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. ,
  • 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-used docking tools in the early stage of modern drug discovery. It uses a Monte-Carlo based iterated search method and multithreading parallelism scheme on multicore machines to improve docking accuracy and speed. However, virtual screening from huge compound databases is common for modern drug discovery, which puts forward a great demand for higher docking speed of AutoDock VINA. Therefore, we propose a fast method VINA-GPU, which expands the Monte-Carlo based docking lanes into thousands of ones coupling with a largely reduced number of search steps in each lane. Furthermore, we develop a heterogeneous OpenCL implementation of VINA-GPU that leverages thousands of computational cores of a GPU, and obtains a maximum of 403-fold acceleration on docking runtime when compared with a quad-threaded AutoDock VINA implementation. In addition, a heuristic function was fitted to determine the proper size of search steps in each lane for a convenient usage. The VINA-GPU code can be freely available at https://github.com/DeltaGroupNJUPT/Vina-GPU for academic usage.

Version notes

Fixed some typos and url link of source code

Content

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