17
    • 33746275630 scopus 로고    scopus 로고
    • In silico classification of hERG channel blockers: A knowledge-based strategy
    • Dubus, E, Ijjaali, I, Petitet, F and Michel, A. 2006. In silico classification of hERG channel blockers: A knowledge-based strategy. ChemMedChem, 1: 622-630.
    • (2006) ChemMedChem , vol.1 , pp. 622-630
    • Dubus, E.1    Ijjaali, I.2    Petitet, F.3    Michel, A.4
  • 18
    • 33745147614 scopus 로고    scopus 로고
    • Determination of hERG channel blockers using a decision tree
    • Gepp, MM and Hutter, MC. 2006. Determination of hERG channel blockers using a decision tree. Bioorg. Med. Chem., 14: 5325-5332.
    • (2006) Bioorg. Med. Chem. , vol.14 , pp. 5325-5332
    • Gepp, M.M.1    Hutter, M.C.2
  • 19
    • 33747505086 scopus 로고    scopus 로고
    • Insights for human ether-a-go-go-related gene potassium channel inhibition using recursive partitionning and Kohonen ana Sammon mapping techniques
    • Ekins, S, Balakin, KV, Savchuk, N and Ivanenkov, Y. 2006. Insights for human ether-a-go-go-related gene potassium channel inhibition using recursive partitionning and Kohonen ana Sammon mapping techniques. J. Med. Chem., 49: 5059-5071.
    • (2006) J. Med. Chem. , vol.49 , pp. 5059-5071
    • Ekins, S.1    Balakin, K.V.2    Savchuk, N.3    Ivanenkov, Y.4
  • 20
    • 84859890850 scopus 로고    scopus 로고
    • Generative topographic maps (GTM): Universal tool for data visualization, structure-activity modeling and database comparison
    • Kireeva, N, Baskin, II, Gaspar, HA, Horvath, D, Marcou, G and Varnek, A. 2012. Generative topographic maps (GTM): Universal tool for data visualization, structure-activity modeling and database comparison. Mol. Inf., 31: 301-312.
    • (2012) Mol. Inf. , vol.31 , pp. 301-312
    • Kireeva, N.1    Baskin, I.I.2    Gaspar, H.A.3    Horvath, D.4    Marcou, G.5    Varnek, A.6
  • 22
    • 84887006810 scopus 로고
    • A nonlinear mapping for data structure analysis
    • Sammon, JW. 1969. A nonlinear mapping for data structure analysis. IEEE Trans. Comput., 18: 401-409.
    • (1969) IEEE Trans. Comput. , vol.18 , pp. 401-409
    • Sammon, J.W.1
  • 27
    • 0347963789 scopus 로고    scopus 로고
    • GTM: The generative topographic mapping
    • Bishop, CM and Svensen, M. 1998. GTM: The generative topographic mapping. Neural Comput., 10: 215-234.
    • (1998) Neural Comput. , vol.10 , pp. 215-234
    • Bishop, C.M.1    Svensen, M.2
  • 30
    • 58149086468 scopus 로고    scopus 로고
    • Combining cluster analysis, feature selection and multiple support vector machine models for the identification of human ether-a-go-go related gene channel blocking compounds
    • Nisius, B, Gts{cyrillic}ller, AH and Bajorath, J. 2009. Combining cluster analysis, feature selection and multiple support vector machine models for the identification of human ether-a-go-go related gene channel blocking compounds. Chem. Biol. Drug Des., 73: 17-25.
    • (2009) Chem. Biol. Drug Des. , vol.73 , pp. 17-25
    • Nisius, B.1    Gtsller, A.H.2    Bajorath, J.3
  • 31
    • 85194997104 scopus 로고    scopus 로고
    • Chemaxon Standardizer; software available at
    • Chemaxon Standardizer; software available athttp://www.chemaxon.com/library/scientific-presentations/standardizer/
  • 32
    • 85195008674 scopus 로고    scopus 로고
    • Instant JChem, software available at
    • Instant JChem, software available athttp://www.chemaxon.com/products/instant-jchem/
  • 35
    • 79958834912 scopus 로고    scopus 로고
    • ISIDA property-labelled fragment descriptors
    • Ruggiu, F, Marcou, G, Varnek, A and Horvath, D. 2010. ISIDA property-labelled fragment descriptors. Mol. Inform., 29: 855-868.
