Introduction

To make Uni-Dock more user-friendly and compatible with more ligand input formats and scoring functions, we have introduced UniDockTools. Now, UniDockTools has two new functions:

• support SDF format

  UniDockTools has a built-in molecular preparation function, so users can use the original SDF files as the input for ligand files, provided that the compound structures in the original SDF files are reasonable.

• support gnina CNNscores

  Gnina CNNscores is a scoring function known for its outstanding screening performance. UniDockTools offers a workflow for Uni-Dock to generate ligand conformations and subsequently re-score them using Gnina CNNscores.

Installation

1. Install Uni-Dock and UniDockTools

To install UniDock, please follow Uni-Dock installation docs.

To install UniDockTools, please execute the following command in Uni-Dock/unidock_tools directory:

python setup.py install

2. Install MGLTools

If you want ro run Uni-Dock with receptor in PDB format, you need to install mgltools. Please use the command below:

conda create -n mgltools mgltools -c bioconda

3. Install gnina

If you want to use gnina CNNscores to rescore docking poses, you should install gnina.

• binary install gnina by download binary file from gnina's release page
• source code install gnina from source code according to gnina installation document

Usage

By installing UniDockTools, you have obtained an executable file called Unidock (note the capitalized U), which you can use just like running unidock.

Input ligands with origin sdf format

Unidock --receptor receptor.pdbqt --gpu_batch ligand1.sdf ligand2.sdf --center_x 9 --center_y -5 --center_z -5 --size_x 20 --size_y 20 --size_z 20 --search_mode balance --dir .

Use gnina CNNscores to rescore docking poses

Unidock --receptor receptor.pdbqt --gpu_batch ligand1.sdf ligand2.sdf --scoring gnina --center_x 9 --center_y -5 --center_z -5 --size_x 20 --size_y 20 --size_z 20 --search_mode balance --dir .

Use ligands structure as bias

Unidock --receptor receptor.pdbqt --gpu_batch ligand1.sdf ligand2.sdf --reference ref1.sdf ref2.sdf --scoring gnina --center_x 9 --center_y -5 --center_z -5 --size_x 20 --size_y 20 --size_z 20 --search_mode balance --dir .

Other usage

To lower users' learning cost, the other usage methods of Unidock remain consistent with the usage of unidock.

License

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