ZINC-22 rearrangement of May-24: Difference between revisions
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This is our first news report for a long time. | This is our first news report for a long time. | ||
**DRAFT** | |||
== Enamine Macrocycles == | |||
* We have released a new layer /zinc-22w/, Enamine macrocycles. There are about 5000 macrocycles. We have no idea whether these are any good for docking. Please let us know. Unusually, we have allowed up to H39, whereas for small molecules we only load and build up to H29. | * We have released a new layer /zinc-22w/, Enamine macrocycles. There are about 5000 macrocycles. We have no idea whether these are any good for docking. Please let us know. Unusually, we have allowed up to H39, whereas for small molecules we only load and build up to H29. | ||
== 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/. | * 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. | * 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 == | |||
* 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 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. | * 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. | 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. | * 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. | ||
* new SDI files in /zinc-22x/sets/ as of 2024-05- | == Freshly pdated SDI files == | ||
* new SDI files in /zinc-22x/sets/ as of 2024-05-20 | |||
(preparation in progress, will be released soon) | |||
== New feedback form == | |||
So you can tell us how we are doing, report bugs, lightweight, all in a | |||
[https://forms.gle/LZV1FCmLWxUWznVi9 simple google form]. | |||
== Wiki restructuring and cleanup == | |||
Long overdue wiki cleanup has begun. It is a never-ended task. | |||
== /zinc-22c/ zwitterions == | |||
Recently updated to H19. | |||
== /zinc-22a/ Enamine in stock. | |||
Update is in progress and will appear soon. This is "the other informer set" | |||
[[Category:ZINC-22-news]] | [[Category:ZINC-22-news]] | ||
Revision as of 22:03, 16 May 2024
This is our first news report for a long time.
- DRAFT**
Enamine Macrocycles
- We have released a new layer /zinc-22w/, Enamine macrocycles. There are about 5000 macrocycles. We have no idea whether these are any good for docking. Please let us know. Unusually, we have allowed up to H39, whereas for small molecules we only load and build up to H29.
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
- 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.
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)
New feedback form
So you can tell us how we are doing, report bugs, lightweight, all in a simple google form.
Wiki restructuring and cleanup
Long overdue wiki cleanup has begun. It is a never-ended task.
/zinc-22c/ zwitterions
Recently updated to H19.
== /zinc-22a/ Enamine in stock. Update is in progress and will appear soon. This is "the other informer set"