Resource Report

URL: http://www.bindingmoad.org/

Proper Citation: Binding MOAD (RRID:SCR_002294)

Description: Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques.

Abbreviations: Binding MOAD

Synonyms: BindingMOAD.org, Binding Mother of All Databases

Resource Type: data or information resource, database

Defining Citation: PMID:18055497, PMID:16168689, PMID:15971202

Keywords: drug, enzymatic, affinity, binding, binding-affinity, biological, chemical, cheminformatic, crystal, crystallography, intermolecular interaction, signaling pathway, ligand, protein, ligand-protein binding, protein crystal structure, protein-ligand, protein-ligand complex