ZINC-22 rearrangement of May-24: Difference between revisions
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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. | 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. | ||
== | == More ZINC-22 3D structures for docking == | ||
* We have begun to release a new layer, /zinc-22y/. | * For background information about layers, see [[ZINC22:Layers]]. | ||
* We have begun to release a new layer, /zinc-22y/. | |||
* This is an incremental update. | |||
* We took all the molecules in 2D registered in ZINC to H24 and ask how many of these are _not_ available in 3D ready to dock formats. | |||
* We found about 4 billion such molecules, just up to H24. | |||
* /zinc-22y/ is available to H19 as of May 23, 2024. We expect to get up to H24 fully updated by summer. Then we will turn to H25-29. | |||
== Molecule counts in 2D tranche browser == | == Molecule counts in 2D tranche browser == | ||
* We have updated 2D molecule counts in ZINC-22. | * We have updated 2D molecule counts in ZINC-22. | ||
* Thus the 2D browser is now a correct summary of what we have loaded. | |||
* ZINC-22 2D is now about 50% bigger. Old count was around 37B. Now around 55B. | |||
== Smallworld and Arthor databases == | == Smallworld and Arthor databases == | ||
* We have rearranged Smallworld and Arthor databases. The information is here: [[Smallworld_and_Arthor_Databases]] | * We have rearranged Smallworld and Arthor databases. The information is here: [[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 | There are now five servers 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. | ||
== Cartblanche22.docking.org == | == Cartblanche22.docking.org == | ||
* There have been a lot of bug fixes in Cartblanche22.docking.org. It is much more | * There have been a lot of bug fixes in Cartblanche22.docking.org. It is much more reliable now than earlier versions. If you had trouble with it, please try again. | ||
== Freshly | == Freshly updated SDI files == | ||
* new SDI files in /zinc-22x/sets/ as of 2024-05-20 | * new SDI files in /zinc-22x/sets/ as of 2024-05-20 | ||
* also available on Wynton. | |||
* will be on AWS by June 1, 2024. | |||
/wynton/group/bks/sets/ and | |||
/nfs/exd/zinc-22x/sets/ | |||
/wynton/group/bks/sets/ and | |||
/nfs/exd/zinc-22x/sets/ | |||
They contain lists of ZINC-22 tranches organized by | They contain lists of ZINC-22 tranches organized by | ||
Line 48: | Line 46: | ||
* suffix is txt (our lab), wyn (wynton) and s3 (AWS) | * suffix is txt (our lab), wyn (wynton) and s3 (AWS) | ||
== /zinc- | == /zinc-22c/ zwitterions == | ||
* Recently updated to H19. | |||
== | |||
[[Category:News]] | [[Category:News]] |
Revision as of 21:09, 23 May 2024
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.
More ZINC-22 3D structures for docking
- For background information about layers, see ZINC22:Layers.
- We have begun to release a new layer, /zinc-22y/.
- This is an incremental update.
- We took all the molecules in 2D registered in ZINC to H24 and ask how many of these are _not_ available in 3D ready to dock formats.
- We found about 4 billion such molecules, just up to H24.
- /zinc-22y/ is available to H19 as of May 23, 2024. We expect to get up to H24 fully updated by summer. Then we will turn to H25-29.
Molecule counts in 2D tranche browser
- We have updated 2D molecule counts in ZINC-22.
- Thus the 2D browser is now a correct summary of what we have loaded.
- ZINC-22 2D is now about 50% bigger. Old count was around 37B. Now around 55B.
Smallworld and Arthor databases
- We have rearranged Smallworld and Arthor databases. The information is here: Smallworld_and_Arthor_Databases
There are now five servers 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.
Cartblanche22.docking.org
- There have been a lot of bug fixes in Cartblanche22.docking.org. It is much more reliable now than earlier versions. If you had trouble with it, please try again.
Freshly updated SDI files
- new SDI files in /zinc-22x/sets/ as of 2024-05-20
- also available on Wynton.
- will be on AWS by June 1, 2024.
/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-22c/ zwitterions
- Recently updated to H19.