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Open Access Highly Accessed Open Badges Research article

The influence of the inactives subset generation on the performance of machine learning methods

Sabina Smusz12, Rafał Kurczab1 and Andrzej J Bojarski1*

Author Affiliations

1 Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, Kraków, 31-343, Poland

2 Faculty of Chemistry, Jagiellonian University, R. Ingardena 3, Kraków, 30-060, Poland

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Journal of Cheminformatics 2013, 5:17  doi:10.1186/1758-2946-5-17

Published: 5 April 2013



A growing popularity of machine learning methods application in virtual screening, in both classification and regression tasks, can be observed in the past few years. However, their effectiveness is strongly dependent on many different factors.


In this study, the influence of the way of forming the set of inactives on the classification process was examined: random and diverse selection from the ZINC database, MDDR database and libraries generated according to the DUD methodology. All learning methods were tested in two modes: using one test set, the same for each method of inactive molecules generation and using test sets with inactives prepared in an analogous way as for training. The experiments were carried out for 5 different protein targets, 3 fingerprints for molecules representation and 7 classification algorithms with varying parameters. It appeared that the process of inactive set formation had a substantial impact on the machine learning methods performance.


The level of chemical space limitation determined the ability of tested classifiers to select potentially active molecules in virtual screening tasks, as for example DUDs (widely applied in docking experiments) did not provide proper selection of active molecules from databases with diverse structures. The study clearly showed that inactive compounds forming training set should be representative to the highest possible extent for libraries that undergo screening.