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DBMAKER: a set of programs to generate three-dimensional databases based upon user-specified criteria

C M Ho1, G R Marshall

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

Journal of Computer-Aided Molecular Design
|February 1, 1995
PubMed
Summary
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DBMAKER, combined with CONCORD, creates 3D structural databases from user-defined constraints. This program efficiently generates and manages random compounds, ensuring high-quality structures and database expansion without duplication.

Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Structural biology

Background:

  • Generating 3D structural databases is crucial for drug discovery and molecular modeling.
  • Existing methods may lack flexibility in compound generation and database management.

Purpose of the Study:

  • To introduce DBMAKER, a program designed for generating 3D structural databases.
  • To enable the creation of diverse compound libraries within user-defined parameters.
  • To ensure efficient database expansion and prevent duplication.

Main Methods:

  • DBMAKER utilizes user-defined parameters to control compound content, composition, size, and connectivity.
  • SMILES string representations are generated for compounds.
  • CONCORD software converts SMILES strings into high-quality 3D structures.

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  • Methods for compound registration and database expansion are implemented.

    • Main Results:

    • DBMAKER successfully generates 3D structural databases with user-specified constraints.
    • The program produces SMILES string representations that are accurately converted to 3D structures by CONCORD.
    • Efficient compound registration and database expansion without duplication are achieved.

    Conclusions:

    • DBMAKER offers a flexible and efficient solution for constructing 3D structural databases.
    • The integration with CONCORD ensures high-quality 3D structures and broad format compatibility.
    • The described methods support scalable database growth for research applications.