TM-score: Assessment of quality of protein structure templates and full-length model predictions

TM-score is an algorithm to calculate the similarity of topologies of two proteins/models. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. A single score between (0,1] is assigned to each comparison. Based on statistics, if a template/model has a TM-score around or below 0.17, it means the prediction is nothing more than a random selection from PDB library.

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.

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

  • Click here 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 here to download the source of the entire program coded in Fortran77, which you can compile in your computer.
  • Click here to download the subroutine code that can quickly calculate TM-score and be conveniently included as a subroutine in any Fortran program.
    Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, 2004 57: 702-710 (download the PDF file).