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Cross-posted on AI Stack Exchange.


We are running alphafold2 multimer on Google Colab to predict the association between two proteins.

It generally works fine, but we get an asymmetric PAE plot for a specific pair. Does anyone know why this might happen? I assumed these must always be symmetrical.

I have provided a figure below:

enter image description here

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Predicted alignment error is not always symmetric. This page from the European Bioinformatics Institute says:

"predicted_aligned_error: The PAE value of the residue pair, rounded to the closest integer. For the PAE value at position (i, j), i is the residue on which the structure is aligned, j is the residue on which the error is predicted."

So if when aligning on residue i we get a bad prediction at residue j, but when aligning on residue j we get a good prediction at residue i, then the PAE plot will be asymmetric.

Below I present two PAE plots from this website by Tom Goddard (5 April 2022) hosted by UCSF. The first one looks quite symmetric at first, but I did find some subtle asymmetries, which I've boxed with a red outline:

enter image description here





The second one is more obviously asymmetric:


enter image description here

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