Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

PAE and pCMAP order of residues pair definition #53

Open
St3451 opened this issue Dec 16, 2024 · 1 comment
Open

PAE and pCMAP order of residues pair definition #53

St3451 opened this issue Dec 16, 2024 · 1 comment
Labels
high High priority

Comments

@St3451
Copy link
Collaborator

St3451 commented Dec 16, 2024

Issue
The PAE is not a symmetric matrix, for a pair of residue (i, j), the PAE matrix includes the predicted error of i when the structure is aligned to j. Now, the problem is that we are not sure if the order of residues is the one just mentioned above and, therefore, j and j could be flipped. In fact, we did implemented the calculation of the probability of contact map matrix (pc) assuming the opposite, i.e., pc(i, j) = probability of j to be in contact with i, considering pae(i, j) as the error of j when the structure is aligned to i.

https://github.com/bbglab/clustering_3d/blob/93600fb275ab9f0b049bc37e8945e432dddfa60b/scripts/datasets/prob_contact_maps.py#L130-L168

Potential solution
We should first check what is the real order for the relationship between each pair of residues in the PAE object. If pae(i, j) represents the error of j when the structure is aligned to i, then our calculation is correct. If it is the other way around, we should flip the residues in our code.

Probably, swapping the residues in the PAE matrix in line 166 could be enough:

m[i, j] = get_prob_contact(pae[j, i], d, distance)

Disclaimer
It is important to note that while the PAE matrix is indeed not symmetric, the difference between (i, j) and (j, i) is marginal. This asymmetry has a negligible impact on the 3D clustering analysis and does not significantly affect the overall results.

@St3451 St3451 added the high High priority label Dec 16, 2024
@St3451
Copy link
Collaborator Author

St3451 commented Dec 16, 2024

@koszulordie

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
high High priority
Projects
None yet
Development

No branches or pull requests

1 participant