Question is on the applicability of TM-score from TM-align for the quantification of structural similarities among proteins which are non-identical in sequences.
I wanted to compare three proteins. First two are identical in sequence (protein-1 and protein-2) and the third one (protein-3) is non-identical homologous protein to the first two proteins. If I wanted compare protein-2 with protein-3 in terms of how close they are with protein-1, can I use TM-score for such comparison?
Let say TM-score for protein-2 with protein-1 is 0.87 and TM-score for protein-3 with protein-1 is 0.79. Can I say protein-2 is closer to protein-1 than protein-3?
This is basically to compare comparative model with templates that are used in comparative/homology modeling in terms of how structurally they are close to native crystal structure of comparative model.
Thank you.