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Related Experiment Videos

Binding MOAD (Mother Of All Databases).

Liegi Hu1, Mark L Benson, Richard D Smith

  • 1Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA.

Proteins
|June 23, 2005
PubMed
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Binding MOAD is the largest database of protein-ligand complexes, offering extensive binding affinity data. This resource aids in understanding molecular recognition and advancing drug discovery.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) contains numerous protein-ligand complexes.
  • High-quality binding affinity data is crucial for understanding molecular interactions.
  • Existing databases may lack comprehensive or curated binding data.

Purpose of the Study:

  • To present Binding MOAD, the most extensive collection of curated protein-ligand complexes.
  • To compile and report binding affinity data for these complexes.
  • To create a non-redundant dataset for robust analysis.

Main Methods:

  • Compiled data from over 5000 structures in the Protein Data Bank.
  • Extracted and curated binding affinity data from crystallography papers.

Related Experiment Videos

  • Developed a non-redundant dataset by selecting representative proteins from each family.

    • Main Results:

    • Binding MOAD contains 5331 protein-ligand complexes, 1780 unique protein families, and 2630 unique ligands.
    • Binding affinity data was compiled for 1375 (26%) complexes, spanning 13 orders of magnitude.
    • A non-redundant dataset of 1780 complexes was created, with 475 (27%) containing binding data.

    Conclusions:

    • Binding MOAD represents the largest compilation of binding data to date.
    • The dataset facilitates the study of molecular recognition and enzymatic regulation.
    • It serves as a valuable resource for developing improved scoring functions and structure-based drug discovery techniques.