dinc-ensemble: docking incrementally to an ensemble of receptors

dinc-ensemble is a toolkit for molecular docking. It provides a meta-docking incremental docking approach with an ensemble of input receptors. Currently implemented docking engine is Vina, but can be extended to other docking approaches.

Install with mamba

• Conda install

1. Pull the github repo.

2. Mamba install (start from this directory).

mamba env create --file ./installation/environment.yml
conda activate dinc-ensemble
pip install -e . 

3. Test the installation.

• Run tests

pytest dinc_ensemble

• Run the CLI

dinc-ensemble --help

Check more details for installing dinc-ensemble here.

Run dinc-ensemble CLI

• Try running the command-line interface.

dinc-ensemble dock {LIGAND_PATH} [{RECEPTOR_PATH}] {OUTPUT_DIR}

• 1OHR xample:

dinc-ensemble dock ./sample-data/small_tests_data/1ohr_ligand.mol2 ./sample-data/small_tests_data/1ohr_receptor.pdb ./tmp_test_out --replica-num 1

Folder structure

• ./dinc_ensemble The python package with all the modules.

• ./installation Different install options and files including conda/mamba install, pulling or building a docker image.

• ./tutorial-notebooks Jupyter notebook tutorials showcasing dinc-ensemble use as a python package and different modules.

• ./sample-data Contains some minimal-example data that can be used to run and test dinc-ensemble.