How to evaluate the confidence of a multimer ？

facebookresearch / esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

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How to evaluate the confidence of a multimer ？ #484

Open genomicsgroup opened 1 year ago

genomicsgroup commented 1 year ago

Dear developer. Thank you for ESM and ESMFold! The AlphaFold-multimer program generate the iptm & ptm score to evaluate the confidence of prediction multimers，but ESMFold only generate pLDDT & pTM score in stdout, how to evaluate the confidence of ESMFold multimers？

nikitos9000 commented 1 year ago

Hi, ESMFold doesn't support multimer-specific evaluation metrics at the moment. The multimer inference is implemented via simple linking.

genomicsgroup commented 1 year ago

Is there any other way to calculate the iptm or dockQ/pdockQ value for multimer? Your opinions are very important to me!

nikitos9000 commented 1 year ago

Yes it's possible to calculate DockQ score, please follow https://github.com/bjornwallner/DockQ/ – it only requires ESMFold .pdb output to compute this score against natural structure.