In this work, we formalize and validate the flexible treatment of macrocyclic rings in AutoDock-GPU on a large set of diverse macrocyclic molecules from the PDB. The method leverages an improved preparation protocol for the ligands for flexible docking of macrocyclic structures, which is now enabled by default in Meeko, our recently developed interface between AutoDock and RDKit. Meeko streamlines the ligand preparation workflow, enabling users to use RDKit molecule objects to manage the AutoDock input and output data. Given the popularity and wide use of RDKit, this interface enables users to more easily integrate AutoDock with other software that supports the RDKit library. For docking methods requiring pseudo atoms, such as the macrocycle flexibility described herein, having streamlined input and output in a well-established molecular representation (as opposed to running scripts to add and remove pseudo-atoms from AutoDockspecific file formats) reduces the burden on the user and makes it easy to use docked poses as input for other modeling tools, such as molecular dynamics simulations. Docking macrocycles flexibly greatly increases the number of conformations that are scored during the search. In comparison to rigid docking, there is a greater chance of finding wrong conformers with good scores, which would be detrimental to docking performance. However, we found no evidence of this being the case (Figure ), which we attribute to the fact that the anisotropic closure potential used here retains bonding information and prevents deformations in bonding geometry from erroneously being scored favorably. Thus, our data suggests that the method does not introduce scoring functions issues.