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The results obtained in this study indicate that the quantum mechanical\/molecular mechanics docking protocol well describes the charge\u2010driven interactions occurring in the binding of nicotinic agonists, and it is able to represent the polarization effects on the ligand exerted by the surrounding atoms of the receptor at the binding site. This makes it possible to properly score agonists of \u03b14\u03b22\u2010nAChR and to reproduce the experimental binding affinity data with good accuracy, within a mean error of 2.2 kcal\/mol. Moreover, applying the QM\u2010polarized docking to an ensemble of nAChR conformations obtained from MD simulations enabled us to accurately capture nAChR\u2010ligand induced\u2010fit effects. \u00a9 2009 Wiley Periodicals, Inc. 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