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Related Experiment Videos

The Binding Database: data management and interface design.

Xi Chen1, Yuhmei Lin, Ming Liu

  • 1Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.

Bioinformatics (Oxford, England)
|February 12, 2002
PubMed
Summary
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A new public database, BindingDB, now provides access to measured biomolecular binding affinities. This resource enables structure and sequence homology searches, improving drug discovery and molecular design.

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Drug Discovery

Background:

  • Vast experimental data on biomolecular binding is crucial for molecular biology and therapeutics.
  • Existing data is largely inaccessible in published literature.
  • No public database offers measured binding affinities with structure/sequence search capabilities.

Purpose of the Study:

  • To create a public, web-accessible database of measured binding affinities.
  • To enable advanced querying, including chemical structure and sequence homology.
  • To facilitate molecular design and therapeutic development.

Main Methods:

  • Developed BindingDB based on a relational data specification for binding measurements (e.g., Isothermal Titration Calorimetry, enzyme inhibition).

Related Experiment Videos

  • Utilized an XML Document Type Definition (DTD) for data interchange and deposition.
  • Implemented an online query interface using Java Servlet technology for SQL, structure, and homology searches.

    • Main Results:

    • Created BindingDB, a public database of measured binding affinities.
    • Implemented efficient online deposition and query interfaces.
    • Achieved brisk response times for diverse search functionalities.

    Conclusions:

    • BindingDB provides a valuable, accessible resource for biomolecular binding data.
    • The database supports structure and sequence homology searches, aiding research.
    • BindingDB is well-suited for continued development and enhancement in molecular biology and drug design.