Selecting tranches in ZINC22

Current method to select tranches to dock in ZINC 22 .

platforms

We support three platforms:

• our cluster, .txt suffix
• Wynton, .wyn suffix
• AWS, .s3 suffix

If you are on another platform, we suggest using and adapting one of these three.

Prepared subsets in "sets"

• by HAC by number of atoms
• by calculated LogP within 0.1 units.
• by charge -4 to +4.

Look in /nfs/exd/zinc-22/sets/

e.g. to dock neutrals (N), H17, lead-like, on Wynton, you would use

/wynton/group/bks/sets/N-H17.lead-like.wyn

similarly, to dock mono cations, H23-H25, lead-like, on our cluster, use

/nfs/exd/sets/O-H2[345].lead-like.txt

and to dock all charges of fragment-like, H07 to H16, on AWS, use

sets/?-H0[789].frag-like.s3 sets/?-H1[0-6].frag-like.s3

more granularity use "dirs"

Thus, use /wynton/group/bks/sets/dirs/ or /nfs/exd/sets/dirs.

The format is <charge>-<logPbin>-<Hbin>.<layer>.<suffix> where

• suffix is one of s3, wyn, txt
• layer is a-z see ZINC22:Layers
• Hbin is H04 to H49
• charge is N=0, O=+1, M=-1, etc from J to R.
• logP bin is
  • P359 = LogP 3.5 to 3.99
  • P304 = logP 3.0 to 3.49
  • P012 = LogP 0-2
  • M = LogP < 0
  • P4 = LogP 4.0 to 4.99
  • P56789 = logP > 5.0

You can learn about how the sets were assembled using make-sets.csh make-sets.csh in turn uses files in /nfs/exd/jjiwork/dirs/ these in turn are created using make-files2.csh in /nfs/exd/jjiwork/

We can adjust these subsets based on what people want. It is easy, we just need to do it.