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 Email: yangzhanglabumich.edu.

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)

• 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 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).

• 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:
  • 2013/05/11: Fix a bug in array overflow (TMtools20130511.tar.gz).
  • 2013/05/08: Update TM-align so that it can read all alternate location indicators and residue insertions (TMtools20130508.tar.gz).
  • 2012/07/07: Add an option '-I align.txt' to allow user to STICK TO the inital alignment. This is different from '-i align.txt' where initial alignment can be optimized. (TMtools20120707.tar.gz).
  • 2012/05/07: Improved RMSD calculation subroutine which speeds up TM-algin program by 10%. (TMtools20120507.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 C-alpha traces (TMtools20120419.tar.gz).

    >> Read all TM-align update history ...

• 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).