In
bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combine ...
, the template modeling score or TM-score is a measure of similarity between two
protein structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer ma ...
s. The TM-score is intended as a more accurate measure of the global similarity of full-length protein structures than the often used
RMSD
The root-mean-square deviation (RMSD) or root-mean-square error (RMSE) is a frequently used measure of the differences between values (sample or population values) predicted by a model or an estimator and the values observed. The RMSD represents ...
measure. The TM-score indicates the similarity between two structures by a score between
, 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
The posterior probability is a type of conditional probability that results from updating the prior probability with information summarized by the likelihood via an application of Bayes' rule. From an epistemological perspective, the posterior ...
of 37% in the same
CATH
The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and coll ...
topology family and of 13% in the same
SCOP
A (
or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designa ...
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
: