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Ligand-protein database: linking protein-ligand complex structures to binding data.

O Roche1, R Kiyama, C L Brooks

  • 1Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Journal of Medicinal Chemistry
|October 19, 2001
PubMed
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This study introduces the Ligand-Protein DataBase (LPDB), a resource for improving computational drug design scoring functions. The database aids in developing more accurate and reliable scoring functions by providing structural and binding data for protein-ligand complexes.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Scoring functions are crucial for computational structure-based drug design.
  • Empirical scoring functions, while fast, often yield too many false positives.
  • Existing methods lack comprehensive datasets for reliable scoring function development.

Purpose of the Study:

  • To introduce the Ligand-Protein DataBase (LPDB), a novel resource for computational drug design.
  • To facilitate the design, parametrization, and assessment of scoring functions.
  • To enable the evaluation of scoring function performance using diverse ligand poses.

Main Methods:

  • Developed a World Wide Web accessible database (LPDB).
  • Integrated structural information from the Protein Data Bank (PDB).

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  • Incorporated experimental binding data for known protein-ligand complexes.
  • Included a continuum of ligand positions for each complex.

    • Main Results:

    • The LPDB provides a curated collection of protein-ligand complex structures with binding data.
    • The database allows filtering complexes by receptor and ligand properties.
    • It facilitates the assessment of scoring function accuracy and reliability.
    • Enables the evaluation of energetic behavior across various ligand positions.

    Conclusions:

    • The LPDB is a valuable resource for advancing computational drug design.
    • It supports the development of more accurate and reliable scoring functions.
    • The database aids in overcoming limitations of current empirical scoring functions.