Applicability domains for classification problems: Benchmarking of distance to models for ames mutagenicity set

Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Artem Cherkasov, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus Robert Müller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Roberto Todeschini, Pavel Polishchuk, Anatoliy ArtemenkoVictor Kuz'Min, Todd M. Martin, Douglas M. Young, Denis Fourches, Eugene Muratov, Alexander Tropsha, Igor Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexander Varnek, Volodymyr V. Prokopenko, Igor V. Tetko

Research output: Contribution to journalArticle

146 Citations (Scopus)

Abstract

The estimation of accuracy and applicability of QSAR and QSPR models for biological and physicochemical properties represents a critical problem. The developed parameter of "distance to model" (DM) is defined as a metric of similarity between the training and test set compounds that have been subjected to QSAR/QSPR modeling. In our previous work, we demonstrated the utility and optimal performance of DM metrics that have been based on the standard deviation within an ensemble of QSAR models. The current study applies such analysis to 30 QSAR models for the Ames mutagenicity data set that were previously reported within the 2009 QSAR challenge. We demonstrate that the DMs based on an ensemble (consensus) model provide systematically better performance than other DMs. The presented approach identifies 30-60% of compounds having an accuracy of prediction similar to the interlaboratory accuracy of the Ames test, which is estimated to be 90%. Thus, the in silico predictions can be used to halve the cost of experimental measurements by providing a similar prediction accuracy. The developed model has been made publicly available at http://ochem.eu/models/1.

Original languageEnglish
Pages (from-to)2094-2111
Number of pages18
JournalJournal of Chemical Information and Modeling
Volume50
Issue number12
DOIs
Publication statusPublished - 2010 Dec 27

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

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    Sushko, I., Novotarskyi, S., Körner, R., Pandey, A. K., Cherkasov, A., Li, J., Gramatica, P., Hansen, K., Schroeter, T., Müller, K. R., Xi, L., Liu, H., Yao, X., Öberg, T., Hormozdiari, F., Dao, P., Sahinalp, C., Todeschini, R., Polishchuk, P., ... Tetko, I. V. (2010). Applicability domains for classification problems: Benchmarking of distance to models for ames mutagenicity set. Journal of Chemical Information and Modeling, 50(12), 2094-2111. https://doi.org/10.1021/ci100253r