meeko 0.7.1

Python package for preparing small molecule for docking

Meeko: interface for AutoDock

Meeko prepares the input for AutoDock and processes its output. It is developed alongside AutoDock-GPU and AutoDock-Vina. Meeko parameterizes both small organic molecules (ligands) and proteins and nucleic acids (receptors).

Meeko is developed by the Forli lab at the Center for Computational Structural Biology (CCSB) at Scripps Research.

Documentation

The docs are hosted on meeko.readthedocs.io

Reporting bugs

Please check if a similar bug has been reported and, if not, open an issue.

Installation

Visit the docs for a more complete description. One option is conda or mamba:

micromamba install meeko

or from PyPI:

pip install meeko

Usage

Meeko exposes a Python API to enable scripting. Here we share very minimal examples using the command line scripts just to give context. Please visit the meeko.readthedocs.io for more information.

Parameterizing a ligand and writing a PDBQT file:

mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt

Parameterizing a receptor with a flexible sidechain and writing a PDBQT file as well as a JSON file that stores the entire receptor datastructure. In this example, the -o option sets the output base name, -j triggers writing the .json file, -p triggers writting the .pdbqt file, and -f makes residue 42 in chain A flexible.

mk_prepare_receptor.py -i nucleic_acid.cif -o my_receptor -j -p -f A:42

Finally, converting docking results to SDF for the ligand, and PDB for the receptor with updated sidechain positions:

mk_export.py vina_results.pdbqt -j my_receptor.json -s lig_docked.sdf -p rec_docked.pdb