I just received the Sigma Aldrich catalog of small bioactives molecules you can purchase. It contains over 3000 chemical products, including 300 new ones.
Pretty good, you think to yourself. Except that the ZINC databases of bioactive compounds are far far bigger. We call them "Oxymoronicules", because they are based on non-purchasable catalogs like ChEMBL and FDA, and yet are purchasable (thus an oxymoron). We think if we had paid attention in marketing class we might have come up with a different name.
Happy New Year - and with the new year come new licenses from our commercial colleagues who kindly supply us with software so we can bring you ZINC. Unfortunately, we have not received one of the new licenses yet, so several things are not working, including drawing molecules in ZINC using WebME. You can still use the old Java version (click on the use Java Editor link in the lower left corner).
Dear DOCK Blaster Users
If you tried to use DOCK Blaster from last Friday (Dec 3) through today Wednesday at 6pm, your job failed. This was because, when we updated the database on Friday, we made a mistake, and a critical table was missing from the database.
The solution is to simply re-launch your job.
We regret any inconvenience caused.
Thank you for your interest in and support of DOCK Blaster.
Dear ZINC Fans
The "all purchasable" subset (#6) was updated this morning. All the major subsets of ZINC have been updated within the last month or so.
Since we have loaded about a quarter of a million new molecules in the past month, we will immediately begin with new exports again. Subsets will appear in decreasing order of speed, thus: fragment-like, then lead-like, then drug-like, then everything.
The subsets are available for download here:
Thank you for your interest in ZINC!
Dear ZINC Fans
We have just released updates of some ZINC subsets, as follows:
Lead like (#1) - 4.2 M
Clean-drug-like (#13) - 3.75 M
Everything (#10) - 19.5 M
We have been informed that "clean drug like" is not fully exported. We regret this error, and have re-started the export. It should be ready on Monday.
Dear ZINC Users
It is Thanksgiving, time to remember all we are grateful for:
* our participating vendors who send us regular updates of their catalogs, so that we can provide you with timely information. http://zinc.docking.org/vendor0/
* our commercial software colleagues who make their software available to us, so that we can provide you with ZINC. http://zinc.docking.org/ack.shtml
* our users, i.e. YOU! Thanks for your helpful feedback, your patience, and for pushing us to improve.
In the last week or so we have updated the following subsets:
* drug-like (#3) - 13.4M
Dear ZINC Fans
We do not know how carbanions ever got into ZINC, but there they are. Today, we finally put them out of their misery. We deleted 23,565 molecules matching the following embarassing patterns:
The sum is not equal to 23,565 because some molecules had two pathologies.
Actually, most of these molecules should have been invisible to you, they were lurking, silently in the shadows. They are all gone now. All future subsets will have these removed.
Due to bookkeeping and other accumulated errors, about 80,000 molecules were not visible in ZINC.
We have fixed this by rebuilding these molecules. They will appear in ZINC search starting on Dec 1st. They will start to appear in ZINC subsets effective immediately (but it takes time to update all the subsets)
We cleaned up the 2-aminopyridines, which often only had the protonated form and not the netural form, which is nearly always wrong. There were 24,464 cases of these molecules that we found. They have all been rebuilt, and should not be a problem any more. All future subsets will have this problem fixed.