Selecting tranches in ZINC22: Difference between revisions

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


== arbitrary subsets ==
== Prepared subsets in "sets" ==
We have created subsets for you (see below, but you can select subsets at a very fine grain level:
* by HAC by number of atoms
* by HAC by number of atoms
* by calculated LogP within 0.1 units.
* by calculated LogP within 0.1 units.
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Look in /nfs/exd/zinc-22/sets/
Look in /nfs/exd/zinc-22/sets/


== lead-like ==
e.g.  to dock neutrals (N), H17, lead-like, on Wynton, you would use
* if you want to dock lead-like, you want
  /wynton/group/bks/sets/N-H17.lead-like.wyn
  /sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above
similarly, to dock mono cations, H23-H25, lead-like, on our cluster, use
/sets/H20-23.lead-like.<suffix>
  /nfs/exd/sets/O-H2[345].lead-like.txt
Then, depending on whether you want to include H24 and H25, you can optionally include
and to dock all charges of fragment-like, H07 to H16, on AWS, use
  /sets/H24.lead-like.<suffix>
  sets/?-H0[789].frag-like.s3 sets/?-H1[0-6].frag-like.s3
  /sets/H25.lead-like.<suffix>
If you want to add on compounds from calculated LogP from 4.0 to 4.9
/sets/H17-19.greasy-leads.<suffix> and so on as above


== fragment-like ==
== more granularity use "dirs" ==
* if you want to dock fragments H10-H16, LogP<4
Thus, use /wynton/group/bks/sets/dirs/ or /nfs/exd/sets/dirs.  
/sets/frag-like.<suffix>


== greasy molecules ==
The format is  <charge>-<logPbin>-<Hbin>.<layer>.<suffix>  
* if you want to dock calculated logP > 5
where
/sets/H04-H19.greasy.<suffix>
* suffix is one of s3, wyn, txt
/sets/H20-29.greasy.<suffix>
* layer is a-z see [[ZINC22:Layers]]
 
* Hbin is H04 to H49
* if you want to dock big monsters (not recommended, but who knows)
* charge is N=0, O=+1, M=-1, etc from J to R.
/sets/H26-H29.big.<suffix>
* logP bin is
/sets/H26-H29.big-greasy.<suffix>
** 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
You can learn about how the sets were assembled using make-sets.csh
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We can adjust these subsets based on what people want. It is easy, we just need to do it.  
We can adjust these subsets based on what people want. It is easy, we just need to do it.  
== real life example ==
So, supposing I want to dock lead-like (H17-H25) in AWS using my S3 bucket results2021.
I assemble a file database210325.txt from four files:
cat H17-19.lead-like.s3 H20-23.lead-like.s3 H24.lead-like.s3 H25.lead-like.s3 > database210325.txt
I upload this to s3
aws s3 cp database210325.txt s3://results2021/
Then I go on AWS and I follow the instructions in [[DOCK on AWS]].
I monitor the job as it runs.
Then I harvest the results and download them to my computer.




[[Category:ZINC22]]
[[Category:ZINC22]]
[[Category:DOCK3.8]]
[[Category:DOCK3.8]]

Latest revision as of 17:56, 12 June 2024

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.

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