  This article introduces a novel protein structure alignment method (named
TALI) based on the protein backbone torsion angle instead of the more
traditional distance matrix. Because the structural alignment of the two
proteins is based on the comparison of two sequences of numbers (backbone
torsion angles), we can take advantage of a large number of well-developed
methods such as Smith-Waterman or Needleman-Wunsch. Here we report the result
of TALI in comparison to other structure alignment methods such as DALI, CE,
and SSM ass well as sequence alignment based on PSI-BLAST. TALI demonstrated
great success over all other methods in application to challenging proteins.
TALI was more successful in recognizing remote structural homology. TALI also
demonstrated an ability to identify structural homology between two proteins
where the structural difference was due to a rotation of internal domains by
nearly 180$^\circ$.
