docking.org

Piperazines and other molecules with proximal aliphatic protonatable nitrogens are being reprocessed in ZINC. Before, they were often doubly charged, which is generally not the biologically relevant form. Now, we believe, they are being prepared in forms that are more biologically relevant.

ZINC is a living database that we are now updating daily with new compounds. We are also removing compounds that are no longer available. The good news is that this should give you a higher rate of success when you come to purchase compounds, particularly if you check ZINC just prior to ordering. The less good news is that you can no longer find compounds that were there just a little while ago.

docking.org is undergoing maintenance tonight (Fri Nov 7, 8-10pm). Sorry for the lack of warning. Some things may just hang until 10. Sorry.

--John

We have updated many of the vendor catalogs in ZINC this month. We deleted about 3M (out of 30M total) catalog entries from ZINC which have been dropped in the latest vendor catalogs.

What does this mean for you? ZINC contains fewer entries that you can no longer buy.

The by-property subsets will by updated next (not done yet).

We have recently upgraded to Epik 1.6, are are presently recalculating the relevant biological form of molecules that were previously poorly handled. If you have a particularly favorite functional group, write us! We would like to hear from you.

We like to test actual drugs for off target effects from time to time, so we were thrilled to see the new Bioactive database from InterBioScreen appear. (www.interbioscreen.com) They offer 728 known potent enzyme substrates, inhibitors and activators, receptor agonists and antagonists, bioregulators and other biologically active compounds for use in assay development and validation and HTS.

This is huge! or, for our colleagues in the British Isles, "quite nice".

One problem in ZINC has been the representation of di-amine cations, matching the patterns (occurrences) :

[NHv4][NHv4] (2811)
[NHv4]*[NHv4] (7750)
[NHv4]**[NHv4] (268,328)

These molecules are not in a biologically relevant form, due to their improbable if not impossible protonation state. We are now loading these in their biologically relevant protonation states.

When, in the course of human events, it becomes necessary for us to dissolve the physical property constraints have been used to select screening subsets and to assume among the powers of earth, blah blah blah, subset definitions that make sense, a decent respect to the users of the ZINC website requires that we should declare the causes which impel us to this change.

Until now, we have been making all old ZINC versions available. The purpose was to allow people to look up molecules if they did not download a purchasing spreadsheet when they downloaded the subset (hint: good idea!). This has started to create problems of clarity, and frankly an increasing burden on our systems.

We are making the final changes in ZINC8, since ZINC9 will take over in January. Here is quick round up:

* Subset re-defintion (think "lead-like", "fragment-like") to better conform to expert opinion in the field. A longer article about this will appear soon

* Subset pruning - we have streamlined the list of available subsets for clarity.

* Depletion - we have depleted over 1M compounds this month. i.e. the compound is no longer available. This will take a while to show up everywhere on our site.

Dear ZINC Fans

A common complaint is that compounds in ZINC cannot be purchased. To try to improve the ratio of compounds you can actually buy, we continually a. load the latest catalogs and b. purge compounds no longer listed in a supplier's catalogs.

During September, we will be retiring catalog entries (and thus possibly compounds) that are no longer for sale, as far as we know. Here is the progress so far. I am using the ZINC short names for brevity. (updated: Sept 5, 2008)

acb, 76; acdisc, 395; acros, 3289; adesis, 19; cdiv 132,000; florida 4; frinton 111; frontier 12;