In bioinformatics, the template modeling score or TM-score is a measure of similarity between two protein structures. The TM-score is intended as a more accurate measure of the global similarity of full-length protein structures than the often used RMSD, 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.

The TM-score equation

TM-score between two protein structures (e.g., a template structure and a target structure) is defined by

is a distance scale that normalizes distances. The maximum is taken over all possible structure superpositions of the model and template (or some sample thereof).

reads from the C-alpha order number of the structure files (i.e., Column 23-26 in Protein Data Bank (file format)). When comparing two protein structures that have different sequences and/or different residue orders, a structural alignment is usually performed first, and TM-score is then calculated on the commonly aligned residues from the structural alignment.

Other measures

An often used structural similarity measure is root-mean-square deviation 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. 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.

See also

• RMSD a different structure comparison measure

• GDT a different structure comparison measure

• Longest continuous segment (LCS) A different structure comparison measure

• Global distance calculation (GDC_sc, GDC_all) Structure comparison measures that use full-model information (not just α-carbon) to assess similarity

• Local global alignment (LGA) Protein structure alignment program and structure comparison measure

References

External links

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

• GDT and LGA description services and documentation on structure comparison and similarity measures.