Subject: New Data at BindingDB

From: "Michael K. Gilson" <[email-masked]>
Date: Fri, 12 Apr 2002 17:42:03 -0400

Dear Colleagues,

The Binding Database (www.bindingdb.org) now includes nearly 170 measured affinities of HIV-1 protease for cyclic urea inhibitors, measured by enzyme inhibition.*

This series should be particularly useful for parameterizing and testing computational models of binding because the measurements were all done with the same assay and the inhibitors are all expected to have a similar binding mode.

You can find these data by typing "HIV" into the search bar at www.bindingdb.org.  If you want an MDL Molfile for an entry, click "more" in the corresponding line of the data table and use the JChem applet at the bottom of the page.  (In JChem, use "Edit"--> "Source".)

The PDB contains several structures that illustrate the binding mode. (Search the PDB for "cyclic urea".) Examples include 1dmp and 1hvr.

We hope you will find these binding data interesting and useful. Please let me know of any problems you may have accessing them.

If you have binding data in electronic form that could be published at BindingDB-- for example, data already published in J. Med. Chem. -- we would be happy to include them in BindingDB, so please send them along.  This is a good way to help BindingDB grow.

Finally, please let me know if there are any specific classes of data (e.g., kinase binding) you think BindingDB should try to collect and make available on-line.

With best regards,

Mike Gilson
Center for Advanced Research in Biotechnology
University of Maryland Biotechnology Insitute

* Thanks to the DuPont Merck Pharmaceutical Company for providing these data in electronic format several years ago.