There are two three kinds of metabolite docking databases at docking.org, and from each type, there are multiple actual databases.
*NB this work is still in progress*
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. http://hmdb.org
- 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, http://covalent.docking.org.