Template modeling score: Difference between revisions
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The '''Template Modeling Score''' or '''TM-score''' is a measure of similarity between two [[protein structure]]s with different [[tertiary structure]]s. The TM-score is intended as a more accurate measure of the quality of full-length protein structures than the often used [[Root mean square deviation (bioinformatics)|RMSD]] and [[Global distance test|GDT]] measures. The TM-score indicates the difference between two structures by a score between <math>(0,1]</math>, where 1 indicates a perfect match between two structures<ref name="zhang2004">{{cite journal |author=Zhang Y and Skolnick J |title=Scoring function for automated assessment of protein structure template quality |journal=Proteins |volume=57 |pages=702–710 |year=2004 |pmid=15476259}}</ref>. 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<ref name="zhang2005">{{cite journal |author=Zhang Y and Skolnick J |title=TM-align: a protein structure alignment algorithm based on the TM-score |journal=Nucleic Acids Res |volume=33 | issue=7 |pages=2302–2309 |year=2005 |pmid=15849316}}</ref>. |
The '''Template Modeling Score''' or '''TM-score''' is a measure of similarity between two [[protein structure]]s with different [[tertiary structure]]s. The TM-score is intended as a more accurate measure of the quality of full-length protein structures than the often used [[Root mean square deviation (bioinformatics)|RMSD]] and [[Global distance test|GDT]] measures. The TM-score indicates the difference between two structures by a score between <math>(0,1]</math>, where 1 indicates a perfect match between two structures<ref name="zhang2004">{{cite journal |author=Zhang Y and Skolnick J |title=Scoring function for automated assessment of protein structure template quality |journal=Proteins |volume=57 |pages=702–710 |year=2004 |pmid=15476259 |doi=10.1002/prot.20264 |issue=4}}</ref>. 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<ref name="zhang2005">{{cite journal |author=Zhang Y and Skolnick J |title=TM-align: a protein structure alignment algorithm based on the TM-score |journal=Nucleic Acids Res |volume=33 | issue=7 |pages=2302–2309 |year=2005 |pmid=15849316 |doi=10.1093/nar/gki524 |pmc=1084323}}</ref>. |
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A quantitative study |
A quantitative study |
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<ref name="xu2010">{{cite journal |author=Xu J and Zhang Y |title=How significant is a protein structure similarity with TM-score=0.5? |journal=Bioinformatics |volume=26 | issue=7 |pages= |
<ref name="xu2010">{{cite journal |author=Xu J and Zhang Y |title=How significant is a protein structure similarity with TM-score=0.5? |journal=Bioinformatics |volume=26 | issue=7 |pages=889–895 |year=2010 |pmid=20164152 |doi=10.1093/bioinformatics/btq066}}</ref> |
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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. |
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. |
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Revision as of 18:39, 3 May 2010
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 , where 1 indicates a perfect match between two 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 probabilities increase rapidly when TM-score >0.5. The TM-score is designed to be independent of protein lengths.
![{\displaystyle (0,1]}](https://wikimedia.org/enwiki/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/enwiki/api/rest_v1/media/math/render/svg/b4060343d9326c07d0b109346b3cc7f9fbce6333)
where and are the lengths 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/enwiki/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
- LCS — a different 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. PMID 20164152.
External links
- TM-score webserver — by the Yang Zhang research group. Calculates TM-score and supplies source code.