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DOVIS: an implementation for high-throughput virtual screening using AutoDock.

Shuxing Zhang1, Kamal Kumar, Xiaohui Jiang

  • 1Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. shuzhang@mdanderson.org

BMC Bioinformatics
|February 29, 2008
PubMed
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DOVIS is a new application that streamlines molecular docking for drug discovery. It enables efficient, automated, and parallel screening of millions of compounds using high-performance computing clusters.

Area of Science:

  • Computational Chemistry
  • Drug Discovery
  • Bioinformatics

Background:

  • Molecular docking is crucial for drug discovery, reducing the chemical compounds needing investigation.
  • Screening millions of compounds requires high-performance computing (HPC) for efficiency.
  • Integrating HPC systems for virtual screening presents technical challenges.

Purpose of the Study:

  • To develop an integrated and automated system for large-scale virtual screening.
  • To address the computational challenges of high-throughput virtual screening.
  • To provide an efficient solution for AutoDock users on Linux clusters.

Main Methods:

  • Developed DOVIS, an application utilizing AutoDock (version 3) as the docking engine.
  • Implemented parallel processing on a Linux cluster for high-throughput screening.

Related Experiment Videos

  • Integrated a graphical user interface for input specification and results visualization.

    • Main Results:

    • DOVIS efficiently docks millions of small molecules (ligands) to receptors.
    • Achieved screening rates of 500 to 1,000 compounds per processor per day.
    • Fully automated docking sessions with integrated queuing system and queryable results.

    Conclusions:

    • DOVIS simplifies complex, large-scale virtual screening processes.
    • Offers a convenient and efficient solution for AutoDock users on HPC platforms.
    • Facilitates high-throughput virtual screening in drug discovery research.