Yes, We can Perform Molecular Docking of these molecules using Autodock

You can use FastDRH server for docking in easy way and MMPBSAGBSA also available there.

While AutoDock is primarily designed for protein-ligand docking, it's not the ideal tool for docking microRNA (miRNA) and mRNA.

Do check out this article (https://www.biorxiv.org/content/10.1101/2023.07.28.551063v3)

Yes, We can Perform Molecular Docking of these molecules using Autodock