Template modeling score

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 measure. The TM-score indicates the similarity between two structures by a score between

(

0

,

1

]

{\displaystyle (0,1]}

, 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

TM-score

=

max

[

1

L

target

∑

i

L

common

1

1

+

(

d

i

d

0

(

L

target

)

)

2

]

{\displaystyle {\text{TM-score}}=\max \left[{\frac {1}{L_{\text{target}}}}\sum _{i}^{L_{\text{common}}}{\frac {1}{1+\left({\frac {d_{i}}{d_{0}(L_{\text{target}})}}\right)^{2}}}\right]}

where

L

target

{\displaystyle L_{\text{target}}}

is the length of the amino acid sequence of the target protein,

and

L

common

{\displaystyle L_{\text{common}}}

is the number of residues that appear in both the template and target structures.

d

i

{\displaystyle d_{i}}

is the distance between the

i

{\displaystyle i}

th pair of residues in the template and target structures, and

d

0

(

L

target

)

=

1.24

L

target

−

15

3

−

1.8

{\displaystyle d_{0}(L_{\text{target}})=1.24{\sqrt[{3}]{L_{\text{target}}-15}}-1.8}

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).