GPU-Accelerated Flexible Molecular Docking

J Phys Chem B. 2021 Feb 4;125(4):1049-1060. doi: 10.1021/acs.jpcb.0c09051. Epub 2021 Jan 26.

Abstract

Virtual screening is a key enabler of computational drug discovery and requires accurate and efficient structure-based molecular docking. In this work, we develop algorithms and software building blocks for molecular docking that can take advantage of graphics processing units (GPUs). Specifically, we focus on MedusaDock, a flexible protein-small molecule docking approach and platform. We accelerate the performance of the coarse docking phase of MedusaDock, as this step constitutes nearly 70% of total running time in typical use-cases. We perform a comprehensive evaluation of the quality and performance with single-GPU and multi-GPU acceleration using a data set of 3875 protein-ligand complexes. The algorithmic ideas, data structure design choices, and performance optimization techniques shed light on GPU acceleration of other structure-based molecular docking software tools.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computer Graphics
  • Ligands
  • Molecular Docking Simulation
  • Proteins
  • Software*

Substances

  • Ligands
  • Proteins