TM-align is a highly optimized algorithm for protein structure comparison and alignment.
For two protein structures of unknown equivalence, TM-align first generates the
residue-to-residue alignment based on structural simularity using dynamic programming iterations.
An optimal superposition of the two structures, as well as the
TM-score value which
scales the structural simularity, will be finally returned.
The TM-score value lies in (0,1].
In general, a TM-score < 0.2
indicates that there is no similarity between two structures; a TM-score
> 0.5 means the structures share the same SCOP/CATH fold.
TM-align is in active development.
Despite the high efficiency, TM-align is not yet perfect and it may not
generate the optimal alignments for some protein pairs.
We welcome users to report us examples which they believe the alignment by
TM-align is incorrect or not optimal.
This will help us to improve TM-align to generate the best structural
alignment algorithm for nearly all protein structures.
You can report to us any problem by
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
>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++ (last update on 2012/01/24).
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.
- 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, 2005 33: 2302-2309
(download the PDF file).