How to evaluate the confidence of a multimer ？

[genomicsgroup]

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？

[nikita-smetanin]

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

[genomicsgroup]

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

[nikita-smetanin]

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.