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New ZINC Lead-Like subsets now available

Dear ZINC Users

Today we are releasing new lead-like subsets of the ZINC database. These are by far our most popular subsets, as they attempt to capture the current thinking of the field for what constitutes a good virtual screening library. Download page is here: http://zinc.docking.org/subset1/

The statistics are:

Set 1: "lead like" 3.7 M
Set 11: "clean leads" 727K
Set 21: "leads now" 1.8M

To recap:

* "leads now" are for immediate delivery. Subset 1 includes "make on demand" which typically take 6-8 weeks for delivery due to synthesis.

528 nitroguanines (NC(=N)N[N+](=O)[O-]) were repaired today

Dear ZINC Users

Today we repaired 528 nitroguanines that were incorrectly represented in ZINC. These changes are visible immediately in ZINC, and will be incorporated in new subsets as they are created going forward over the next month.

The problem was that some nitroguanines were cationic, some were anionic, and some were neutral.

692 isothiocyanates (R-N=C=S) were repaired today

Dear ZINC Users

We rebuilt 692 isothiocyanates that were broken today. These are available now in ZINC, and will be incorporated into static exported subsets going forward over the coming month.

The problem was that the isothiocyanates were often incorrectly protonated, thus R-[NH+]=C=S. The corrected form is neutral.

Please see our general notes on ZINC repair for terms and conditions and more background information: http://wiki.compbio.ucsf.edu/wiki/index.php/Notes_on_ZINC_repair

171 molecules removed from ZINC during cleanup today

We found 171 molecules that were mangled in ways that were not simple to fix. Thus we have deleted these molecules from ZINC. The source molecules will be reloaded with new ZINC IDs very soon. Some may already be loaded.

A good way to find molecules is to use the ZINC search feature, which has recently been improved, and which will continue to improve in the coming weeks and months.

A second good idea is to download purchasing information with each subset you download so that you have static information available in perpetuity.

ZINC Fragments subsets updated (again)

Dear ZINC Users

In the past week we have been housekeeping, resulting in better representations of the biologically relevant forms molecules and fewer errors. We have therefore released new versions of three ZINC fragment subsets as follows:

2 - "fragment like" - 374K (was 405K)
12 - "clean fragments" - 72K (was 81K)
22 - "frags now" - 335K (was 361 K)

(download here: http://zinc.docking.org/subset1/)

You will note a reduction of about 9%. These were incorrect duplicate representations of molecules. The new version is in our view much closer to correct.

New "fragment like" subsets available today

Dear ZINC Users

New versions of three ZINC subsets were released this morning:

2 - "fragment like" - 405K
12 - "clean fragments" - 81K
22 - "frags now" - 361 K

(download here: http://zinc.docking.org/subset1/)

A few points to note:

1. The number of fragments is about the same as it was, but don't be fooled: there has been tremendous turnover. At least 100,000 of these are new and about the same number are no longer available.

Sunny days for ZINC

Dear ZINC Users

It may be cloudy in cool in San Francisco today, but it is sunshine for ZINC users. The hardware upgrade last night has given us a huge performance boost. We hope you will begin to notice the difference in the days and weeks to come.

We want to publicly thank Pascal, our legendary system administrator, who suggested the hardware configuration we are using. Here's the secret: pssst. RAID10, and lots and lots of memory for your MySQL server.

-- John

Problems with DOCK Blaster following ZINC upgrade now fixed

Dear DOCK Blaster Users

As a result of the ZINC upgrade last night, and job that was submitted from midnight through about 1pm San Francisco time today Tuesday October 5, 2010 probably failed. The workaround is to please re-submit your job.

Thanks for your interest in docking.org services.

John
UCSF ZINC / DOCK Blaster Team

ZINC is back up

ZINC came up last night just after midnight San Francisco time. It looks fine to us, and searches seems a little faster. Let us know if you notice anything wrong.

John

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