Difference between revisions of "Dockable metabolites libraries"

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It's a big topic, I didn't know exactly what you wanted.
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http://zinc.docking.org/subsets/zmd
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these are the ZINC 12 metabolites. The download links are on the page.
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For instance to download mol2 format, you would use:
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http://zinc.docking.org/db/special/97/usual.sdf.csh
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For ZINC15, the answer depends on three questions:
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a. purchasable vs all
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b. endogenous human vs all
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c. format (sdf, mol2, db.gz, db2.gz, pdbqt)
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d. assuming near pH 6-8 but if low pH or high pH must specify
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The syntax will get much clearer soon. for now:
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For instance, all endogenous human metabolites:
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zinc15.docking.org/protomers.mol2.gz?catalog.np=3
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all endogenous human metabolites you can buy
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http://zinc15.docking.org/protomers.mol2.gz?catalog.np=3&substance.purchasability=for-sale&count=all
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Good enough?  Lots more options...
  
 
[[Category:Metabolites]]
 
[[Category:Metabolites]]
 
[[Category:Docking]]
 
[[Category:Docking]]
 
[[Category:Libraries]]
 
[[Category:Libraries]]

Latest revision as of 17:56, 22 June 2015

sure, of course, except KEGG contains a lot of things that are not metabolites. But sure, http://zinc.docking.org/catalogs/keggviapc. If you want to consider individual databases and catalogs, some of which contain some metabolites, then there's also HMDB. Biocyc.

Here is a list of metabolite databases in ZINC 15

http://zinc15.docking.org/catalogs/subsets/metabolite/

Here are the catalogs that contain only endogeous human metabolites as far as we know: http://zinc15.docking.org/catalogs/subsets/endogenous/

here are the ones that contain natural products, many of which are metabolites

http://zinc15.docking.org/catalogs/subsets/biogenic/


http://zinc.docking.org/subsets/zmd

these are the ZINC 12 metabolites. The download links are on the page. For instance to download mol2 format, you would use: http://zinc.docking.org/db/special/97/usual.sdf.csh


For ZINC15, the answer depends on three questions: a. purchasable vs all b. endogenous human vs all c. format (sdf, mol2, db.gz, db2.gz, pdbqt) d. assuming near pH 6-8 but if low pH or high pH must specify

The syntax will get much clearer soon. for now: For instance, all endogenous human metabolites:

zinc15.docking.org/protomers.mol2.gz?catalog.np=3

all endogenous human metabolites you can buy

http://zinc15.docking.org/protomers.mol2.gz?catalog.np=3&substance.purchasability=for-sale&count=all

Good enough? Lots more options...