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. 2008 Jan;36(Database issue):D674-8.
doi: 10.1093/nar/gkm911. Epub 2007 Nov 30.

Binding MOAD, a high-quality protein-ligand database

Mark L Benson  1 , Richard D Smith, Nickolay A Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, Heather A Carlson
Affiliations

Binding MOAD, a high-quality protein-ligand database

Mark L Benson et al. Nucleic Acids Res. 2008 Jan.

Abstract

Binding MOAD (Mother of All Databases) is a database of 9836 protein-ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org.

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Figures

Figure 1.
Figure 1.
Distribution of binding affinities in Binding MOAD. Data is labeled as Kd (blue), IC50 (yellow) and Ki (red). For this figure, binding affinities were simply converted to free energies by RT × ln(affinity). While this conversion not strictly appropriate for Ki or IC50, it provides a comparison for the reader.
Figure 2.
Figure 2.
Distribution of the sizes of 5074 unique ligands in Binding MOAD. The largest ligands are peptides, short oligonucleotides and complex sugars.
Figure 3.
Figure 3.
Screenshot of the data page for 3ERK, showing the additional ligand data and the connectivity to proteins with similar structure and function.
Figure 4.
Figure 4.
EolasViewer for 3ERK. The SB4 ligand is shown in ball in stick inside the pocket. The surfaces shown are the ligand surface in blue, the binding site in red and the solvent-exposed regions of the binding site are in green. (Top) The protein backbone is shown as a gray ribbon, and in the close-up (Bottom), the backbone is colored by B-factors.
See this image and copyright information in PMC

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