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Python package for preparing small molecule for docking

Project description


License PyPI version

The Python package meeko is a new type of package developped and maintained by the Forli lab also at the Center for Computational Structural Biology (CCSB). It provides tools covering other docking aspects not handled by the ADFR software suite. This package provides addtionnal tools for the following docking protocols:

  • Hydrated docking
  • Macrocycles


You need, at a minimum (requirements):

  • Python (>=3.5)
  • Numpy
  • Openbabel (>=3)

Installation (from source)

$ git clone
$ cd Meeko
$ python build install

Quick tutorial

from meeko import MoleculePreparation
from meeko import obutils

input_molecule_file = 'example/BACE_macrocycle/BACE_4.mol2'
mol = obutils.load_molecule_from_file(input_molecule_file)

preparator = MoleculePreparation(merge_hydrogens=True, macrocycle=True, hydrate=True)

output_pdbqt_file = "test_macrocycle_hydrate.pdbqt"

Project details

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