There have been various tools and methods developed to assist with setup, docking and analysis with AutoDock and Vina. A collection of such resources for legacy AutoDock4.2.6 and Vina v1.1.2 can be found at:

https://autodock.scripps.edu/resources/

More recently, the Forli lab have been developing command-line tools and Python bindings for interoperability with RDKit, SQLite and other modern cheminformatics utility tools:

Meeko: https://github.com/forlilab/Meeko

Meeko streamlines the processing of ligand coordinate files for use in docking. It reads an RDKit molecule object and writes a PDBQT string (or file) for AutoDock-Vina and AutoDock-GPU. It converts the docking output to RDKit molecules and SD files, without loss of bond orders.

Ringtail: https://github.com/forlilab/Ringtail

Ringtail reads collections of Docking Log Files (DLG) or PDBQT results from virtual screenings performed with AutoDock-GPU and AutoDock-Vina, respectively, and deposits them into a SQLite database. It then allows for the filtering of results with numerous pre-defined filtering options, generation of a simple result scatterplot, export of molecule SDFs, and export of CSVs of result data. Result file parsing is parallelized across the user’s CPU.

For the latest developments and information, please visit the linked project Github pages or our new navigation & resource site at https://rsd3.scripps.edu/.