Difference between revisions of "Selecting tranches in ZINC22"

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Current method to select tranches to dock in ZINC 22 .
 
Current method to select tranches to dock in ZINC 22 .
  
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== platforms ==
 
We support three platforms:
 
We support three platforms:
 
* our cluster, .txt suffix
 
* our cluster, .txt suffix
 
* Wynton, .wyn suffix
 
* Wynton, .wyn suffix
 
* AWS, .s3 suffix
 
* AWS, .s3 suffix
 +
If you are on another platform, suggest using one of these three.
  
We have created subsets, but you can select subsets at a fine grain level, by HAC and calculated LogP within 0.1 units.
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== arbitrary subsets ==
 
+
We have created subsets for you (see below, but you can select subsets at a very fine grain level:
Look in  
+
* by HAC by number of atoms
/nfs/exd/zinc-22/sets
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* by calculated LogP within 0.1 units.
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* by charge -4 to +4.
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Look in /nfs/exd/zinc-22/sets/
  
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== lead-like ==
 
* if you want to dock lead-like, you want
 
* if you want to dock lead-like, you want
 
  /sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above
 
  /sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above
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  /sets/H17-19.greasy-leads.<suffix> and so on as above
 
  /sets/H17-19.greasy-leads.<suffix> and so on as above
  
 +
== fragment-like ==
 
* if you want to dock fragments H10-H16, LogP<4
 
* if you want to dock fragments H10-H16, LogP<4
 
  /sets/frag-like.<suffix>
 
  /sets/frag-like.<suffix>
  
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== greasy molecules ==
 
* if you want to dock calculated logP > 5
 
* if you want to dock calculated logP > 5
 
  /sets/H04-H19.greasy.<suffix>
 
  /sets/H04-H19.greasy.<suffix>
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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.  
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 +
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== real life example ==
 +
So, supposing I want to dock lead-like (H17-H25) in AWS using my S3 bucket results2021.
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I assemble a file database210325.txt from four files:
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 +
cat H17-19.lead-like.s3 H20-23.lead-like.s3 H24.lead-like.s3 H25.lead-like.s3 > database210325.txt
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I upload this to s3
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aws s3 cp database210325.txt s3://results2021/
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Then I go on AWS and I follow the instructions in [[DOCK on AWS]].
 +
 +
I monitor the job as it runs.
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Then I harvest the results and download them to my computer.
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[[Category:ZINC22]]
 
[[Category:ZINC22]]
 
[[Category:DOCK3.8]]
 
[[Category:DOCK3.8]]

Latest revision as of 22:19, 25 March 2021

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, suggest using one of these three.

arbitrary subsets

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 calculated LogP within 0.1 units.
  • by charge -4 to +4.

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

lead-like

  • if you want to dock lead-like, you want
/sets/H17-19.lead-like.<suffix> where <suffix> is txt, wyn or s3 as above
/sets/H20-23.lead-like.<suffix>

Then, depending on whether you want to include H24 and H25, you can optionally include

/sets/H24.lead-like.<suffix>
/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

  • if you want to dock fragments H10-H16, LogP<4
/sets/frag-like.<suffix>

greasy molecules

  • if you want to dock calculated logP > 5
/sets/H04-H19.greasy.<suffix>
/sets/H20-29.greasy.<suffix>
  • if you want to dock big monsters (not recommended, but who knows)
/sets/H26-H29.big.<suffix>
/sets/H26-H29.big-greasy.<suffix>

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.


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.