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New molecular shape descriptors: application in database screening

A C Good1, T J Ewing, D A Gschwend

  • 1School of Pharmacy, Department of Pharmaceutical Chemistry, University of California at San Francisco 94143-0446, USA.

Journal of Computer-Aided Molecular Design
|February 1, 1995
PubMed
Summary
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New geometric descriptors quantify molecular shape similarity for rapid database screening. These methods enhance the identification of potential drug candidates by enriching shape-based searches.

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Molecular shape descriptors are increasingly used for database screening and clustering.
  • These descriptors offer condensed representations for rapid comparison.
  • Efficient methods are needed for shape-based virtual screening.

Purpose of the Study:

  • To introduce novel geometric descriptors and methods for quantifying molecular shape similarity.
  • To evaluate the utility of these descriptors for prescreening shape-based database searches.
  • To compare the performance of these methods against established tools like DOCK.

Main Methods:

  • Development of new geometric descriptors for molecular shape quantification.
  • Application of these descriptors to two distinct biological systems.

Related Experiment Videos

  • Comparison of results with shape-based searches using the DOCK program.
  • Analysis of enriched potential hits in prescreened databases.

    • Main Results:

    • The new descriptors effectively quantify molecular shape similarity.
    • Shape similarity evaluations successfully identified molecules with complementary shapes.
    • Prescreening using these descriptors enriched the number of potential DOCK hits compared to original databases.
    • The study identified limitations in the utility of DOCK prescreens.

    Conclusions:

    • Geometric descriptors offer a valuable approach for rapid molecular shape similarity assessment.
    • These methods can significantly improve the efficiency of shape-based virtual screening.
    • Further development is needed to address limitations and enhance the utility of DOCK prescreens.