Probing the binding of ligands to estrogen receptor using an empirical system

The estrogen receptor (ER) is a ligand-regulated transcription factor whose activity as an inducer or repressor of gene transcription depends on the nature of the ligand to which it is bound. The aim of this work is to evaluate the behavior of a set of compounds (antagonist molecules), using different docking experiments, in order to understand the relationship between ERα and such new ligands. With regard to the chemical properties of the ligands analyzed, we defined a specific guideline procedure designed for docking experiments. In our approach, we propose the use of the HINT scoring function in docking methodologies as a means of assessing the consistency of a docking solution, to discriminate correctly or near-correctly docked orientations from incorrectly docked ones, thus compensating for the lack of experimental data.