ZINC Database Updates

Questions, comments, and feedback.

ZINC Database Updates

Postby dkoes » March 29th, 2012, 8:42 am

Every couple of months the ZINC people update the purchasable subset. Every update results in a few million compounds being removed and a few million new compounds being added. Up until now I have been silently pushing out the updates to ZINCPharmer. From this point on I will post to this thread when the ZINCPharmer database is changed.

The general process when a new subset is made available is to
  1. Download SMILES
  2. Generate top ten conformers (using omega -rms .7) for new compounds
  3. Create a set of structures consisting only of those compounds in the new purchasable set
  4. Generate the Pharmer index
  5. Restart the search engine to use the new index
  6. Post here

This whole process takes several days.
dkoes
Site Admin
 
Posts: 24
Joined: May 27th, 2011, 11:29 am

Re: ZINC Database

Postby dkoes » March 29th, 2012, 8:44 am

ZINCPharmer has been updated to use the ZINC All Purchasable subset dated 2012-03-15.

There are 170,896,974 conformations of 17,818,291 compounds.
dkoes
Site Admin
 
Posts: 24
Joined: May 27th, 2011, 11:29 am

Re: ZINC Database Updates

Postby dkoes » January 17th, 2013, 10:24 am

ZINCPharmer has been updated to use the ZINC All Purchasable subset dated 2013-01-11.

There are 187,981,253 conformers of 19,581,769 compounds.

Additionally, I have added a subset selector under the filters tab. In addition to the full purchasable set, this allows you to search the following ZINC subsets:
ZINC Drug Database
ZINC In Man
ZINC Drug Database (Metabolites)
ZINC Natural Derivatives
ZINC Natural Products

The descriptions for these subsets can be found here.
dkoes
Site Admin
 
Posts: 24
Joined: May 27th, 2011, 11:29 am

Re: ZINC Database Updates

Postby limon720 » February 26th, 2013, 9:21 am

Can you give little information about omega -rms .7.
thanks :!:

limon
Last edited by limon720 on February 28th, 2013, 9:28 am, edited 1 time in total.
limon720
 

Re: ZINC Database Updates

Postby dkoes » February 26th, 2013, 11:38 pm

limon720 wrote:Can you give little information about omega -rms .7.
thanks :!:


omega is a conformer generator from OpenEye software. The -rms .7 option requires that the generated conformers deviate by at least 0.7 RMSD. You can read more in the omega documentation. I use .7 (instead of the default .5) to get a better sampling conformational space. In my limited testing I have found that this setting results in better enrichment in pharmacophore searches compared to the default when generating 10 conformers. I have also found that omega generally does a little better than rdkit and ballon.
dkoes
Site Admin
 
Posts: 24
Joined: May 27th, 2011, 11:29 am


Return to Discussion

Who is online

Users browsing this forum: No registered users and 2 guests

cron

x