The current release is the 2006 version

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

Statistics

Binding MOAD currently contains:
  • 9836 Protein-Ligand Structures
  • 2964 Structures with Binding Data
  • 4659 Different Ligands

High Quality Dataset

We've created a dataset of the highest quality
protein/ligand complexes from
BindingMOAD/PDBbind databases and associated
binding data. As part of the selection
process we used DPI, and (Rfree - R) as given
by Hawkins, P. C. D.; Warren, G. L.;
Skillman, A. G.; Nicholls, A. J. Comput. Aided
Mol. Des. (2008) 22:179-190. We also hand
curated the entire set as part of the
selection process.

We wish to thank Chemical Computing Group
and Openeye for the use of their software.
Dr. Gregory Warren for the use of his DPI and Rfree code.
We also wish to thank Dr. Shaomeng Wang and
Dr. Chao-Yie Yang for the use of PDBbind and
assistance in processing the dataset.
It is available from the download area as HiQ set.
  • 536 Protein-Ligand Structures
  • 108 Structures with a cofactor or second molecule in the crystal structure
  • <0.5 DPI
  • <0.05 (Rfree-R)