protein ordering changes the pdockQ score

[akdess]

Hi,

Thanks a lot for developing this great tool.

I am trying to run interaction analysis on two proteins.

bash predict_single.sh A.fasta B.fasta gives pdockQ score of 0.5
bash predict_single.sh B.fasta A.fasta gives pdockQ score of 0
How should I interpret this score?

Additionally running bash predict_single.sh A.fasta B.fasta also sometimes give inconsistent results, sometimes higher than 0.5 and sometimes around 0. It might be related to the Alphafold algorithm random features.

Thanks a lot!

[patrickbryant1]

Hi,

This is interesting. Yes, the MSAs are samples which can result in different results, but it should not differ this much on average. Can you please run it 5 times in each order and confirm that the scores remain the same?