In bioinformatics, the template modeling score or TM-score is a measure of similarity between two protein structures.
[1] Generally scores below 0.20 corresponds to randomly chosen unrelated proteins whereas structures with a score higher than 0.5 assume roughly the same fold.
[2] A quantitative study [3] shows that proteins of TM-score = 0.5 have a posterior probability of 37% in the same CATH topology family and of 13% in the same SCOP fold family.
The TM-score is designed to be independent of protein lengths.
is the length of the amino acid sequence of the target protein, and
is the number of residues that appear in both the template and target structures.
th pair of residues in the template and target structures, and
The maximum is taken over all possible structure superpositions of the model and template (or some sample thereof).
When comparing two protein structures that have the same residue order,
reads from the C-alpha order number of the structure files (i.e., Column 23-26 in Protein Data Bank (file format)).
An often used structural similarity measure is root-mean-square deviation (RMSD).
) with equal weight over all residue pairs, a large local error on a few residue pairs can result in a quite large RMSD.
which makes the magnitude of TM-score length-independent for random structure pairs, while RMSD and most other measures are length-dependent metrics.
The Global Distance Test (GDT) algorithm, and its GDT TS score to represent "total score", is another measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures.
[4] GDT score has the same length-dependence issue as RMSD, because the average GDT score for random structure pairs has a power-law dependence on the protein size.