Python package for preparing small molecule for docking
Project description
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
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