unidock_tools

Introduction

Based on Uni-Dock, we have developed several user-friendly and enhanced applications in Uni-Dock Tools. Main features are:

• Individual receptor and ligand preparation applications

• End-to-End Uni-Dock pipeline starting from common formats receptor and ligands

• Multi-Conformation Docking (mcdock): See MCDock Introduction

Installation

Dependency

• Uni-Dock
• Python >= 3.6
• RDKit
• networkx
• MGLTools, if you want to use AD4 scoring function in Uni-Dock
• mcdock dependencies, see MCDock Installation

Install

• pip install .

Docker

We provide docker image with all the dependencies installed. You can pull the docker image from the following link:

docker pull dptechnology:unidocktools

And run the docker container using the following command:

docker run --gpus 0 -it -v $(pwd):/workpsace unidocktools:v1.0.0 cd /workspace && <Your command>

Applications

1. ProteinPrep

Prepare and Convert PDB-format receptor protein into PDBQT format

unidocktools proteinprep -r <Input PDB File> -o <Output PDBQT File Path>

2. LigandPrep

Prepare ligands to be used in Uni-Dock

unidocktools ligandprep -l <Input SDF ligand files, use commas to seperate> -sd <output_dir> -bs <batch_size=1200>

or write a list of ligand files in a text file and use the following command:

unidocktools ligandprep -i <Txt File> -sd <output_dir>

3. Uni-Dock Pipeline

End-to-End pipeline to run Uni-Dock with common-format receptor and ligands

unidocktools unidock_pipeline -r <receptor file> -l <ligand files> -sd <output_dir> -cx <center_x> -cy <center_y> -cz <center_z>

Parameters

IO Parameters

• -r, --receptor: Path to the receptor file in PDBQT format.
• -l, --ligands: Path to the ligand file in SDF format. For multiple files, separate them by commas.
• -i, --ligand_index: A text file containing the path of ligand files in sdf format.
• -sd, --savedir: Save directory (default: 'unidock_results').

Pocket Parameters

• -cx, --center_x: X-coordinate of the docking box center.
• -cy, --center_y: Y-coordinate of the docking box center.
• -cz, --center_z: Z-coordinate of the docking box center.
• -sx, --size_x: Width of the docking box in the X direction (default: 22.5).
• -sy, --size_y: Width of the docking box in the Y direction (default: 22.5).
• -sz, --size_z: Width of the docking box in the Z direction (default: 22.5).

Docking Parameters

• -sf, --scoring_function: Scoring function (default: 'vina').
• -ex, --exhaustiveness: exhaustiveness (default: 128).
• -ms, --max_step: max_step (default: 20)
• -nm, --num_modes: Number of poses to output (default: 3).
• -rs, --refine_step: Refine step (default: 3).
• -topn, --topn: Top N pose results to keep (default: 100).

Others

• -wd, --workdir: Working directory (default: 'unidock_workdir').
• -bs, --batch_size: Batch size (default: 20).

4. Multi-Conformation Docking (mcdock)

See MCDock Usage

License

This project is licensed under the terms of Apache license 2.0. See LICENSE for additional details.