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ZINC 3D updated

Dear Dockers

We are announcing today a major update of the 3D docking libraries in ZINC15, accessible via the Tranche Browser: http://zinc15.docking.org/tranches/home/

The following numbers of molecules are available in ready to dock formats as follows: stock / on-demand / boutique

Lead-like: 2.9M / 52M / 56M
Fragment-like: 795K / 6.8M / 8.1M
Drug-like: 7.8M / 69M / 74M
All: 8.7M / 70M / 76M

There's more. We expect ZINC 3D lead like to grow by an average of 5 M per week for the rest of 2016.

Thank you for your interest in ZINC.


ZINC15 bigger than ever

ZINC15 has been updated.
The 2D version (SMILES) is ready for download.

A few highlights:
13 million compounds in stock, 233 M including make-on-demand and 331 M including boutique.

Leads: 3.4 M stock, 93 M including on demand, 133 M including boutique.

Fragments: 824 K in stock, 7M including on demand and 24 M including boutique.

We will be updating the 2D tranches continuously going forward. We will announce substantial revisions.

The 3D updates will be available later this month. "very soon".



Molecular excipients

Dear All

We have created a new tool for research in the area of molecular excipients.

We have just published a paper about it.

The website is online and ready to use:

This work is sponsored by the US Food and Drug Administration (FDA).

We're happy to talk to you if you have any questions about this new facility.

We hope you find it useful.

-- John

Did you ever wonder how many molecules were added to ZINC today?

Dear ZINC Fans

We all know ZINC keeps growing. It now contains 218 M purchasable molecules.

And if you ask me, I'll tell you that we add tens of thousands of molecules to ZINC every day, certainly averaged over a year.

Did you ever wonder how many molecules were added today? Now you can easily find out. For instance, suppose you are interested just in "in stock" molecules, whether available directly from vendors or via procurement agents, such as MolPort or eMolecules. For May 31st, the answer is:

ZINC15 is back up! thanks for your patience

We are back! We promise to do our utmost to avoid that kind of outage in future!

-- John

ZINC15 undergoing maintenance

Dear ZINC Fans

ZINC15 is offline this morning as we undo some maintenance we did last night. We hope to be back up again very soon, but right now, we're not sure how long it is going to take.

Thanks for your patience!

ZINC Database Team

PAINS questioned

Peter Kenny @pwk2013 just brought an interesting paper to my attention:

Privileged Scaffolds or Promiscuous Binders: A Comparative Study on Rhodanines and Related Heterocycles in Medicinal Chemistry


In short, hydantoins, rhodanines, thiohydantoins, and thiazolidinediones might not be as problematic (PAINs-y) as is often widely assumed. Interesting data, definitely worth a look before you throw out that baby with your bathwater.

Free tool to find PAINS patterns

Dear Ligand Discovery Fans

There is a new tool to help you find PAINS patterns, part of ZINC15:


Enter the molecule (SMILES, ZINC ID, Name or Draw it) and click "Identify". If a PAINS pattern matches, it will be shown. An empty result indicates no match. Since it is in ZINC15, it is scriptable. You can run it on millions of molecules, for free.

new 3D models for ZINC15 being released tomorrow (Wed Dec 9, 2015)

Dear ZINC15 Fans

Thank you to everyone who has written us asking about 3D models in ZINC15. As we said in the paper and on our wiki, we would start updating the 3D models in December 2015. Tomorrow is day 1.

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