Metabolites databases

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There are two three kinds of metabolite docking databases at, and from each type, there are multiple actual databases.

*NB this work is still in progress*

Ground state

These are the regular databases prepared in ZINC. The molecules are represented in biologically relevant protonation states and tautomeric forms. The databases currently available include

  • HMDB - the human metabolome database.
  • Biocyc/Metacyc - the SRI (Stanford Research International) database of metabolites. These are organized by organism. We have the human subset
  • Zmd - ZINC metabolite database

High energy intermediates

HEI - There are a number of these, each of which has been prepared for a specific purpose. We document them here.


There are databases of metabolites prepared for covalent docking. They can be used by the covalent docking program,