Binding MOAD, a high-quality protein–ligand database

By Mark L. Benson, Richard D. Smith, N. Khazanov, Brandon Dimcheff, John E. Beaver, Peter Dresslar, Jason Nerothin, Heather A. Carlson. 2007

166 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Jianyi Yang
2. Yang Zhang
3. Ambrish Roy
4. Robin Pearce
5. Chengxin Zhang
6. Zhihai Liu
7. Yan Li
8. Alfonso Valencia

Citations in the corpus

• ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “PDBBind (9), Binding MOAD (10) and AffinDB (11) contain binding affinity information for protein–ligand complexes found in the Protein Data Bank (PDB, 12).”
• Predicting the locations of cryptic pockets from single protein structures using the PocketMiner graph neural network (2022, methodology): “The use of MOAD-identified compounds excluded small hydrophilic molecules such as DMSO, glycerol, and ethylene glycol which are miscible in water and are often added as cryoprotectants, as well as small ions.”
• BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions (2012, background): “Binding MOAD (5) is a ligand-binding affinity database that selects ligands based on a combination of automated procedure and manual validation.”
• PDB-wide collection of binding data: current status of the PDBbind database (2015, background): “2005) are two outstanding databases created for this purpose.”
• FireDB: a compendium of biological and pharmacologically relevant ligands (2013, background): “Binding MOAD (6) uses pre-established criteria (manually curated lists) but does not take metals into account.”