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FOUNDATION: a program to retrieve all possible structures containing a user-defined minimum number of matching query

C M Ho1, G R Marshall

  • 1Center for Molecular Design, Washington University, St. Louis, MO 63130.

Journal of Computer-Aided Molecular Design
|February 1, 1993
PubMed
Summary

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This study introduces a novel program for searching 3D structural databases. It retrieves structures matching user-defined chemical and environmental constraints, aiding in the discovery of new drug candidates.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Accurate 3D structural data is crucial for understanding molecular interactions.
  • Identifying novel compounds with specific binding affinities requires efficient database searching tools.

Purpose of the Study:

  • To present a new computational program for searching three-dimensional structural databases.
  • To enable the retrieval of structures based on user-defined chemical and spatial constraints.

Main Methods:

  • The program accepts queries comprising 3D coordinates of atoms and/or bonds.
  • It incorporates numerous constraints, including atom type, occupancy, RMS-fit, and active site accessibility.
  • Queries were tested using thermolysin-inhibitor complex data against the Cambridge Crystallographic Database.

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Main Results:

  • The program successfully retrieved compounds satisfying various query aspects, including active site fitting.
  • Demonstrated the ability to identify structures with specific pharmacophoric elements and environmental conditions.
  • Validated the program's utility in a practical drug discovery context.

Conclusions:

  • The developed program offers a powerful method for exploring 3D structural databases.
  • It facilitates the identification of potential drug candidates by matching structural and chemical properties.
  • Combining partial query matches can lead to the generation of unique compounds with targeted affinities.