Zusammen

If you've ever thought how useful it would be to have a single database of binding affinity data compiled from the peer-reviewed literature, today's stop on our continuing tour of free chemical databases and Web services may come in handy. BindingDB hosts a growing collection of binding assay results that can be browsed and searched. From the about page:

The Binding Database projects aims to make experimental data on the noncovalent association of molecules in solution searchable via the WWW. The initial focus is on biomolecular systems, but data on host-guest and supramolecular systems are also important and will be included in time.

BindingDB is organized around the concept of the binding assay. As of this writing, over 54,000 binding determinations with over 28,000 mostly small molecule ligands are available.

The contents of BindingDB can be accessed by either browsing or searching. For example, the Histamine H3 Receptor assay page lists binding assay results for just over 100 compounds. We can view details of any assay, for example, this one with JNJ-7777120. Each record contains a link to the primary literature and the experimental details of the assay determination. In the case of the JNJ-7777120 assay, the link points to a PubMed record linking to a J. Med. Chem. article. If we wanted to see all of the data from that paper that were in BindingDB, we can do that as well.

Records can also be found through BindingDB's search interfaces. For example, a substructure search of piperazine gives over 1,300 results. Likewise, records can be found by using compound name, Ki, IC50, molecular weight, and a number of other fields.

The BindingDB dataset is available for download. The data are licensed for noncommercial use only, although the creators suggest that other arrangements can be discussed.

Although for the most part navigating BindingDB is straightforward and reveals a multitude of interesting relationships, there appear to be some connections among datapoints that are not enabled. Going back to the Histamine H3 example, let's say we wanted to see what other assays JNJ-7777120 had been tested at. Although clicking on the structure does take us the expected compound summary page, this page has no summary of the assays that the compound was run at. Another possible limitation is the lack of control over the order in which records appear. For example, it's not immediately clear how to sort assay results by decreasing activity.

BindingDB is an excellent concept and deserves much more attention. Although the site itself may have some limitations, overall its a well-thought tool. This review only covers a portion BindingDB's many features. For anyone looking for information on cross-activity of their target molecules or just insights into a single target, BindingDB makes an excellent choice.

Kudos

• Richly-connected web of assays, targets, and small molecules that can be explored through hyperlinks.
• Downloadable results sets.
• Links to the primary literature.
• Detailed information on individual assay conditions.
• Free dataset download.

Ideas for Improvement

• More options for sorting results sets - one way to do this would be to make table headings clickable. Clicking would toggle whether the table was sorted in ascending or descending order by the field.
• Compound detail view should list all assays the compound was tested in.
• Structure search returns two tables - one below the other. Each table has a different format and it's not clear why they're both necessary.
• Although this page suggests that the scientific community may deposit results into BindingDB, how this is done is not quite clear.
• New results/assays feeds to help users keep up-to-date.