Ligand Database For Compounds Present In Human Food
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11.4 years ago
Flow ★ 1.5k

For protein-ligand docking calculations one can use free databases such as ZINC (http://zinc.docking.org). But I need to find databases of compounds that are present in human food. In zinc I can see there is the "natural products" subset, but I would like to focus just on some "food" subset. Are there other databases available for such compounds?

PS: I mean databases where one can download the compounds in any of the standar formats (mol2, sdf, smiles, etc)

docking database • 3.8k views
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11.4 years ago
cdsouthan ★ 1.9k

Try http://www.foodb.ca/

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This looks good but I could only find around 127 compounds

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My guess is they are waiting for funding in sequence after DrugBank and HMDB. As you can see below your question cannot be answered from any current database even the FDA (additives yes but not food chemistry). This is a massive gap (considering eating is our biggest chemical exposure bar none) that I hope FOODB will plug soon. Given the size of the global food/nutrition industry you'd of thought they might offer to help, but there are also reasons why they might not. I guess some of those 1000 to 50000 substances in food will turn out not to be so good for us as we thought. No harm in asking Nestle if they have made their own database though.

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11.4 years ago

Maybe there is something on Food and Drug Administration or its European equivalent. Let us now.

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I could not find any structural information in such databases

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EDIT : I just saw that you wanted only downloadable files. But if you tend to construct your compound database, this comment is still good.

Ok. But did you get the compound names ? It may be a good start since FDA tend to use INN names. For example, a list of substance generally recognized as safe exist http://www.accessdata.fda.gov/scripts/fcn/fcnNavigation.cfm?rpt=grasListing&displayAll=true and food contact substances http://www.accessdata.fda.gov/scripts/fcn/fcnNavigation.cfm?filter=&sortColumn=&rpt=fcsListing

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