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Articles

Hybrid reduced graph for SAR studies

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Pages 201-214 | Received 02 Nov 2012, Accepted 20 Dec 2012, Published online: 25 Feb 2013

References

  • Todeschini , R. , Consonni , V. , Mannhold , R. , Kubinyi , H. and Timmerman , H. 2008 . Handbook of Molecular Descriptors , Weinheim, Germany : John Wiley & Sons .
  • Todeschini , R. , Consonni , V. , Mannhold , R. , Kubinyi , H. and Folkers , H. 2009 . Molecular Descriptors for Chemoinformatics , Weinheim, Germany : John Wiley & Sons .
  • Bonchev , D. 2000 . Overall connectivities/topological complexities: A new powerful tool for QSPR/QSAR . J. Chem. Inf. Comp. Sci , 40 : 934 – 941 .
  • Bonchev , D.G. and Rouvray , D.H. 2003 . Complexity: Introduction and Fundamentals , London and New York : Taylor & Francis .
  • Carrasco-Velar , R. , Padrón , J.A. and Gálvez , J. 2004 . Definition of a novel atomic index for QSAR: The refractotopological state . J. Pharm. Pharmaceut. Sci , 7 : 19 – 26 .
  • Adhikari , N. , Maiti , M.K. and Jha , T. 2010 . Predictive comparative QSAR modelling of (phenylpiperazinyl-alkyl) oxindoles as selective 5-HT1A antagonists by stepwise regression, PCRA, FA-MLR and PLS techniques . Eur. J. Med. Chem , 45 : 1119 – 1127 .
  • Jha , T. , Samanta , S. , Basu , S. , Halder , A.K. , Adhikari , N. and Mait , M.K. 2008 . QSAR study on some orally active uracil derivatives as human gonadotropin–releasing–hormone receptor antagonists . Internet Electron. J. Mol. Des , 7 : 234 – 250 .
  • Samanta , S. , Alam , S.M. , Panda , P. , Jha , T. and Panda , P. 2006 . Pharmacophore mapping of tricyclic isoxazoles for their affinity towards alpha–2 adrenoreceptors . Internet Electron. J. Mol. Des , 5 : 503 – 514 .
  • Randić , M. and Razinger , M. 1996 . Molecular shapes and chirality . J. Chem. Inf. Comp. Sci , 36 : 429 – 441 .
  • Escalona , J.C. , Carrasco , R. , Guerra , K. and Centeno , J. 1999 . Estudio QSAR de flavonoides con actividad estrogénica . Rev. Cub. Quím , 11 : 13 – 21 .
  • Hammett , L.P. 1938 . Linear free energy relationships in rate and equilibrium phenomena . Trans. Faraday Soc , 34 : 156 – 165 .
  • Hansch , C. and Fujita , T. 1964 . P-σ-π Analysis. A method for the correlation of biological activity and chemical structure . J. Am. Chem. Soc , 86 : 1616 – 1626 .
  • Free , S. and Wilson , J. 1964 . A mathematical contribution to structure–activity studies . J. Med. Chem , 7 : 395 – 399 .
  • Birchall , K. , Gillet , V.J. , Willett , P. , Ducrot , P. and Luttmann , C. 2009 . Use of reduced graphs to encode bioisosterism for similarity-based virtual screening . J. Chem. Inf. Mod. , 49 : 1330 – 1346 .
  • Friedman , H. 1951 . “ Influence of isosteric replacements upon biological activity ” . In On Chemical Biological Correlation , Edited by: Symposium , First . 296 – 358 . Washington : DCNational Research Council .
  • Thornber , C.W. 1979 . Isosterism and molecular modification in drug design . Chem. Soc. Rev , 8 : 563 – 580 .
  • Melville , P. and Mooney , R.J. 2003 . Constructing diverse classifier ensembles using artificial training examples, in Proceedings of the 18th International Joint Conference on Artificial Intelligence , Acapulco , Mexico : Morgan Kaufmann Publishers . pp. 505–510
  • Melville , P. and Mooney , R.J. 2005 . Creating diversity in ensembles using artificial data . Inf. Fusion , 6 : 99 – 111 .
  • Breiman , L. 1996 . Bagging predictors . Mach. Learn , 24 : 123 – 140 .
  • Bolton , E. , Kim , S. and Bryant , S. 2011 . PubChem3D: Diversity of shape . J. Cheminf. , 3 : 9
  • R. Carrasco-Velar, Nuevos descriptores atómicos y moleculares. Aplicaciones [New atomic and molecular descriptors. Applications] Ciudad de La Habana: Editorial Universitaria, 2003. pp. 35–36.
  • Randic , M. 1991 . Resolution of ambiguities in structure-property studies by use of orthogonal descriptors . J. Chem. Inf. Comp. Sci , 31 : 311 – 320 .
  • Ghose , A.K. and Crippen , G.M. 1986 . Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships I. Partition coefficients as a measure of hydrophobicity . J. Comput. Chem , 7 : 565 – 577 .
