article · Journal of Chemical Information and Modeling · 2023
DSDP: A Blind Docking Strategy Accelerated by GPUs
Yupeng Huang, Hong Zhang, Siyuan Jiang, Dajiong Yue, Xiaohan Lin, Jun Zhang, Yi Qin Gao
Cited by 36Abstract and details only
Abstract
Virtual screening, including molecular docking, plays an essential role in drug discovery. Many traditional and machine-learning-based methods are available to fulfill the docking task. However, the traditional docking methods are normally extensively time-consuming, and their performance in blind docking remains to be improved. Although the runtime of docking based on machine learning is significantly decreased, their accuracy is still limited. In this study, we take advantage of both traditional and machine-learning-based methods and present a method, deep site and docking pose (DSDP), to improve the performance of blind docking. For traditional blind docking, the entire protein is covered by a cube, and the initial positions of ligands are randomly generated in this cube. In contrast, DSDP can predict the binding site of proteins and provide an accurate searching shape and initial positions for further conformational sampling. The sampling task of DSDP makes use of the score function and a similar but modified searching strategy of AutoDock Vina, accelerated by implementation in GPUs. We systematically compare its performance in redocking, blind docking, and virtual screening tasks with state-of-the-art methods, including AutoDock Vina, GNINA, QuickVina, SMINA, and DiffDock. In the blind docking task, DSDP reaches a 29.8% top-1 success rate (root-mean-squared deviation < 2 Å) on an unbiased and challenging test dataset with 1.2 s wall-clock computational time per system. Its performances on the DUD-E dataset and the time-split PDBBind dataset used in EquiBind, TANKBind, and DiffDock are also evaluated, presenting a 57.2 and 41.8% top-1 success rate with 0.8 and 1.0 s per system, respectively.
Cite this paper
Huang, Y., Zhang, H., Jiang, S., Yue, D., Lin, X., Zhang, J., & Gao, Y. Q. (2023). DSDP: A Blind Docking Strategy Accelerated by GPUs. Journal of Chemical Information and Modeling, 63(14), 4355–4363. https://doi.org/10.1021/acs.jcim.3c00519
Huang, Yupeng, et al. “DSDP: A Blind Docking Strategy Accelerated by GPUs.” Journal of Chemical Information and Modeling, vol. 63, no. 14, 2023, pp. 4355–63, https://doi.org/10.1021/acs.jcim.3c00519.
Huang, Yupeng, Hong Zhang, Siyuan Jiang, Dajiong Yue, Xiaohan Lin, Jun Zhang, and Yi Qin Gao. 2023. “DSDP: A Blind Docking Strategy Accelerated by GPUs.” Journal of Chemical Information and Modeling 63 (14): 4355–63. https://doi.org/10.1021/acs.jcim.3c00519.
Huang, Y. et al. (2023) ‘DSDP: A Blind Docking Strategy Accelerated by GPUs’, Journal of Chemical Information and Modeling, 63(14), pp. 4355–4363. Available at: https://doi.org/10.1021/acs.jcim.3c00519.
@article{huang2023dsdp,
title = {{DSDP: A Blind Docking Strategy Accelerated by GPUs}},
author = {Huang, Yupeng and Zhang, Hong and Jiang, Siyuan and Yue, Dajiong and Lin, Xiaohan and Zhang, Jun and Gao, Yi Qin},
journal = {Journal of Chemical Information and Modeling},
volume = {63},
number = {14},
pages = {4355--4363},
year = {2023},
doi = {10.1021/acs.jcim.3c00519}
}Made from the index record. Check names, capitalisation and page numbers against the paper. Need another style? AI for Research has over 10,000.