“Template modeling score”的意思、由来-开放百科全书

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]

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]

The equation

where

and

are the lengths of the target protein and the aligned region respectively.

is the distance between the

th pair of residues and

See also

References

1. ^{{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}}
2. ^{{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}}
3. ^{{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 |pmc=2913670 |doi=10.1093/bioinformatics/btq066}}
4. ^{{cite journal |author=Zemla A |year=2003 |title=LGA: A method for finding 3D similarities in protein structures |journal=Nucleic Acids Research |volume=31 |issue=13 |pages=3370–3374 |pmid=12824330 |pmc=168977 |doi=10.1093/nar/gkg571}}

The equation

See also

References

External links