Metabolite Docker

This is a public access service that uses molecular docking as a basis for predicting the function of enzymes. It supports docking both ground state and high energy intermediate forms of metabolites and commercially available compounds to protein structures.

The Metabolite Docker is supported by the Enzyme Function Initiative developed by the Irwin and Shoichet Laboratories at the University of California San Francisco; the tool is built on the DOCK Blaster suite. To cite the latter, please reference: Irwin, Shoichet, Mysinger et al., "Automated docking screens: a feasibility study.", J. Med. Chem. 2009, 52(18), pp 5712-5720.
Examples of a successful metabolite docking may be found in:

  • Hermann JC, Marti-Arbona R, Fedorov AA, Fedorov E, Almo SC, Shoichet BK, Raushel FM., "Structure-based activity prediction for an enzyme of unknown function.", Nature. 2007, 448(7155):775-9.
  • Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM., "Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes.", Biochemistry. 2013 Sep 4..
  • Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP., "Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.", Proc Natl Acad Sci U S A. 2012, 109(11):4122-7.

You may also be interested in covalent docking, in which some metabolites may be docked covalently. You may also be interested in our regular docking server, DOCK Blaster, in which there is a different range of choices of databases to dock.

There is sample data to use.