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 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 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 on-line (view an example of output)

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.

  • Input Structure 1 in PDB format (mandatory):
    Please copy and paste your structure file here. Sample input

    Or upload the stucture file:

  • Input Structure 2 in PDB format by which TM-score will be normalized (mandatory):
    Please copy and paste your structure file here. Sample input

    Or upload the stucture file:

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

TM-align download

  • 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:
  • 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). | (734) 647-1549 | 100 Washtenaw Avenue Ann Arbor, MI 48109-2218