Binding datasets for protein-ligand complexes were first used in computational chemistry to develop scoring functions for ligand docking and de novo design of enzyme inhibitors. The earliest relevant dataset was only 45 complexes and more recent sets are 200-800. Some of these sets have been made available online, changing their nature from a flat list of data in a paper to a dynamic and searchable tool for the scientific community.
Binding MOAD (Mother of All Databases) is the largest collection of high-quality, protein–ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein–ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. More than 5000 studies of crystallography structures were compiled, for 1375 protein–ligand complexes. This is the largest collection of binding data reported to date in the literature. The redundancy in the data was addressed by choosing one protein from each of the 1780 protein families as a representative. This significant collection of protein–ligand complexes will be very 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. The dataset can be accessed at http://www.BindingMOAD.org
Applications and Advantages
- Searching for high-quality, protein-ligand-nl-complexes
- Large range of complexes
- Biologically relevant ligands with resolution-nl-of 2.5 angstrom or better