ZINC-22 rearrangement of May-24

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A few things have happened recently, which we describe below.

Enamine Macrocycles

  • We have released a new layer /zinc-22w/, Enamine macrocycles. These are based on a private library of about 150K from Enamine as follows:
  • 104,060 H19 to H39.
  • 45,985 H40 to H49
  • 654 H50-H54

We have built to H39. Next time (summer) we will build to H49.

The 104,060 expand to 144,978K with steroisomers. That's dockable today in /zinc-22w/ To be clear, this number double-counts protonation states with different charges, thus if there is an imidazole and there is one protonated and one unprotonated, it counts as two. So maybe 140K really.

Incremental update of 3D structures

  • We have begun to release a new layer, /zinc-22y/. This is an incremental update. What we did was to take all the molecules in 2D registered in ZINC and ask how many of these are _not_ available in 3D ready to dock formats. We found about billions of such molecules, even just up to H24. We have begun to process them and make them available. We are currently complete up to H15. H16 and H17 are well underway. H18 and H19 have started to appears. H20 and H21 are still in the building stage, and H22, H23 and H24 have not started to be built. We will attempt to process everything up to H24, while at the same time, we attempt to finish H25-H29 in the first generation, represented mostly by /zinc-22x/ and /zinc-22n/.

Molecule counts in 2D tranche browser

  • We have updated 2D molecule counts in ZINC-22. Thus the 2D browser is now a pretty correct summary of what we have loaded. (It is working on H25 as I write, expecting to finish H26-H29 later today). ZINC-22 2D is now about 30% bigger. Old count was around 37B. Now around 50B.

Smallworld and Arthor databases

There are five of each, thus: sw (public, no pw), swp (private, pw, but available), swcc (chemistry commons), swbb (building blocks) and one more that is private to UCSF. For Arthor it is the same thing: arthor, arthorp, arthorcc, arthorbb and a UCSF only one.

3D tranche updates to follow

  • We have been building and updating 3D tranches for about a year, and are now starting to push them to public servers.

This will happen over the coming weeks and we will announce when it is done.

Cartblanche22.docking.org

  • There have been a lot of bug fixes in Cartblanche22.docking.org. It is much more reliably now than earlier versions. If you had trouble with it, please try again.

Freshly pdated SDI files

  • new SDI files in /zinc-22x/sets/ as of 2024-05-20

(preparation in progress, will be released soon)

/zinc-22c/ zwitterions

Recently updated to H19.

new "sets" and "dirs" directory

There is a new "sets" directory in /wynton/group/bks/sets/ and /nfs/exd/zinc-22x/sets/

They contain lists of ZINC-22 tranches organized by charge-HAC-name.suffix where

  • charge: N=neutral, M= -1, O= +1 and so on.
  • HAC is H04 to H39
  • name is lead-like (HAC 17-25), frag-like (HAC 04-16), also big, greasy-leads, big-greasy
  • suffix is txt (our lab), wyn (wynton) and s3 (AWS)

== /zinc-22a/ Enamine in stock. Update is in progress and will appear soon. This is "the other informer set"

== /zinc-22g/ ZINC20 in stock The informer sets. This will be updated in June.

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