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Custom DDG parsing fail due to name mismatch #25

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2 of 4 tasks
St3451 opened this issue Mar 4, 2024 · 3 comments
Closed
2 of 4 tasks

Custom DDG parsing fail due to name mismatch #25

St3451 opened this issue Mar 4, 2024 · 3 comments
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bug Something isn't working low Low priority

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@St3451
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St3451 commented Mar 4, 2024

Currently, we are downloading pre-predicted data but it would be nice if we can make our own predictions

https://github.com/bbglab/clustering_3d/blob/16ab785a795810e40800cc3a3795bb1fcee6221e/scripts/plotting/stability_change.py#L39-L41

  • Try to install RaSP and make it work
  • Add a step to the annotation pipeline that predict the mutations
  • If the previous one is not sustainable, make predictions ones for humans V4 and mouse V4 and make the data available somewhere to download
  • If everything is too complex (GPU availability etc), ask them to make the predictions for us
@St3451
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St3451 commented Apr 11, 2024

Predicted all MANE structures and human proteome V4 + mouse proteome V4.
We only miss a step where we add as arg the possibility to load the ddG predicted from us.

@St3451
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St3451 commented May 10, 2024

Added custom dir for ddG predictions but we miss:

  • test it
  • predict the fragments of the fragmented structures

@St3451
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St3451 commented Jun 4, 2024

There is a bug in the parsing of the new arrays, they have different names than original.
To make it simple, change the name in the output of the predictions.

@St3451 St3451 added the bug Something isn't working label Jun 4, 2024
@St3451 St3451 changed the title DDG is only available for AF human proteome v2 Custom DDG parsing fail due to name mismatch Jun 4, 2024
@St3451 St3451 added the low Low priority label Nov 20, 2024
@St3451 St3451 closed this as completed Jan 27, 2025
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