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TM-score is a metric for assessing the topological similarity of protein structures. It is designed to solve two major problems in traditional metrics such as root-mean-square deviation (RMSD): (1) TM-score weights smaller distance errors stronger than larger distance errors and makes the score value more sensitive to the global fold similarity than to the local structural variations; (2) TM-score introduces a length-dependent scale to normalize the distance errors and makes the magnitude of TM-score length-independent for random structure pairs. TM-score has the value in (0,1], where 1 indicates a perfect match between two structures. Following strict statistics of structures in the PDB, scores below 0.17 correspond to randomly chosen unrelated proteins whereas structures with a score higher than 0.5 assume generally the same fold in SCOP/CATH. The equation of TM-score can be found at Wikipedia or the original publication. Please read "Problem and Solution", if you have problem on how to calculate TM-score for protein/RNA/DNA structures.

News: TM-score allows for input structure with either PDB or PDBx/mmCIF format. Meanwhile C++ version of TM-score is available now.

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TM-score on-line (view an example of output)

Input Structure 1, Template/model in PDB format or PDBx/mmCIF format (mandatory):
Please copy and paste your structure file here. Sample input

Or upload the stucture file:



Input Structure 2, Experimental structure in PDB format (mandatory):
Please copy and paste your structure file here. Sample input

Or upload the stucture file:


These are complex structures (server will merge all chains and compare them as monomers).


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

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TM-score download

• Click TMscore.cpp (last update: 2022/2/27) to download the newest version of the TM-score source code in C++. You can compile the program in your Linux computer by (you can ignore the '-static' option for some machines, such as Mac, which does not support static build):
  
  >g++ -static -O3 -ffast-math -lm -o TMscore TMscore.cpp
• Click TMscore.f (last update: 2019/8/22) to download the newest version of the TM-score source code in Fortran77. You can compile the program in your Linux computer by (you can ignore the '-static' option for some machines, such as Mac, which does not support static build):
  
  $ gfortran -static -O3 -ffast-math -lm -o TMscore TMscore.f
  or
  $ g77 -static -O3 -lm -o TMscore TMscore.f
  
• Click TMscoreLinux.zip, TMscoreWin.zip, and TMscoreMac.zip to download the executable program for Linux, Windows and Mac OS systems. Nevertheless, it is recommended to download the TM-score source code and compile it on your machine, which gives you higher speed to run the program (See above step). If Mac OS complaint about "cannot be opened because the developer cannot be verified", run the following to change the permission:
  $ gzip TMscore
  $ gzip -d TMscore.gz
• Click TMscore_subroutine.f to download the subroutine code that can quickly calculate TM-score and be conveniently included as a subroutine in any Fortran program.
• Click RMSD.f to download the source code for calculating RMSD only.
• Click TMscore.jar.tar.gz to download a java version of the TM-score program (last update: 2012/05/02).

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TM-score other information

• How to calculate TM-score if your model and native structures are mislabelled?
• Click TM-score Help to view a brief instruction on how to run TM-score program.
• Click here to view Frequently Asked Questions on TM-score.
• What is the difference between TM-score and TM-align?
  The TM-score program is to compare two protein structures based on their given residue equivalency (i.e., based on the residue index in the PDB file). 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; however, the TM-score value reported by TM-align is usually higher than that reported by TM-score program due to the optimized alignment in TM-align.
• Why is TM-score different when normalized by different proteins?
  Suppose we compare the following two structures:

  AAAAAABBBBBB
  AAAAAA
  

  Apparently, the structural similarity is a relative quality in this example, i.e., the structural similarity (i.e., the full-match in the N-terminal domain) is 100% to the second structure while the similarity is only 50% relative to the first structure. This is the reason that we need to specify which protein the TM-score is normalized by, when we report a TM-score value. Be default, TM-score program reports the TM-score that is normalized by the length of the second protein.
• Update history (please always download the newest version of TMscore.f and TMscore programs):
  • 2005/10/19: the program was reformed so that the score values are not dependent on the specific compilers.
  • 2006/06/20: selected 'A' if there is altLoc when reading PDB file.
  • 2007/02/05: fixed a bug with length<15 in TMscore_32.
  • 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
  • 2007/12/06: GDT-HA score was added, fixed a bug for reading PDB.
  • 2010/08/02: A new RMSD matrix was used and obsolete statement removed.
  • 2011/01/03: The length of pdb file names were extended to 500.
  • 2011/01/30: An open source license is attached to the program.
  • 2012/05/07: Improved RMSD calculation subroutine which speeds up TM-score program by 30%.
  • 2012/06/05: Added an option '-l L' which calculates TM-score (and maxub and GDT scores) normalized by a specific length 'L'.
  • 2012/12/17: Added 'TM.sup_atm' to superpose full-atom structures. The former superposition is for CA-trace only.
  • 2013/05/08: Update TM-score so that it can read all alternate location indicators and residue insertions.
  • 2013/05/11: Fix a bug in array overflow.
  • 2016/03/23: Extended the program to allow calculating TM-score for complex structure comparisons, where multiple-chains are merged into a single chain. Real chain ID (instead of artificial ones) is now included in the output files.
  • 2019/07/08: Enabled TM-score to support both PDB and mmCIF formats, and updated structure reading which makes program faster.
  • 2019/08/18: Fixed multiple bugs associated with mmCIF formats.
  • 2019/08/22: Added output scripts for pymol, C++ version was included.
  • 2022/04/15: The C++ version program can now calculate TM-score for proteins, RNAs and DNA structures. A new option "-seq" was added to the C++ version program for calculating TM-score based on sequence alignment. This option was specifically designed for calculating TM-scores for structures with incorrect order number (see Problem and Solution on Calculating TM-score for protein/RNA/DNA Structures).
  
  
• References:
  • Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, 57: 702-710 (2004) (download the PDF file and Correction).
    
  • J. Xu, Y. Zhang, How significant is a protein structure similarity with TM-score=0.5? Bioinformatics, 26, 889-895 (2010) (download the PDF file).