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A Database of High Energy Intermediates for Substrate Docking

Welcome to HEI, a database of high energy intermediates for docking. This first version of HEI anticipates a single reaction class, where the first step is nucleophilic attach of a hydroxide nucleophile leading to a high energy intermediate. Moreover, we have selected in this version only certain chemotypes that are known or thought to be recognized and turned over by amidohydrolases.

HEI is provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF). To cite HEI, please reference Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ and Shoichet BK, Predicting substrates by docking high-energy intermediates to enzyme substuctures. J Am Chem Soc. 128, 15882-91 (2006). PDF. We are grateful to NIGMS for support via GM093342 (John Gerlt, PI). HEI is provided in the hope that it will be useful, but you must use it at your own risk. We thank NIGMS for financial support (GM71896).

HEI is drawn extensively from KEGG, so many of these compounds may not be commercially available. The molecules have been processed via a modified form of the ZINC scripts, specially adapted for high energy intermediates by Johannes Hermann.

Future versions of HEI will address other reaction classes and schemes. For now, we only support nucleophilic attack of hydroxide for a limited number of reaction types. You may download HEI, the scripts used to prepare it, and other information, below. We hope you find this useful.


The documentation on HEI continues to be more limited than we would like. Please refer to the paper, and the wiki, and contact us if you have any questions.
A product of BCIRC, the Bioinfomatics and Chemical Informatics Research Center @ UCSF. Last updated Jan 2, 2008. Please direct email as follows: bug reports to support at docking.org; comments to comments at docking.org; questions and discussion to blaster-fans at docking.org.