Python scripts to automate molecular docking

Installation

pip install moldock

or the latest version

pip install git+https://github.com/ci-lab-cz/docking-scripts.git

Dependencies

from conda

conda install -c conda-forge python=3.9 numpy=1.20 rdkit scipy dask distributed vina

from pypi

pip install meeko

Installation of gnina is described at https://github.com/gnina/gnina

Description

Fully automatic pipeline for molecular docking.

• two major scripts vina_dock and gnina_dock which support docking with vina and gnina (gnina also supports smina and its custom scoring functions)
• can be used as command line scripts or imported as a python module
• support distributed computing using dask library
• if calculation was interrupted it can be continued by invoking the same command, but everything except output DB may be omitted (these will be ignored nevertheless if DB exists) because all data is stored in DB at the first call
• get_sdf_from_db is used to extract data from output DB

Pipeline:

• input SMILES are converted in 3D by RDKit embedding, if input is 3D structures in SDF their conformations wil be taken as starting without changes.
• ligands are protonated by chemaxon at pH 7.4 and the most stable tautomers are generated (optional, requires a Chemaxon license)
• molecules are converted in PDBQT format
• docking with vina/gnina
• output poses are converted in MOL format and stored into output DB along with docking scores

Example

Both scripts vina_dock and gnina_dock have similar common arguments.

Docking using input SMILES, prepared protein and config files. Ligands will not be protonated with Chemaxon, so their supplied charged states will be used. 4 CPU cores will be used. When docking will finish an SDF will be created with top docking poses for each ligand.

vina_dock -i input.smi -o output.db -p protein.pdbqt -s vina_config --no_protonation -c 4 --sdf 

Retrieve second poses for compounds mol_id_1 and mol_id_2 with their docking scores in SDF format:

get_sdf_from_db -i output.db -o out.sdf -d mol_id_1,mol_id_4 --fields docking_score --poses 2 

Instead of a comma-separated list of ids a text file can be supplied as an argument -d.

Retrieve top poses for compounds with docking score less then -10:

get_sdf_from_db -i output.db -o out.sdf --fields docking_score --poses 1 --add_sql 'docking_score < -10' 

Use as a Python module

from moldock import vina_dock

vina_dock.iter_docking(dbname='output.db', receptor_pdbqt_fname='protein.pdbqt', protein_setup='vina_config.txt', protonation=False, exhaustiveness=8, seed=-1, n_poses=10, ncpu=4)

Changelog

0.1.2

• (bugfix) docking of macrocycles is rigid (in future may be changed)

Licence

CC BY-NC-SA 4.0