TM-align: A protein structure alignment algorithm using TM-score rotation matrix

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 comparing 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 TM-align program will be made available online soon. Thanks for the patience!!

  • 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.
  • Click TMalign.f to download the source of the entire program coded in Fortran77, which you can compile in your computer.
  • Click here 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.
    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).