Take into account pLDDT into TM-score

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mariaartlle
Posts: 1
Joined: Fri Dec 09, 2022 10:25 am

Take into account pLDDT into TM-score

Post by mariaartlle »

Hi, I am currently superimposing protein structures of different species with TM-Align and using a TM-score threshold to filter. However, I have realized that, since I am using AlphaFold structures, the TM-score is heavily influenced by low pLDDT regions that appear as disordered coils. As I am trying to annotate proteins, I would like to still get a global TM-score that somehow penalizes the poor predicted regions, as long as they don't represent a large proportion of the protein.

For instance, I have a candidate protein that has an almost perfect superimposition with the core of the reference protein, but as it also has a disordered terminal region, the global TM-score drops and it does not overcome the threshold I defined to filter. Is there a correction measure that takes into account the pLDDT regions when computing the TM-score?
jlspzw
Posts: 114
Joined: Tue May 04, 2021 5:04 pm

Re: Take into account pLDDT into TM-score

Post by jlspzw »

Dear user,

If you make sure some areas are disordered, you can remove those residues both from the model and native, only keep the core region that you mentioned, then you will get a good score.

The pLDDT score and TM-score are completely different things, pLDDT score is a predicted LDDT score, so we may not integrate it in TM-score calculation. so you may want to use the method I mentioned to re-calculate the scores.

Best
IT Team
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