biocheming / uni-dock

Uni-Dock: a GPU-accelerated molecular docking program

DeepModeling

Introduction

Uni-Dock

Uni-Dock is a GPU-accelerated molecular docking program developed by DP Technology. It supports various scoring functions including vina, vinardo, and ad4. Uni-Dock achieves more than 1000-fold speed-up on V100 GPU with high-accuracy compared with the AutoDock Vina running in single CPU core. The paper has been accepted by JCTC (doi: 10.1021/acs.jctc.2c01145).

Check this subfolder for instructions on installing Uni-Dock.

UniDockTools

UniDockTools is a python package developed to handle the inputs and outputs of Uni-Dock. In the future, UniDockTools will support more input formats and scoring functions. We hope it could be an easy-to-use virtual screening workflow for all users.

Check this subfolder for more details.

Changelog

• 2023-08-21: Upload source codes of Uni-Dock.
• 2023-08-14: Add unidock_tools to support SDF format input for vina and vinardo scoring functions.

Citation

If you used Uni-Dock in your work, please cite:

Yu, Y., Cai, C., Wang, J., Bo, Z., Zhu, Z., & Zheng, H. (2023). Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening. Journal of Chemical Theory and Computation. https://doi.org/10.1021/acs.jctc.2c01145

Tang, S., Chen, R., Lin, M., Lin, Q., Zhu, Y., Ding, J., ... & Wu, J. (2022). Accelerating autodock vina with gpus. Molecules, 27(9), 3041. DOI 10.3390/molecules27093041

J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings, J. Chem. Inf. Model. (2021) DOI 10.1021/acs.jcim.1c00203

O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J. Comp. Chem. (2010) DOI 10.1002/jcc.21334