Take into account pLDDT into TM-score
Posted: Fri Dec 09, 2022 11:13 am
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?
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?