John Irwin's blog

zinc15 restarted Weds Aug 23 9am SF time due to overload

Dear ZINC15 fans

ZINC15 has been slow recently, perhaps after my talk at ACS. I just restarted the server. I hope it is now faster. Please write us on twitter or elsewhere if you are having persistent performance problems.



No more logins

Dear fans

We have blocked new user registration on, as used by We did this because we are being hit so heavily by people who are just trying to sell watches and shoes.

If you need an account, please write me at chemistry4biology at gmail dot com including a bit about yourself and your affiliation.


blog back up - sorry for the interruption

Dear fans

We were seeing a lot of hacking attempts, so I tightened up security in a bit of a panic. Unfortunately, I also broke this blog. Now that my paper is submitted and I am returning to other things, I have fixed the blog.

I am rededicating myself to making things better. We have a lot of new tools, released or soon to be released, and I will be telling you about them here.


power outage tonight Mon Nov 21 pm - Tues Nov 22 am

Dear users

We are having a building powerdown tonight. Some of our services may go offline. They will be re-started tomorrow morning (Tuesday) by 10am San Francisco time.

-- John

Download ZINC15 by catalog

Dear ZINC Fans

An important missing feature in ZINC15 has been the ability to download dockable libraries by catalog.

Today, we are announcing a new feature that gives you a lot of flexibility to download 3D models for docking.

Please read more here:

We are preparing the files in increasing order of size. All small catalogs < 100,000 molecules are ready. We expect catalogs under 1,000,000 molecules will be ready by the weekend. Larger catalogs will take longer.

* consider using libraries by property (the Tranche Browser)

ZINC 3D updated

Dear Dockers

We are announcing today a major update of the 3D docking libraries in ZINC15, accessible via the Tranche Browser:

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:

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