Difference between revisions of "ZINC-22 Clean Up in Jan 2022"

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(Provisional description of major changes in the ZINC-22 database.)
 
m (Update)
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We started builing ZINC-22 before we really had all of the catalogging apparatus ready. As a result, some tranches were damaged, have been lost, and must be rebuilt.  
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We started builing ZINC-22 before all of the cataloging apparatus was ready. As a result, some tranches were damaged, have been lost, and must be rebuilt.  
  
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We cleaned up ZINC-22 in the first week of January 2022 as follows:
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We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable.
  
 
  generation tranche.        count
 
  generation tranche.        count
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  zinc-22u | H22P320_390  | 1097048
 
  zinc-22u | H22P320_390  | 1097048
  
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A total of 47.6 M 3D molecules were deleted.  If you docked ZINC_22 before Jan 4, 2022, you may have docked these molecules.
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molecules in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org.  
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These molecules will not look up correctly in Cartblanche22.docking.org. However, you can still look for them using
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However, they CAN be found by searching the SMILES in the swp.docking.org service.  
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the SMILES lookup feature.  
 
  
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At the time of writing (Jan 4 noon) there are still problems with H26 to H29. These will be resolved asap.
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* we still must build a new smallworld and arthor index based on ZINC-22 2d-12.  (JJ, Ben)
  
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We are currently investigating whether 2d-0? (1-8), representing the pre-2022 database, are complete and correct.  
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* there are remaining problems with H26-H29 that we are aware of and are working on.  
  
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The current 2d database is /nfs/exb/zinc22/2d-12. We are currently investigating whether anything from 2d-0? is missing.  
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* We have found a bug in which a few thousand molecules have been incorrectly treated as radicals.  
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We are working to fix this.  For now, ignore.  
  
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There are a small number of molecules in the 3D production /nfs/exd/zinc-22? that are not present in 2d-0? and 2d-12.
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If a molecule does not look up correctly, you can always use its SMILES code.
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We are working on figuring out how many, and what to do about them.  
 
  
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If a molecule does not look up correctly, you can always use its SMILES code.
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Thank you for reading.

Revision as of 01:01, 5 January 2022

We started builing ZINC-22 before all of the cataloging apparatus was ready. As a result, some tranches were damaged, have been lost, and must be rebuilt.

We cleaned up ZINC-22 in the first week of January 2022, deleting 47.6 million 3D molecules that you have likely docked. We are sorry but this was unavoidable. 

generation tranche.        count
-----------------------------------
zinc-22x | H24P200_230   | 38034845
zinc-22u | H24P200_230   | 2105987
zinc-22k | H24P200_230   | 81295
zinc-22l | H24P200_230   | 39679
zinc-22m | H24P200_230   | 52743
zinc-22o | H24P200_230   | 751764
zinc-22p | H24P200_230   | 2105987
zinc-22x | H22P320_390   | 3895304
zinc-22u | H22P320_390   | 1097048

molecules in these tranches will NOT be findable by ZINC code in Cartblanche22.docking.org. However, they CAN be found by searching the SMILES in the swp.docking.org service.

  • we still must build a new smallworld and arthor index based on ZINC-22 2d-12. (JJ, Ben)
  • there are remaining problems with H26-H29 that we are aware of and are working on.
  • We have found a bug in which a few thousand molecules have been incorrectly treated as radicals.

We are working to fix this. For now, ignore.

If a molecule does not look up correctly, you can always use its SMILES code.

Thank you for reading.

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