Ecotoxicity prediction by adaptive fuzzy partitioning: comparing descriptors computed on 2D and 3D structures

SAR and QSAR in Environmental Research
Nadège PiclinJ R Chrétien

Abstract

Classification models were established on four endpoints, i.e. trout, daphnia, quail and bee, including from 100 to 300 pesticides subdivided into 3 toxicity classes. For each species, five separate sets of molecular descriptors, computed by several software, were compared, including parameters related to 2D or 3D structures. The most relevant descriptors were selected with help of a procedure based on genetic algorithms. Then, structure-activity relationships were built by Adaptive Fuzzy Partition (AFP), a recursive partitioning method derived from Fuzzy Logic concepts.Globally, satisfactory results were obtained for each animal species. The best cross-validation and test set scores reached values of about 70-75%. More important, the relationships derived from the descriptors calculated from 2D structures were superior or similar to those computed from 3D structures. These results underline that the long computational time employed to compute 3D descriptors is often useless to improve the prediction ability of the ecotoxicity models. Finally, the differences in the prediction ability between the different software used were quite reduced and show the possibility to use different descriptor packages for obtaining similar satisf...Continue Reading

References

Mar 7, 2001·European Journal of Medicinal Chemistry·M PintoreJ R Chrétien
May 1, 2001·SAR and QSAR in Environmental Research·J Devillers
Jul 20, 2001·European Journal of Medicinal Chemistry·M PintoreJ R Chrétien
Jan 30, 2002·SAR and QSAR in Environmental Research·J Devillers
Jan 30, 2002·SAR and QSAR in Environmental Research·E BenfenatiM R Varì
Feb 23, 2002·Journal of Molecular Graphics & Modelling·Alexander Golbraikh, Alexander Tropsha
Jul 23, 2002·Journal of Chemical Information and Computer Sciences·Li Xing, Robert C Glen
Mar 12, 2003·Environmental Toxicology and Chemistry·T Wayne Schultz, Mark T D Cronin
May 17, 2003·European Journal of Medicinal Chemistry·Marco PintoreJacques R Chrétien
Aug 20, 2003·Environmental Toxicology and Chemistry·Roger PerkinsWilliam J Welsh
Oct 12, 2004·Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes·Alessandra RoncaglioniMark Clook
Feb 26, 2005·Journal of Computer-aided Molecular Design·Nadège PiclinJacques R Chrétien
Mar 5, 2005·International Braz J Urol : Official Journal of the Brazilian Society of Urology·K T BalasteghinC R Padovani

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Citations

Dec 9, 2008·SAR and QSAR in Environmental Research·A RoncaglioniE Benfenati
Aug 4, 2010·Chemistry Central Journal·Antonio CassanoEmilio Benfenati
Mar 1, 2012·Cellular and Molecular Bioengineering·Nripen S SharmaMartin L Yarmush
Apr 24, 2012·Toxicology and Applied Pharmacology·Angelo VedaniMartin Smieško
Jan 27, 2011·Journal of Separation Science·Dorina CasoniCostel Sârbu
Sep 23, 2014·Toxicology Letters·Angelo VedaniMartin Smieško
Dec 19, 2009·Alternatives to Laboratory Animals : ATLA·Angelo Vedani, Martin Smiesko

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