In bioinformatics, the template modeling score or TM-score is a measure of similarity between two protein structures with different tertiary structures. The TM-score is intended as a more accurate measure of the quality of full-length protein structures than the often used RMSD and GDT measures. The TM-score indicates the difference between two structures by a score between ( 0 , 1 ] , where 1 indicates a perfect match between two structures (thus the higher the better). 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. A quantitative study 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 probabilities increase rapidly when TM-score > 0.5. The TM-score is designed to be independent of protein lengths.
TM-score = max [ 1 L target ∑ i L aligned 1 1 + ( d i d 0 ( L target ) ) 2 ] where L target and L aligned are the lengths of the target protein and the aligned region respectively. d i is the distance between the i th pair of residues and
d 0 ( L target ) = 1.24 L target − 15 3 − 1.8 is a distance scale that normalizes distances.
