protocol or parameters for PR docking using Unimol/Unidock

[CLG68]

Hi,

In your paper:
"Synergistic application of molecular docking and machine learning for improved binding pose": https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10936200/

you used a combination of Unimol docking and Unidock: PR Docking

There is no detail in the Methods section or in supp 1.4, on how to setup Uni-dock to accept Unimol Docking results as the input. It says in the paper that the details about the method are in suppl 1.4 but there are just figures...no details.

My other question is on the reason for using pdbqt with unidock instead of sdf like with Unimol docking V2... It is not very convenient to have to convert to or from pdbqt, with large libraries. Is this because you are using an old autodock scoring function? While Vina accept pdbqt files, it does not use the partial charges in its evaluation. When you do PR docking, do you convert the Unimol docking results to pdbqt files be compatible with Uni-dock or you do not have to because the molecule will already be loaded and then transferred to Unidock? The partial charges could be different once docked, so do you calculate the partial charges of the ligand in the docking pose or you use a generic tool like Meeko that does not care about the pose for converting to pdbqt?

Thanks,
Christian