Biological and Medicinal Chemistry

Vina-GPU 2.0:further accelerating AutoDock Vina and its derivatives with GPUs

Authors

  • Ji Ding Nanjing University of Posts and Telecommunications ,
  • Shidi Tang Nanjing University of Posts and Telecommunications ,
  • Lingyue Wang Nanjing University of Posts and Telecommunications ,
  • Qinqin Huang Nanjing University of Posts and Telecommunications ,
  • Haifeng Hu Nanjing University of Posts and Telecommunications ,
  • Ming Ling Southeast University ,
  • Jiansheng Wu Nanjing University of Posts and Telecommunications

Abstract

Modern drug discovery typically faces large virtual screens from huge compound databases where multiple docking tools are involved for meeting various real scenes or improving the precision of virtual screens. Among these tools, AutoDock Vina and its numerous derivatives are the most popular and have become the standard pipeline for molecular docking in modern drug discovery. Our recent Vina-GPU method realized 14-fold acceleration against AutoDock Vina on a piece of NVIDIA RTX 3090 GPU in one virtual screening case. Further speedup of AutoDock Vina and its derivatives with GPUs is beneficial to systematically push their popularization in large-scale virtual screens due to their high benefit-cost ratio and easy operation for users. Thus, we proposed the Vina-GPU 2.0 method to further accelerate AutoDock Vina and the most common derivatives with new docking algorithms (QuickVina 2 and QuickVina-W) with GPUs. Caused by the discrepancy of their docking algorithms, our Vina-GPU 2.0 adopts different GPU acceleration strategies. In virtual screening for two hot protein kinase targets RIPK1 and RIPK3 from the DrugBank database, our Vina-GPU 2.0 reaches an average of 65.6-fold,1.4-fold and 3.6-fold docking acceleration against the original AutoDock Vina, QuickVina 2 and QuickVina-W while ensuring their comparable docking accuracy. In addition, we develop a friendly and installation-free graphical user interface (GUI) tool for their convenient usage. The codes and tools of Vina-GPU 2.0 are freely available at https://github.com/DeltaGroupNJUPT/Vina-GPU-2.0, coupled with explicit instructions and examples.

Content

Thumbnail image of Vina-GPU2.0.pdf

Supplementary material

Thumbnail image of Supplementary_Data.7z
Docking scores for our Vina-GPU 2.0 and baseline methods
Supplementary data includes the docking scores of all 9125 molecules for our Vina-GPU 2.0 and baseline methods on RIPK1 and RIPK3.