sokrypton / sokrypton/ColabFold

Is it possible to get iPTM for pairs within a multimer?

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Description

I'm looking to calculate iPTM for each pair of proteins in a given complex (using the below formula from the Alphafold-Multimer paper). Currently, the Colabfold version of Alphafold-Multimer only gives a single iPTM score for the entire complex...

To do this, I believe I would need the logits, breaks, and asym_id from Alphafold to recalculate it to be pairwise...which it doesn't seem like Colabfold currently gives? Is it possible to access this information?

Screen Shot 2023-01-12 at 1 47 57 PM

This is where the function in Alphafold is called
https://github.com/deepmind/alphafold/blob/0be2b30b98f0da7aecb973bde04758fae67eb913/alphafold/model/model.py#L48

confidence_metrics['iptm'] = confidence.predicted_tm_score(
          logits=prediction_result['predicted_aligned_error']['logits'],
          breaks=prediction_result['predicted_aligned_error']['breaks'],
          asym_id=prediction_result['predicted_aligned_error']['asym_id'],
          interface=True)

This is the function it's calling:
https://github.com/deepmind/alphafold/blob/0be2b30b98f0da7aecb973bde04758fae67eb913/alphafold/common/confidence.py#L111

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Research direction

Start with the cited AlphaFold model.py call and alphafold/common/confidence.py predicted_tm_score function, then inspect how ColabFold exposes prediction_result data. Determine whether logits, breaks, and asym_id are available for pairwise calculations; done means the access path or its limitation is clearly established.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
bioinformatics, machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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