Biological and Medicinal Chemistry

Accelerating AutoDock VINA with GPUs

Authors

  • Tang Shidi Nanjing University of Posts and Telecommunications ,
  • Chen Ruiqi VeriMake Research, Nanjing Renmian Integrated Circuit Technology Co., Ltd. ,
  • Lin Mengru VeriMake Research, Nanjing Renmian Integrated Circuit Technology Co., Ltd. ,
  • Lin Qingde Southeast University ,
  • Zhu Yanxiang VeriMake Research, Nanjing Renmian Integrated Circuit Technology Co., Ltd. ,
  • Ding Ji Nanjing University of Posts and Telecommunications ,
  • Wu Jiansheng Nanjing University of Posts and Telecommunications ,
  • Hu Haifeng Nanjing University of Posts and Telecommunications ,
  • Ling Ming Southeast University

Abstract

AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern drug discovery is facing the most common scenario on large virtual screening of drug hits from huge compound databases. Due to the seriality characteristic of the AutoDock Vina algorithm, there is no successful report on its parallel acceleration with GPUs. Current acceleration of AutoDock Vina typically relies on the stack of computing power as well as the allocation of resource and tasks, such as the VirtualFlow platform. The vast resource expenditure and the high access threshold of users will seriously limit the popularity of AutoDock Vina and the flexibility of usage in modern drug discovery. Thus, the design of a new method for accelerating AutoDock Vina with GPUs is greatly needed for reducing the investment for large virtual screens, and also for a wide application in large-scale virtual screening on personal computers, station servers orcloud computing etc. Our proposed method Vina-GPU greatly raises the number of initial random conformations and reduces the search depth of each lane, and then a heterogeneous OpenCL implementation was developed to realize its parallel acceleration leveraging thousands of GPU cores. Large benchmarks show that Vina-GPU reaches a maximum of 403- fold docking acceleration against the original AutoDock Vina while ensuring their comparable docking accuracy, indicating its potential of pushing the popularization of AutoDock Vina in large virtual screens. The Vina-GPU code and tool can be freely available at http:// www.noveldelta.com/Vina_GPU for academic usage.

Version notes

A new version of Vina-GPU paper

Content

Thumbnail image of Vina_GPU.pdf

Supplementary material

Thumbnail image of Vina_GPU_SI.pdf
Vina-GPU Support Information
the support information of the manuscript "Accelerate AutoDock Vina with GPUs"