structural comparison with TM score

Question

[silvia.caprari84]

Hi all,

I am trying to use TM align to make structure comparisons among some of my proteins. I would like to build a similarity matrix to be used as an input to build a hierarchical tree of these proteins based on TM score. My problem is, as far as I saw, TM align runs taking in input just two proteins. So, I was wondering how I can perform the structural comparison if I want to build a matrix similarity based on TM score among more pairs of proteins (and not only one pair).

Thank you very much,

Silvia

Answer 1

[xiaoguang]

Have you got any idea about this question? I think a good idea is to calculate TMscore for each pair of proteins and use these values to build matrix, But a key question maybe the you will be given two Tmscore when perfoming paird alignments