Selecting tranches in ZINC22: Difference between revisions
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Current method to select tranches to dock in ZINC 22 . | Current method to select tranches to dock in ZINC 22 . | ||
== 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 | == 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 | ||
| Line 20: | Line 25: | ||
/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> | ||
| Line 30: | Line 37: | ||
/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.