Welcome to ZINC15 > 99% Dark Matter!

Use this area to download commercially available molecules that have no prediction having pSEA>=40 or MaxTc>=40. These files are refreshed monthly or so, or if you ask us. Each file is dated.

Caveat Emptor: We do not guarantee the quality of any molecule for any purpose and take no responsibility for errors arising from the use of this database. ZINC is provided in the hope that it will be useful, but you must use it at your own risk.

Attention nitpickers: There are actives among the dark matter, it is just mostly dark. We only exclude compounds that are Tc 40 or pSEA 40 to a 10uM or better direct binding annotated active in ChEMBL21. So you will find a few natural products and perhaps drugs in there. This is why we write > 99% dark.

Whereas you are free to share the results of a ZINC search or a screen of molecules from ZINC, you may not redistribute major portions of ZINC without the express written permission of John Irwin: chemistry4biology at gmail dot com.

ZINC 15 - Chemical Dark Matter

Notes:

We generate new versions on a rolling basis.
Each version is timestamped, and the current version is indicated.
Old versions may be retained, but are subject to removal at any time.
Within each version, the files are tranched by physical property and by purchasability.

how to download in 2D

To download all tranches, all purchasabilities, use:

curl "http://files.docking.org/dark-matter/2017-07-05/[A-K][A-K]/{In-Stock,On-Demand,Agent,For-Sale}.txt.gz"
-o "#3-#1#2.txt.gz"

You should be able to see how to generalize from this to get whatever you want.

I have generated db2 and mol2 files for In stock compounds. To get these for say lead-like, use

curl "http://files.docking.org/dark-matter/2017-07-05/A[D-G]/In-Stock-{ref,mid}-x[a-z][a-z].mol2.gz" -o "In-Stock-#2-x#3#4.A#1.mol2.gz"

General instructions for downloading 3D models for docking.

Here are the steps. You must have csh, curl and wget, which are standard on linux. note this script is not yet quite right. We are actively working on it

Get the script, below: http://files.docking.org/catalogs/getfiles.csh
Follow the instructions in that script to
- Get the mapping from ZINC ID to the vendor's codes
- e.g. http://files.docking.org/catalogs/20/fchgroup/fchgroup-info.txt.gz
- The columns are: FCH code, ZINC ID, InChIKey (for cross-referencing)
Choose lead-like or fragment like and get the relevant index files.
- e.g. wget -e robots=off -r -l1 --no-parent "http://files.docking.org/catalogs/1/bitterdb/frag-like/"
Get the 3D models using csh getfiles.csh (this may take a while!)

Any errors, problems, suggestions, please write me.

here's how to explore whether a compound really has no annotated actives:

http://zinc15.docking.org/substances/having/genes/?ecfp4_fp-tanimoto-40=ZINC000087200955
biogenic neighbors: http://zinc15.docking.org/substances/subsets/biogenic?ecfp4_fp-tanimoto-40=ZINC000087200955
in vitro neighbors. http://zinc15.docking.org/substances/subsets/in-vitro/?ecfp4_fp-tanimoto-40=ZINC000087200955

-- John

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