The current release is the 2012 version

Welcome to our new binding MOAD website. The following changes have been made:
- Complete rewrite of the site
- Implemented Jmol as the protein viewer
- New implementation of the Browse functionality

What is Binding MOAD?

We have created a subset of the Protein Data Bank (PDB), containing
every high-quality example of ligand-protein binding. Hence, we call
it the Mother of All Databases (MOAD).

Binding MOAD's goal is to be the largest collection of well resolved
protein crystal structures with clearly identified biologically relevant
ligands annotated with experimentally determined binding data
extracted from literature.

  ...well resolved...
has a resolution of 2.5 Å or better

  ...biologically relevant ligands...
Ligands may be a
  • peptide of 10 amino acids or less
  • oligonucleotide of 4 nucleotides or less
  • small organic molecule (e.g. ibuprofen)
  • cofactor (e.g. NADPH)
Ligands are not:
  • crystallographic additives (e.g. polythylene glycol)
  • salts (Cl-, phosphates)
  • buffers (e.g. Tris, CHAPS)
  • metals (e.g. Rb+, Zn2+)
  • metallic catalytic centers (e.g. FeS, NiFe)
  • solvents (e.g. DMSO)

  ...binding data extracted from literature
We've searched through the primary reference of each
PDB entry looking for Kd, Ki, and IC50 data.
If we've got something wrong or if you have something to add,
Please let us know - we'll correct it, and give you credit.

Citing Binding MOAD:

L Hu, ML Benson, RD Smith, MG Lerner, HA Carlson.
Binding MOAD (Mother Of All Databases).
Proteins 2005, 60, 333-40.
Link to Paper : here
Endnote Citation: Windows Apple
Bibtex Citation: Windows Linux

Additional Reference:
ML Benson, RD Smith, NA Khazanov, B Dimcheff, J Beaver, P Dresslar, J Nerothin, and HA Carlson.
Binding MOAD, A high-quality protein-ligand database.
Nucleic Acids Research 2008, 36, D674-D678.
Link to Paper : here


Binding MOAD currently contains:
  • 21,109 Protein-Ligand Structures
  • 7,284 Binding Data
  • 10,156 Different Ligands
  • 6,443 Different Families
  • See the download area to get just the new structures for 2012. Note: the associated .csv file only has ligand and binding data.
  • We have gone through all the single HET group ligands and updated the SMILES to the current PDB Component Dictionary OpenEye Cannonical form.
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