Zusammen

Chemical database systems become more valuable when they link to other systems. Today's stop on our continuing survey of free chemistry databases and Web services is a case in point: AffinDB. AffinDB was created to help enable the understanding of energetics in biomolecular recognition. From the about page:

The Affinity Database 'AffinDB' contains affinity data for protein-ligand complexes of the PDB [Protein Data Bank]. Its purpose is to provide direct and free access to the experimental affinity of a given complex structure. As of Friday, May 29th, 2009, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex.

AffinDB is organized around the concept of small-molecule/protein interactions, and draws the foundation for its records from the PDB. By providing binding constant data and links to primary literature sources, AffinDB builds on the PDB dataset.

Records can either be browsed or searched. For example, the search form can be used to find all records with reported binding between 1 nM and 1 uM. Similarly, we can find all complexes involving the small molecule phosphoglycolic acid. Records can be sorted and browsed by affinity, PDB code, and year of publication, among others.

One of the most useful features of AffinDB is that each binding record is linked to the primary literature through PubMed. Primary literature citations extend from 1965-2004. For convenience, a summary of the experiment used to make the binding affinity determination is linked to each record.

Although AffinDB appears to be no longer maintained, it offers a valuable add-on to the PDB and a good example of what can be accomplished when larger databases are linked to other resources through third party services.