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 measure. The TM-score indicates the difference between two structures by a score between , 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 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]
![{\displaystyle (0,1]}](https://wikimedia.org/api/rest_v1/media/math/render/svg/7e70f9c241f9faa8e9fdda2e8b238e288807d7a4)
The equation
![{\displaystyle {\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]}](https://wikimedia.org/api/rest_v1/media/math/render/svg/b4060343d9326c07d0b109346b3cc7f9fbce6333)
where and are the lengths of the amino acid sequences of the target protein and the aligned region respectively. is the distance between the th pair of residues and
![{\displaystyle d_{0}(L_{\text{target}})=1.24{\sqrt[{3}]{L_{\text{target}}-15}}-1.8}](https://wikimedia.org/api/rest_v1/media/math/render/svg/6a32e5ceba3bac9ee14b1c0872b3aa65b80470b7)
is a distance scale that normalizes distances.
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
- ^ 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.
- ^ 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.
- ^ 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.
- ^ Zemla A (2003). "LGA: A method for finding 3D similarities in protein structures". Nucleic Acids Research. 31 (13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330.
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.