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TM-score: Quantitative assessment of protein structure similarities
TM-score is an algorithm to calculate the similarity
of topologies of two protein structures. It can be exploited to
quantitatively access the quality of protein structure predictions
relative to native.
Because TM-score weights the close matchs stronger than the
distant matchs, TM-score is more sensitive than root-mean-square
deviation (RMSD) (An illustative example can be found from here).
A single score between (0,1] is assigned to
each comparison. Based on statistics, if a template/model has a
TM-score around or below 0.17, it means the prediction is nothing
more than a random selection from PDB library.
What is the difference between TM-score and TM-align?
The TM-score program is to compare two models based on their given and
known residue equivalency. It is usually NOT applied to compare
two proteins of different sequences.
The TM-align is a structural alignment program for comparing two proteins
whose sequences can be different. The TM-align will first find the
best equivalent residues of two proteins based on the structure similarity
and then output a TM-score.
The TM-score values in both programs have the same definition.
TM-score FAQ
TM-score on-line
Update history (please always download the newest version of TMscore.f and TMscore programs)
- 2005/10/19: the program was reformed so that the score values
are not dependent on the specific compilers.
- 2006/06/20: select 'A' if there is altLoc when reading PDB file
- 2007/02/05: fix a bug with length<15 in TMscore_32
- 2007/02/27: rotation matrix from Chain-1 to Chain-2 is added
- 2007/12/06: GDT-HA score is added, fixed a bug for reading PDB
Click TMscore to download the executable program for Linux system.
Simply running the program itself will give you a brief instruction of how
to use it. (In case that you are using a 32 bit computer and you get warning
message of "bash: ./TMscore: cannot execute binary file", you need to
download a 32-bit version of TMscore which is a little bit slower.)
Click TMscore.f to download the source of the entire program coded in Fortran77, which you can compile in your computer.
Click TMscore_subroutine.f to download the subroutine code that can quickly calculate TM-score and be conveniently included as a subroutine in any Fortran program.
References:
Y. Zhang, J. Skolnick, Scoring function for automated assessment of
protein structure template quality, Proteins, 2004 57: 702-710
(download the PDF file and Correction).
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