HEI

Available data

High-energy intermediate databases in mol2 format can be found at hei.docking.org.

The files available are:

1. rmkh.ohln.tar.gz: KEGG, more than one ring, leaving group neutral
2. rmkh.ohlp.tar.gz: KEGG, more than one ring, leaving group protonated
3. rmpkh.ohln.tar.gz: KEGG, more than one ring rings, leaving group neutral
4. rnkh.ohln.tar.gz: KEGG, no rings, leaving group neutral
5. rnkh.ohlp.tar.gz: KEGG, no rings, leaving group protonated
6. rnpkh.ohln.tar.gz: KEGG, no rings, leaving group neutral
7. rokh.ohln.tar.gz: KEGG, one ring, leaving group neutral
8. rokh.ohlp.tar.gz: KEGG, one ring, leaving group protonated
9. ropkh.ohln.tar.gz: KEGG, one ring, leaving group neutral

The conversion of databases of ground state molecules to their high-energy intermediate forms is described in a tutorial.

References

1. 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 448 (7155), 775-9 (2007).
2. Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM. Resolution of Chiral Phosphate, Phosphonate, and Phosphinate Esters by an Enantioselective Enzyme Library. J Am Chem Soc 128 (49), 15892-902 (2006).
3. Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. Predicting Substrates by Docking High-Energy Intermediates to Enzyme Structures. J Am Chem Soc 128 (49), 15882-891 (2006).

Data on local cluster disk

• fawlty: /nfs/store/users/proust1/in/other_data/kolb/
• /raida/db/hei/

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