Uni-Dock: A GPU-Accelerated Docking Program Enables Ultra-Large Virtual Screening

19 July 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Molecular docking, a structure-based virtual screening method, is a reliable tool to enrich bio-active molecules from molecular databases. With the expansion of the size of virtual libraries, the speed of existing molecular docking programs becomes less than adequate to meet the demand for screening ultra-large libraries containing tens of millions or billions of molecules. Here we propose Uni-Dock, a GPU-accelerated molecular docking program supporting various scoring functions including vina, vinardo, and ad4, which achieves more than 1000-fold speed-up with high accuracy compared with the AutoDock Vina single-CPU-core version, outperforming reported GPU-accelerated docking programs including AutoDock-GPU and Vina-GPU. Uni-Dock divides molecules into batches and simultaneously docks batches of molecules using hundreds of concurrent threads for each molecule. The data flow between GPU and CPU is optimized to eliminate CPU hotspots and maximize GPU utility. We demonstrate and analyze the improved performance of Uni-Dock on the CASF-2016 and DUD-E datasets and recommend three combinations of hyperparameters corresponding to different docking scenarios. To demonstrate Uni-Dock's capability on routinely screening ultra-large libraries, we performed hierarchical virtual screening experiments with Uni-Dock on Enamine Diverse REAL drug-like set containing 38.2 million molecules to a popular target KRAS G12D in 12 hours using 100 NVIDIA V100 GPUs.


Molecular Docking
Virtual Screening
GPU Acceleration


Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.