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Large-Scale Docking in the Cloud.

Benjamin I Tingle1, John J Irwin1

  • 1Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, California 94158-2330, United States.

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|April 18, 2023
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Summary
This summary is machine-generated.

AWS-DOCK enables efficient, large-scale molecular docking in the cloud. This approach screens billions of molecules cost-effectively, accelerating drug discovery by leveraging scalable cloud computing resources.

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Area of Science:

  • Computational Chemistry
  • Drug Discovery
  • Bioinformatics

Background:

  • Molecular docking is crucial for identifying new drug candidates by analyzing protein structures.
  • Screening vast chemical spaces is computationally intensive and challenging for traditional in-house clusters.

Purpose of the Study:

  • To develop and present AWS-DOCK, a protocol for executing UCSF DOCK within Amazon Web Services (AWS) cloud infrastructure.
  • To enable efficient and cost-effective screening of billions of molecules for drug discovery.

Main Methods:

  • Leveraging AWS cloud resources for scalable and cost-efficient computation.
  • Utilizing a low-molecule-cost docking engine for high-throughput screening.
  • Benchmarking the system by docking 50 million molecules against the DRD4 receptor.

Main Results:

  • Screening of 50 million molecules against the DRD4 receptor achieved an average CPU time of approximately 1 second per molecule.
  • Observed up to 3-fold cost variations across different AWS availability zones.
  • Docking 4.5 billion lead-like molecules was completed in approximately one week on AWS for around $25,000, significantly less than purchasing new hardware.

Conclusions:

  • AWS-DOCK offers a scalable and economical solution for large-scale molecular docking, overcoming the limitations of in-house computing.
  • The protocol is presented with clear steps and is potentially adaptable for other molecular docking programs.
  • The necessary tools for AWS-DOCK are freely available, with DOCK 3.8 also free for academic use, promoting accessibility in research.