TMalign.f:

This program is to identify the best alignment of two protein
structures that gives the highest TM-score. Input structures must
be in the PDB format. By default, TM-score is normalized by the
second protein. Users can obtain a brief instruction by simply
running the program without arguments. For comments/suggestions,
please contact email: zhng@umich.edu.

Reference to cite:
Yang Zhang, Jeffrey Skolnick, Nucl. Acid Res. 2005 33: 2303-9

Permission to use, copy, modify, and distribute this program for
any purpose, with or without fee, is hereby granted, provided that
the notices on the head, the reference information, and this
copyright notice appear in all copies or substantial portions of
the Software. It is provided "as is" without express or implied
warranty.

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TMscore.f:

This program is to compare two protein structures and identify the
best superposition that has the highest TM-score. Input structures
must be in the PDB format. By default, TM-score is normalized by
the second protein. Users can obtain a brief instruction by simply
running the program without arguments. For comments/suggestions,
please contact email: zhng@umich.edu.

Reference:
Yang Zhang, Jeffrey Skolnick, Proteins, 2004 57:702-10.

Permission to use, copy, modify, and distribute this program for
any purpose, with or without fee, is hereby granted, provided that
the notices on the head, the reference information, and this
copyright notice appear in all copies or substantial portions of
the Software. It is provided "as is" without express or implied
warranty.