Template modeling score

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).^[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 probabilities increase rapidly when TM-score > 0.5. The TM-score is designed to be independent of protein lengths.

The equation

$\text{TM-score}=\max\left[ \frac{1}{L_\text{target}}\sum_i^{L_\text{aligned}}\frac{1}{1+\left(\frac{d_i}{d_0(L_\text{target})}\right)^2} \right]$

where $L_\text{target}$ and $L_\text{aligned}$ 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

$d_0(L_\text{target})=1.24\sqrt[3]{L_\text{target}-15}-1.8$

is a distance scale that normalizes distances.

See also

• RMSD — a different structure comparison measure
• GDT — a different structure comparison measure
• LCS — a different structure comparison measure

References

1. Zhang Y and Skolnick J (2004). "Scoring function for automated assessment of protein structure template quality". Proteins 57 (4): 702–710. doi:10.1002/prot.20264. PMID 15476259.
2. Zhang Y and Skolnick J (2005). "TM-align: a protein structure alignment algorithm based on the TM-score". Nucleic Acids Res 33 (7): 2302–2309. doi:10.1093/nar/gki524. PMC 1084323. PMID 15849316.
3. Xu J and Zhang Y (2010). "How significant is a protein structure similarity with TM-score = 0.5?". Bioinformatics 26 (7): 889–895. doi:10.1093/bioinformatics/btq066. PMC 2913670. PMID 20164152.

External links

• TM-score webserver — by the Yang Zhang research group. Calculates TM-score and supplies source code.