  • Ghose , A.K. and Crippen , G.M. 1987 . Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions . J. Chem. Inf. Comp. Sci , 7 : 21 – 35 .
  • Ghose , A.K. , Pritchett , A. and Crippen , G.M. 1988 . Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships III: Modeling hydrophobic interactions . J. Comput. Chem , 9 : 80 – 90 .
  • Varnek , A. and Tropsha , A. , eds. 2008 . 9 , Cambridge : Royal Society of Chemistry .
  • Ruggiu , F. , Marcou , G. , Varnek , A. and Horvath , D. 2010 . ISIDA property-labelled fragment descriptors . Mol. Inf. , 29 : 855 – 868 .
  • Avidon , V.V. , Pomerantsev , I.A. , Golender , V.E. and Rozenblit , A.B. 1982 . Structure-activity relationship oriented languages for chemical structure representation . J. Chem. Inf. Comp. Sci , 22 : 207 – 214 .
  • Hall , L.H. , Mohney , B. and Kier , L.B. 1991 . The electrotopological state: Structure information at the atomic level for molecular graphs . J. Chem. Inf. Comp. Sci , 31 : 76 – 82 .
  • R. Carrasco-Velar, Nuevos descriptores atómicos y moleculares para estudios de estructura-actividad: Aplicaciones [New atomic and molecular descriptors for structure-activity studies: Applications], PhD thesis, Havana University, Havana, 2008.
  • N.Rivero, B.Llorente, and R.Carrasco-Velar, Estudio de relacion cuantitativa estructura-actividad en un grupo de quinolonas empleando el indice del estado electrotopologico modificado [Relationship quantitative structure–activity study by using modified Electrotopologico State Index in quinolones], Rev. CENIC, Cienc. Quím. 28 (1997), pp. 1–14.
  • PubChem BioAssay database. Available at http://pubchem.ncbi.nlm.nih.gov/.
  • Ho , T.K. 1998 . The random subspace method for constructing decision forests . IEEE Trans. Pattern Anal. Mach. Intell , 20 : 832 – 844 .
  • J.R. Quinlan, C4.5: Programs for Machine Learning, Morgan Kaufmann, San Mateo, USA, 1993.
  • Rosenblatt , F. 1962 . Principles of Neurodynamics: Perceptrons and the Theory of Brain Mechanisms , Washingotn, D. C. : Spartan Books .
  • Rumelhart , D.E. , Hinton , G.E. and Williams , R.J. 1986 . Learning internal representations by error propagation, in Parallel Distributed Processing: Explorations in the Microstructure of Cognition , Edited by: David , E.R. , James , L.M. and Group , C.P.R. Volume 1 , 318 – 362 . MIT Press Cambridge, MA, USA : MIT Press .
  • Wasserman , P.D. and Schwartz , T. 1988 . Neural networks. II. What are they and why is everybody so interested in them now? . IEEE Expert , 3 : 10 – 15 .
  • Hall , M. , Frank , E. , Holmes , G. , Pfahringer , B. , Reutemann , P. and Witten , I.H. 2009 . The WEKA data mining software: An update . SIGKDD Explor. Newsletter , 11 : 10 – 18 .
  • Burges , C.J.C. 1998 . A tutorial on support vector machines for pattern recognition . Data Min. Knowl. Disc , 2 : 121 – 167 .
  • Vapnik , V.N. 1995 . The nature of statistical learning theory , New York : Springer-Verlag .
  • Ivanciuc , O. 2007 . Applications of support vector machines in chemistry . Rev. Comput. Chem. , 23 : 291 – 400 .
  • Chang , C.-C. and Lin , C.-J. 2011 . LIBSVM: A library for support vector machines . ACM Trans. Intell. Syst. Technol. , 2 : 1 – 27 .
  • Platt , J.C. 1999 . Fast training of support vector machines using sequential minimal optimization, in Advances in Kernel Methods , Cambridge, MA, USA : MIT Press . pp. 185–208
  • StatSoft, STATISTICA (data analysis software system), version 7, 2004; software available at www.statsoft.com.
  • A.L. Maceo-Pixa, R. Carrasco-Velar, R. Alcolea-Nuñez, and L.G. Silva-Rojas, MolVis (software for visualization of topographic atomic indices), Havana, Cuba: Visualization and Virtual Reality Department, University of Informatic Science, Havana, Cuba 2012.
  • Fawcett , T. 2006 . An introduction to ROC analysis . Pattern Recogn. Lett , 27 : 861 – 874 .
  • Zhu , W. , Zeng , N. and Wang , N. 2010 . Sensitivity, specificity, accuracy, associated confidence interval and ROC analysis with practical SAS implementations, in NESUG Proceedings: Health Care and Life Sciences , Maryland : Baltimore .

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