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J Chem Inf Model. 2013 Oct 28;53(10):2681-8. doi: 10.1021/ci400392p. Epub 2013 Sep 24.

Hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens.

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Department of Numerical Analysis and Modelling, ZIB Zuse Institute Berlin , 14195 Berlin, Germany.


With this work we target the development of a predictictive model for the identification of small molecules which bind to the estrogen receptor alpha and, thus, may act as endocrine disruptors. We propose a combined thermodynamic approach for the estimation of preferential binding modes along with corresponding free energy differences using a linear interaction energy (LIE) ansatz. The LIE model is extended by a Monte Carlo approach for the computation of conformational entropies as recently developed by our group. Incorporating the entropy contribution substantially increased the correlation with experimental affinity values. Both squared coefficients for the fitted data as well as the more meaningful leave-one-out cross-validation of predicted energies were elevated up to r(Fit)² = 0.87 and q(LOO)² = 0.82, respectively. All calculations have been performed on a set of 31 highly diverse ligands regarding their structural properties and affinities to the estrogen receptor alpha. Comparison of predicted ligand orientations with crystallographic data retrieved from the Protein database revealed remarkable binding mode predictions.

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