TM-align is an algorithm for sequence-order independent protein structure comparisons.
For two protein structures of unknown equivalence, TM-align first generates
optimized residue-to-residue alignment based on structural similarity using
dynamic programming iterations.
An optimal superposition of the two structures, as well as the
TM-score value which
scales the structural similarity, will be returned.
TM-score has the value in (0,1], where 1 indicates a perfect match between
two structures. Following strict statistics of structures in the PDB, scores
below 0.2 corresponds to randomly chosen unrelated proteins whereas with a score
higher than 0.5 assume generally the same fold in SCOP/CATH.
Note: This server is only for pair-wise structure comparison.
If you want to match one protein structure with all proteins in the PDB
library, you can do it in COFACTOR Server.
- Click TMalign.f to download the newest version of
the source code of TM-align
coded in Fortran77. You can compile the program in your Linux computer by
(you can ignore the '-static' option for some machines, such as Mac, which does not support static build):
>gfortran -static -O3 -ffast-math -lm -o TMalign TMalign.f (recommended)
>g77 -static -O3 -lm -o TMalign TMalign.f
- Click TMalign to download the F77 executable program
for Linux system. Nevetheless, it is strongly recommended to download the
TM-align source code and compile it on your machine, which gives you higher
speed to run the program (See above step).
- Click TMalignc.tar.gz
to download the TM-align package written in c++
(Read about TMalignC,
last update on 2016/05/25).
TM-align other information
- Click TM-align Help
to view a brief instruction on how to run TM-align program.
- Click example
to view an example of TM-align server output.
- Click benchmark to download a set of 200 non-homologous proteins
taken from PDB (sequence identity<30%);
this set of proteins was used as a benchmark test of TM-align method. The
result is summarized in the Table I of the paper below.
- 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.
- Why are there two TM-scores in
Suppose we match the following two structures:
Apparently, the structural similarity is a relative quality in this example, i.e.,
the structural similarity (i.e., the full-match in the N-terminal domain) is 100% to the
second structure while the similarity is only 50%
relative to the first structure. This is the reason that TM-align reports two TM-scores, where the first
TM-score is normalized by the length of the first structure and the second by the length of the second
The newest updates of TM-align program:
- Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm
based on TM-score, Nucleic Acids Research, 33: 2302-2309 (2005)
(download the PDF file).