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Related Experiment Videos

Spresso: an ultrafast compound pre-screening method based on compound decomposition.

Keisuke Yanagisawa1,2, Shunta Komine2,3, Shogo D Suzuki2,3

  • 1Department of Computer Science, School of Computing, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.

Bioinformatics (Oxford, England)
|April 4, 2017
PubMed
Summary

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A new method, Spresso, dramatically speeds up virtual screening by analyzing compound fragments. This rapid pre-screening protocol accelerates the evaluation of millions of compounds for drug discovery.

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • The increasing number of protein structures and compounds necessitates efficient virtual screening methods.
  • Current structure-based virtual screening methods, like docking simulations, are computationally intensive.
  • Existing pre-screening methods are not fast enough to handle large compound libraries (≥10 million).

Purpose of the Study:

  • To develop a novel, rapid pre-screening protocol for structure-based virtual screening.
  • To significantly enhance the computational speed of evaluating large compound libraries.

Main Methods:

  • Introducing Spresso (Speedy PRE-Screening method with Segmented cOmpounds), a docking-based pre-screening protocol.
  • Utilizing common structural fragments of compounds to reduce the number of unique entities for evaluation.

Related Experiment Videos

  • Implementing the protocol in C++ and Python for efficient computation.

    • Main Results:

    • Spresso achieves a speed increase of approximately 200-fold compared to conventional pre-screening methods.
    • The fragment-based approach effectively reduces the computational burden of virtual screening.
    • The protocol is available as open-source software.

    Conclusions:

    • Spresso offers a highly efficient solution for pre-screening large compound libraries in drug discovery.
    • The method addresses the computational limitations of current virtual screening techniques.
    • The open-source availability promotes wider adoption and further development in the field.