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

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: fix a bug of two-point superposition.
    • 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 is added.
    • 2007/04/18: add options with TM-score normalized by average length, shorter length, or longer length of two structures.
    • 2007/05/23: add additional output file 'TM.sup_all' for showing all atoms while 'TM.sup' is only for aligned atoms
    • 2007/09/19: add a new feature alignment to deal with the problem of aligning fractional structures (e.g. protein interfaces).
    • 2007/10/16: fix a bug for irregular bond-length models.
    • 2009/03/14: A new initial alignment is added and previous initial alignments are further enhanced. This change increases accuracy by 4% but increases CPU cost by 40%.
    • 2009/08/20: A bug for asymmetry alignment result was fixed.
  • Click TMalign 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: ./TMalign: cannot execute binary file", you need to download a 32-bit version of TMalign which is a little bit slower.)
  • Click TMalign.f to download the source of the entire program coded in Fortran77, which you can compile in your computer.
  • 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.
    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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