TM-align is an algorithm for sequence 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
heuristic dynamic programming iterations.
An optimal superposition of the two structures built on the detected alignment,
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 correspond to randomly chosen unrelated proteins while those
higher than 0.5 assume generally the same fold in SCOP/CATH.
TM-align now allows for input structure with
C++ version of TM-align
is now officially released.
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 TM-align source code
coded in Fortran77 (or C++). 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
>g++ -static -O3 -ffast-math -lm -o TMalign TMalign.cpp
- 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).
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 residue equivalency (i.e., based on the residue index in the PDB file).
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;
however, the TM-score value reported by TM-align is usually higher than that reported by TM-score
program due to the optimized alignment in TM-align.
- Why are there two TM-scores reported 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).