TM-align is a computer algorithm for protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. The value of TM-score lies in (0,1]. In general, a comparison of TM-score < 0.2 indicates that there is no similarity between two structures; a TM-score > 0.5 means the structures share the same fold.

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-align on-line (example)

Structure 1 in PDB format (mandatory):


Structure 2 in PDB format by which TM-score will be normalized (mandatory):


Email: (optional, where results will be sent to)

  • Update history (please always download the newest version of TMalign.f and TMalign programs):
    • 2005/06/01: A bug of two-point superposition was fixed.
    • 2005/10/19: the program was reformed so that the alignment results are not dependent on the specific compilers.
    • 2006/06/20: select 'A' if there is altLoc when reading PDB file.
    • 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
    • 2007/04/18: added options with TM-score normalized by average length, shorter length, or longer length of two structures.
    • 2007/05/23: added additional output file 'TM.sup_all' for showing all atoms while 'TM.sup' is only for aligned atoms
    • 2007/09/19: added a new feature alignment to deal with the problem of aligning fractional structures (e.g. protein interfaces).
    • 2007/10/16: A bug for irregular bond-length models was fixed.
    • 2009/03/14: A new initial alignment was added and previous initial alignments are further enhanced. This change increased accuracy by 4% but increases CPU cost by 40%.
    • 2009/08/20: A bug for asymmetry alignment result was fixed.
    • 2010/08/02: A new RMSD matrix was used to remove obsolete statements. Staled subroutines were deleted.
    • 2011/01/03: The length of pdb file names were extended to 500.
    • 2011/01/24: Fixed a bug on output file name created on 2011/01/03.
    • 2011/01/30: An open source license is attached to the program (TMtools20110130.tar.gz).
    • 2011/09/03: A new option "-d" is added to allow users to change TM-score normalization scale. A version number is attached to the program from now on (TMtools20110903.tar.gz).
    • 2011/10/11: A new scale (d0) was introduced for alignment search. This is to mainly improve alignment selection for small proteins (e.g. L<50 residues) but also increase alignment coverage of larger proteins. Second, TM-align output format is changed and two TM-scores normalized by both chains are reported. (TMtools20111011.tar.gz).
    • 2011/10/11: Distance cutoff for gap is increased from 3.85A to 4.25A. Added 'TMalign -v' to allow user to check version number. (TMtools20111012.tar.gz).
    • 2012/01/24: Fix a bug for secondary structure definition (TMtools20120124.tar.gz).
    • 2012/04/16: Add an option to allow user to specify seed alignments, e.g. '-i align.txt'. This is used together with other inherent TM-align seeds. An example of the fasta file can be seen at http://zhanglab.ccmb.med.umich.edu/TM-align/align.txt. (TMtools20120416.tar.gz).
    • 2012/04/17: Add an option '-m matrix.txt' to output the rotation matrix in separate file, drop-off secondary-structure smooth procedure, and add one iteration in initial5. This change increases the alignment accuracy (TM-score) by 2%. (TMtools20120417.tar.gz).
    • 2012/04/19: Add additional output file 'TM.sup_atm' for showing all-atom superposition while 'TM.sup' and 'TM.sup_all' are only for (TMtools20120419.tar.gz).
    • 2012/05/07: Improved RMSD calculation subroutine which speeds up TM-algin program by 10%. (TMtools20120507.tar.gz).
  • 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)
      or
      >g77 -static -O3 -lm -o TMalign TMalign.f
  • Click TMalign to download the F77 executable program for Linux system. Nevetheless, it is 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).
  • 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.
  • 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.
    References:
    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).

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