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.
+
== 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
+
* 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
 
* 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>
  
 +
== 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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  /sets/H26-H29.big.<suffix>
 
  /sets/H26-H29.big.<suffix>
 
  /sets/H26-H29.big-greasy.<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.
  
  
 
[[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.