RMSD VALUE AND TM SCORE

[priya]

Hi all, When I work with online servers for my protein, i get an RMSD value of -1 and TM score of -1. What does these values suggest of my protein? can any one of you explain? regards priya    "Success is a journey, not a destination." – Ralph Arbitelle

[Susanna Lamers]

From the I-Tasser web page:

TM-score and RMSD are known standards for measuring structural similarity between two structures which are
usually used to measure the accuracy of structure modeling when the native structure is known. In case
where the native structure is not known, it becomes necessary to predict the quality of the modeling 
prediction, i.e. what is the distance between the predicted model and the native structures? To answer this
question, we tried predicted the TM-score and RMSD of the predicted models relative the native structures
based on the C-score. 

In a benchmark test set of 500 non-homologous proteins, we found that C-score is highly correlated with 
TM-score and RMSD. Correlation coefficient of C-score of the first model with TM-score to the native 
structure is 0.91, while the coefficient of C-score with RMSD to the native structure is 0.75. These data 
actually lay the base for the reliable prediction of the TM-score and RMSD using C-score. Values reported 
in Column 3 & 4 are the estimated values of TM-score and RMSD based on their correlation with C-score. 
Here we only report the quality prediction (TM-score and RMSD) for the first model, because we found that 
the correlation between C-score and TM-score is weak for lower rank models. However, we list the C-score 
of all models just for a reference.

What is TM-score? 

TM-score is a recently proposed scale for measuring the structural similarity between two structures 
(see Zhang and Skolnick, Scoring function for automated assessment of protein structure template quality,
Proteins, 2004 57: 702-710). The purpose of proposing TM-score is to solve the problem of RMSD which
is sensitive to the local error. Because RMSD is an average distance of all residue pairs in two structures,
a local error (e.g. a misorientation of the tail) will araise a big RMSD value although the global topology
is correct. In TM-score, however, the small distance is weighted stronger than the big distance which makes 
the score insensitive to the local modeling error. A TM-score >0.5 indicates a model of correct topology and 
a TM-score<0.17 means a random similarity. These cutoff does not depends on the protein length.

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