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.

Original languageEnglish (US)
Pages (from-to)1049-1060
Number of pages12
JournalJournal of Physical Chemistry B
Issue number4
StatePublished - Feb 4 2021

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry


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