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Structural features of diverse ligands influencing binding affinities to Estrogen α and Estrogen β receptors. Part I: molecular descriptors calculated from minimal energy conformation of isolated ligands

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Abstract

We report a neural network modeling approach combined with genetic algorithm for prediction of experimental binding affinity to human Estrogen Receptor α and β (ER-α and ER-β) of a diverse set of chemicals. The counterpropagation artificial neural network is used as a modeling method. Structural features of ligands having the strongest influence to the binding affinities were investigated. The molecular descriptors have been selected in the variable selection procedure based on the genetic algorithm (GA). The 3D descriptors of molecular structures were calculated for the minimal energy conformation of isolated ligands. All the optimized models were tested by an internal and an external set of compounds. The models served for classification and prediction of binding affinities. The optimized models were 100% correct in the classification part, where the active molecules were separated from the inactive ones. The best predictive model of active molecules was assessed with the internal test set yielding the error in prediction RMS = 0.12, while the predictions for the external test set contain some outliers, which are ascribed to the incompatibility of individual compounds concerning the structural domain of our model. The influence of the receptor on the conformation of the ligands in the ligand–protein complex is described and discussed in the accompanying paper.

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Abbreviations

CP-ANN:

Counterpropagation artificial neuronal network

ER:

Estrogen receptor

GA:

Genetic algorithm

RBA:

Relative binding affinity

RMS:

Root mean square error

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Authors and Affiliations

  1. Mario Negri Institute for Pharmacological Research, Via La Masa, 19-20156, Milan, Italy

    Elena Boriani, Morena Spreafico & Emilio Benfenati

  2. Laboratory for Chemometrics, National Institute of Chemistry, Hajdrihova 19, POB 660, 1001, Ljubljana, Slovenia

    Elena Boriani, Morena Spreafico & Marjana Novič

Authors
  1. Elena Boriani
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  2. Morena Spreafico
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  3. Emilio Benfenati
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  4. Marjana Novič
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Correspondence to Marjana Novič.

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Boriani, E., Spreafico, M., Benfenati, E. et al. Structural features of diverse ligands influencing binding affinities to Estrogen α and Estrogen β receptors. Part I: molecular descriptors calculated from minimal energy conformation of isolated ligands. Mol Divers 11, 153–169 (2007). https://doi.org/10.1007/s11030-008-9069-9

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  • DOI: https://doi.org/10.1007/s11030-008-9069-9

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