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Related Experiment Videos

Exploring protein-ligand recognition with Binding MOAD.

Richard D Smith1, Liegi Hu, Jayson A Falkner

  • 1Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109-1055, USA.

Journal of Molecular Graphics & Modelling
|September 20, 2005
PubMed
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The Binding MOAD database now contains over 6,800 protein-ligand complexes. Analysis reveals that most binding sites and ligands are significantly buried, supporting the importance of molecular contact in recognition.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • The Binding MOAD (Mother of All Databases) is the largest publicly available database of protein-ligand complexes.
  • The database was updated in August 2004, containing 6816 complexes, 2220 protein families, and 3316 unique ligands.
  • Binding data was successfully retrieved for 27% of complexes from over 6000 crystallography papers.

Purpose of the Study:

  • To present the data available on the Binding MOAD website.
  • To analyze the degree of solvent exposure in binding sites within protein-ligand complexes.
  • To introduce GoCAV and the GoCAV viewer tools for data analysis and visualization.

Main Methods:

  • Data mining of the Binding MOAD database.
  • Analysis of solvent exposure for protein binding sites and ligands using GoCAV.

Related Experiment Videos

  • Integration of the GoCAV viewer into the Binding MOAD website.

    • Main Results:

    • Binding MOAD contains 6816 protein-ligand complexes, with binding data available for 1793 (27%).
    • A non-redundant set shows binding data for 630 unique complexes (28%).
    • Analysis indicates that 70-85% of binding cavities and ligands are substantially buried within complexes.

    Conclusions:

    • The extensive data in Binding MOAD facilitates structural biology research.
    • The high degree of solvent burial in binding sites supports the significance of protein-ligand contact in molecular recognition.
    • The integrated GoCAV viewer enhances data accessibility and utility for the research community.