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TM-align is a computer algorithm for protein structure alignment using dynamic
programming and TM-score rotation matrix. An optimal alignment between two
proteins, as well as the TM-score, will be reported for each comparison. The
value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller
0.2 indicates that there is no similarity between two structures; a TM-score
greater 0.5 means the structures share the same fold.
What is the difference between TM-score and TM-align? The TM-score program
is to compare two models based on their given and known residue equivalency.
It is usually NOT applied to compare two proteins of different sequences. The
TM-align is a structural alignment program for comparing two proteins whose
sequences can be different. The TM-align will first find the best equivalent
residues of two proteins based on the structure similarity and then output a
TM-score. The TM-score values in both programs have the same definition.