Introduction

Molecular docking is a method for rapidly evaluating the binding affinity of candidate molecules to protein receptor through computational simulations. Due to its high throughput, fast speed, and good enrichment capabilities, it is widely used in the early stages of drug design for virtual screening to find potential active molecules in large-scale molecular libraries.

Uni-Dock, developed by DPTechnology, is a GPU-accelerated molecular docking engine that can complete virtual screening tasks on GPUs at a speed over 3000X than a single CPU. In June 2023, Uni-Dock was featured as a cover article in the Journal of Chemical Theory and Computation journal[1]. In the latest version, Uni-Dock v1.1, the virtual screening speed can reach 0.03 s/ligand. This means that with a cluster of 100 GPUs, you can complete the virtual screening of 100 million molecules in just 8.3 hours.

Uni-Dock is an open-source software incubated by the DeepModeling community and is available under the LGPL license. Anyone can access the latest version of Uni-Dock at https://github.com/dptech-corp/Uni-Dock.

This app is based on the latest version of Uni-Dock and aims to simplify the installation and deployment process while leveraging Bohrium's massive computational resources to provide end-to-end, fast virtual screening services.

The speed of Uni-Dock for one-ligand molecular docking and multi-ligand virtual screening are shown below:

Best Practice

Example 1

• Inputs：

  • protein
  • ligand
  • box_parameters: {center_x: -16, center_y: -17, center_z: -26, size_x: 25, size_y: 25, size_z: 25}

• Outputs(For reference only, the scores may not be the same)：

  • Result files in outputs folder.
  • Score table:

  

Reference

[1] Yu Y, Cai C, Wang J, et al. Uni-dock: Gpu-accelerated docking enables ultralarge virtual screening[J]. Journal of chemical theory and computation, 2023, 19(11): 3336-3345.

How to Cite

Uni-Dock

@article{yu2023uni,
  title={Uni-dock: Gpu-accelerated docking enables ultralarge virtual screening},
  author={Yu, Yuejiang and Cai, Chun and Wang, Jiayue and Bo, Zonghua and Zhu, Zhengdan and Zheng, Hang},
  journal={Journal of chemical theory and computation},
  volume={19},
  number={11},
  pages={3336--3345},
  year={2023},
  publisher={ACS Publications}
}