Where can I find the confidence value of a Prediction on Omegafold ?

[PierrePaillard]

Heyy,

I've already predicted several protein structures with Alphafold2.0 using a colab-notebook. But I have to predict around 100 protein structures and so I've heard about Omegafold wich can predict protein structures in a very short time compared to Alphafold.

I'm on macOS and I've used the terminal commands in order to do my prediction job. All my proteins have been predicted but I can't find the confidence value of the prediction with Omegafold (I mean the pLDDT score, wich is given by Alphafold).

Do you know if Omegafold gives with the pdb structure prediction, a file containing the confidence value of the prediction (pLDDT) ? If it does, Do you know how to find this file ??

Thank you for any help you can offer Pierre

[EdgarAraya]

The output PDB file that OmegaFold produces has the pLDDT on the bfactor column, you can visualize it with software such as ChimeraX or extract it from the PDB as an average or from the residues you need.

[jonlevi]

Jumping in on this thread. Is there a concept of "pae" in OmegaFold? I know that their version of pLDDT is in the bfactor column (thanks @EdgarAraya ), but I was wondering if the package also has some kind of "predicted aligned error" as well. Those are two distinct confidence metrics, you can see more about the distinction in here