Results from ESM?

[KeyTals]

Hello,

Thank you for creating useful tool. Would it be possible to check pdb files from ESM fold when its is used to as complex for 2 proteins ?
https://github.com/facebookresearch/esm

Thank you,
Keyur

[flyark]

Hi Keyur,

If ESM prediction generates both structure and confidence (like PAE) files, I can implement. Does ESM generate confidence files?

Ah-Ram

[KeyTals]

No it doesnt generate PAE like files. Hence i wanted ask for guidance if any way to visualize the interaction using LIVIA.

Keyur

[flyark]

Unfortunately, without PAE like files, visualization only for confident residues can't be hard since we don't know which residues are confidently predicted or not.

[flyark]

Hi, I tested ESMFold2 recently and this seemed nice for PPI discovery. You can check this out and use LIVIA website for analyzing predicted protein complex. You can find out p53-MDM2 example file.

[KeyTals]

Could you please let me know how you generated json file for ESMFold2 ?

Keyur

[flyark]

You can check these out. There are instructions for API-based prediction, which allows download of PAE matrix.

https://biohub.ai/models/esmfold2
https://github.com/Biohub/esm