    • (2010) Mol. Inform. , vol.29 , pp. 855-868
    • Ruggiu, F.1    Marcou, G.2    Varnek, A.3    Horvath, D.4
  • 36
    • 33846799417 scopus 로고    scopus 로고
    • Chemical informatics functionality in R
    • Guha, R. 2007. Chemical informatics functionality in R. J. Stat. Software, 18: 1-16.
    • (2007) J. Stat. Software , vol.18 , pp. 1-16
    • Guha, R.1
  • 37
    • 85194997377 scopus 로고    scopus 로고
    • R project, software available at
    • R project, software available athttp://www.r-project.org/foundation/
  • 38
    • 0003798635 scopus 로고    scopus 로고
    • An Introduction to Support Vector Machines (and Other Kernel-Based Learning Methods)
    • Cambridge, Cambridge,: Cambridge University Press
    • Cristianini, N and Shawe-Taylor, J. 2000. "An Introduction to Support Vector Machines (and Other Kernel-Based Learning Methods)". In Cambridge Monographs on Applied and Computational Mathematics, Cambridge: Cambridge University Press.
    • (2000) Cambridge Monographs on Applied and Computational Mathematics
    • Cristianini, N.1    Shawe-Taylor, J.2
  • 40
    • 0003450542 scopus 로고    scopus 로고
    • New York and Chichester, New York and Chichester,: Wiley-Interscience
    • Vapnik, V. 1998. Statistical Learning Theory, New York and Chichester: Wiley-Interscience.
    • (1998) Statistical Learning Theory
    • Vapnik, V.1
  • 43
    • 51849156137 scopus 로고    scopus 로고
    • Beyond accuracy, F-score and ROC: A family of discriminant measures for performance evaluation
    • Sokolova, M, Japkowicz, N and Szpakowicz, S. 2006. Beyond accuracy, F-score and ROC: A family of discriminant measures for performance evaluation. Adv. Artif. Intell., 4304: 1015-1021.
    • (2006) Adv. Artif. Intell. , vol.4304 , pp. 1015-1021
    • Sokolova, M.1    Japkowicz, N.2    Szpakowicz, S.3
  • 45
    • 4043137356 scopus 로고    scopus 로고
    • A Tutorial on support vector regression
    • Smola, AJ and Schölkopf, B. 2004. A Tutorial on support vector regression. Stat. Comput., 14: 199-222.
    • (2004) Stat. Comput. , vol.14 , pp. 199-222
    • Smola, A.J.1    Schölkopf, B.2
  • 47
    • 85194993669 scopus 로고    scopus 로고
    • Netlab
    • Netlab,www1.aston.ac.uk/eas/research/groups/ncrg/resources/netlab/
  • 51
    • 78650201311 scopus 로고    scopus 로고
    • The one-class classification approach to data description and to models applicability domain
    • Baskin, II, Kireeva, N and Varnek, A. 2010. The one-class classification approach to data description and to models applicability domain. Mol. Inf., 29: 581-587.
    • (2010) Mol. Inf. , vol.29 , pp. 581-587
    • Baskin, I.I.1    Kireeva, N.2    Varnek, A.3
  • 52
    • 80052912494 scopus 로고    scopus 로고
    • Target-driven subspace mapping methods and their applicability domain estimation
    • Soto, AJ, Vazquez, GE, Strickert, M and Ponzoni, I. 2011. Target-driven subspace mapping methods and their applicability domain estimation. Mol. Inf., 30: 779-789.
    • (2011) Mol. Inf. , vol.30 , pp. 779-789
    • Soto, A.J.1    Vazquez, G.E.2    Strickert, M.3    Ponzoni, I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.