High-throughput virtual molecular docking with AutoDockCloud

Sally R. Ellingson, Jerome Baudry

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


Virtual molecular docking is a computational method used in computer-aided drug discovery that calculates the binding affinity of a small molecule drug candidate to a target protein. High-throughput virtual screenings calculate the binding affinities for a large number of molecules at once and ranks potential drug candidates to greatly reduces the time and cost of suggesting new potential pharmaceuticals. This high-throughput screening is a task parallel process and therefore well-suited for distributed computing. In this study, we use the open source Hadoop framework implementing the MapReduce paradigm for distributed computing on a cloud platform and the widely used molecular docking program, AutoDock. The initial implementation of AutoDockCloud showed a speed-up of 450 on Kandinsky, a cloud computer located at Oak Ridge National Laboratory. Further modifications show promise for a greater speed-up of large chemical library screenings and also incorporates and distributes the pre-docking procedures.

Original languageEnglish
Pages (from-to)907-916
Number of pages10
JournalConcurrency Computation Practice and Experience
Issue number4
StatePublished - Mar 25 2014


  • Hadoop
  • cloud computing
  • drug discovery
  • high-throughput virtual docking

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Software
  • Computer Science Applications
  • Computer Networks and Communications
  • Computational Theory and Mathematics


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