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 that also interfaces with RDKit.
Command line scripts#
There are two scripts to write the input files for docking,
mk_prepare_ligand.py and mk_prepare_receptor.py, and one script to
convert docking output files mk_export.py.
Running a docking#
To run a docking, more packages are required besides Meeko. At a minimum, either Vina or AutoDock-GPU are needed to run the actual docking.
Docking for GPUs. Implements the AutoDock4.2 scoring function. Command line executable only.
Docking on CPUs. Implements Vina and AutoDock4.2 scoring functions. Has a Python API and command line executable.
Store and analyze virtual screening with SQLite. Has a Python API and command line scripts.
Check the tutorials page to learn about using meeko with these other packages to run molecular docking and virtual screening.