To address the mentioned challenges, we introduce DockOpt, a new automated docking pipeline that enables the creation, evaluation, and optimization of docking models using a single tool. DockOpt is part of the Python package Pydock3, a toolkit dedicated to the standardization and enhancement of docking methodologies, specifically designed to complement UCSF DOCK 3.8 and subsequent versions. To evaluate the utility of DockOpt, we benchmarked it against the DUDE-Z dataset .