# Meeko: interface for AutoDock
[](https://shields.io/)
[](https://pypi.python.org/pypi/meeko/)
[](https://meeko.readthedocs.io/en/release/?badge=release)
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](https://forlilab.org/) at the
[Center for Computational Structural Biology (CCSB)](https://ccsb.scripps.edu)
at [Scripps Research](https://www.scripps.edu/).
## Documentation
The docs are hosted on [meeko.readthedocs.io](https://meeko.readthedocs.io/en/release)
## Reporting bugs
Please check if a similar bug has been reported and, if not, [open an issue](https://github.com/forlilab/Meeko/issues).
## Installation
Visit the docs for a more complete description. One option is conda or mamba:
```bash
micromamba install meeko
```
or from PyPI:
```bash
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](https://meeko.readthedocs.io/en/release) for more information.
Parameterizing a ligand and writing a PDBQT file:
```bash
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.
```bash
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:
```bash
mk_export.py vina_results.pdbqt -j my_receptor.json -s lig_docked.sdf -p rec_docked.pdb
```
Raw data
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"description": "# Meeko: interface for AutoDock\n\n[](https://shields.io/)\n[](https://pypi.python.org/pypi/meeko/)\n[](https://meeko.readthedocs.io/en/release/?badge=release)\n\nMeeko prepares the input for AutoDock and processes its output.\nIt is developed alongside AutoDock-GPU and AutoDock-Vina.\nMeeko parameterizes both small organic molecules (ligands) and proteins\nand nucleic acids (receptors).\n\nMeeko is developed by the [Forli lab](https://forlilab.org/) at the\n[Center for Computational Structural Biology (CCSB)](https://ccsb.scripps.edu)\nat [Scripps Research](https://www.scripps.edu/).\n\n\n## Documentation\n\nThe docs are hosted on [meeko.readthedocs.io](https://meeko.readthedocs.io/en/release)\n\n\n## Reporting bugs\n\nPlease check if a similar bug has been reported and, if not, [open an issue](https://github.com/forlilab/Meeko/issues).\n\n\n## Installation\n\nVisit the docs for a more complete description. One option is conda or mamba:\n\n```bash\nmicromamba install meeko\n```\n\nor from PyPI:\n\n```bash\npip install meeko\n```\n\n## Usage\n\nMeeko exposes a Python API to enable scripting. Here we share very minimal examples\nusing the command line scripts just to give context.\nPlease visit the [meeko.readthedocs.io](https://meeko.readthedocs.io/en/release) for more information.\n\nParameterizing a ligand and writing a PDBQT file:\n```bash\nmk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt\n```\n\nParameterizing a receptor with a flexible sidechain and writing a PDBQT file\nas well as a JSON file that stores the entire receptor datastructure. In this\nexample, the `-o` option sets the output base name, `-j` triggers writing the\n.json file, `-p` triggers writting the .pdbqt file, and `-f` makes residue\n42 in chain A flexible.\n\n```bash\nmk_prepare_receptor.py -i nucleic_acid.cif -o my_receptor -j -p -f A:42\n```\n\nFinally, converting docking results to SDF for the ligand, and PDB for the\nreceptor with updated sidechain positions:\n\n```bash\nmk_export.py vina_results.pdbqt -j my_receptor.json -s lig_docked.sdf -p rec_docked.pdb\n```\n",
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