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 == | ||
* For background information about layers, see [[ZINC22:Layers]]. | * For background information about layers, see [[ZINC22:Layers]]. | ||
* We have begun to release a new layer, /zinc-22y/. | * We have begun to release a new layer, /zinc-22y/. | ||
| Line 20: | Line 20: | ||
* /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. | * /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 and 3D 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. | * 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. | * ZINC-22 2D is now about 50% bigger. Old count was around 37B. Now around 55B. | ||
* We are updating the 3D molecule counts in ZINC-22. Work in progress. | |||
== Smallworld and Arthor databases == | == Smallworld and Arthor databases == | ||
* We have rearranged Smallworld and Arthor databases. The information is here: [[ | * We have rearranged Smallworld and Arthor databases. The information is here: [[Smallworld Databases]]. [[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 | 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 == | ||
| Line 39: | Line 36: | ||
* 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. | * also available on Wynton. | ||
* will be on AWS | * will be on AWS in June, 2024. | ||
/wynton/group/bks/sets/ and | /wynton/group/bks/sets/ and | ||
/nfs/exd/zinc-22x/sets/ | /nfs/exd/zinc-22x/sets/ | ||
| Line 53: | Line 50: | ||
* Recently updated to H19. | * Recently updated to H19. | ||
== We updated /wynton/group/bks/2d/ == | |||
54 B smiles in ZINC-22 | |||
== Synced to Wynton == | |||
We sync to AWS in June 2024. | |||
== SMILES available for 3D structures == | |||
We have recomputed SMILES files for each small tranche, e.g. H20/H20P200/*.smi.gz. | |||
By layers, here is where we are (May 29, 2024) | |||
DONE: a,b,c,i, k, l, q, r, t,w,y,z | |||
x: H18 done. stopped. n: H20 done. stopped. p: H20 done stopped. m: H17 done stopped | |||
Almost done but still running: | |||
d H26 | |||
g H28 | |||
h H29 | |||
o H25 | |||
s H25 | |||
u H25 | |||
v H21 | |||
'We will announce when finished. Should be mostly finished except x and n past H25. That last bit will take a while. | |||
[[Category:News]] | [[Category:News]] | ||
Latest revision as of 23:14, 29 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 and 3D 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.
- We are updating the 3D molecule counts in ZINC-22. Work in progress.
Smallworld and Arthor databases
- We have rearranged Smallworld and Arthor databases. The information is here: Smallworld Databases. 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 in June, 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.
We updated /wynton/group/bks/2d/
54 B smiles in ZINC-22
Synced to Wynton
We sync to AWS in June 2024.
SMILES available for 3D structures
We have recomputed SMILES files for each small tranche, e.g. H20/H20P200/*.smi.gz.
By layers, here is where we are (May 29, 2024)
DONE: a,b,c,i, k, l, q, r, t,w,y,z x: H18 done. stopped. n: H20 done. stopped. p: H20 done stopped. m: H17 done stopped
Almost done but still running: d H26 g H28 h H29 o H25 s H25 u H25 v H21
'We will announce when finished. Should be mostly finished except x and n past H25. That last bit will take a while.