Meeko: interface for AutoDock

Parameterization of molecules

Meeko assigns parameters to small organic molecules, referred to as ligands, and to proteins and nucleic acids, referred to as receptors. Parameterization includes assigning atom types, partial charges, setting bonds as rotatable, and making receptor sidechains flexible.

Prepare input and convert output

Meeko writes the input PDBQT files (or strings in Python) for AutoDock-Vina and AutoDock-GPU, and exports docking results in SDF format for ligands and in PDB format for receptor.

Python API

Meeko is written in Python and exposes functions and classes that operate on RDKit molecules for the ligands, leveraging RDKit’s popularity to facilitate integration with external software. Command line scripts are also available.

AutoDock ecosystem

To run a docking, more packages are required besides Meeko:

• AutoDock-Vina

• AutoDock-GPU

• Ringtail