title: TALI: local alignment of protein structures using backbone torsion angles.
abstract: Torsion angle alignment (TALI) is a novel approach to local structural motif alignment, based on backbone torsion angles (phi, psi) rather than the more traditional atomic distance matrices. Representation of a protein structure in the form of a sequence of torsion angles enables easy integration of sequence and structural information, and adopts mature techniques in sequence alignment to improve performance and alignment quality. We show that TALI is able to match local structural motifs as well as identify global structural similarity. TALI is also compared to other structure alignment methods such as DALI, CE, and SSM, as well as sequence alignment based on PSI-BLAST; TALI is shown to be equally successful as, or more successful than, these other methods when applied to challenging structural alignments. The inference of the evolutionary tree of class II aminoacyl-tRNA synthetase shows the potential for TALI in estimating protein structural evolution and in identifying structural divergence among homologous structures.
  
  
  BACKGROUND
  http://redcat.cse.sc.edu/index.php/
  
  
  METHODS
  TALI/.
authors.affiliation: Department of Computer Science and Engineering, University of South Carolina, 301 Main Street, Columbia, SC 29208, USA. miaox@cse.sc.edu
authors.forename: Xijiang
authors.initials: X
authors.lastname: Miao
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Waddell
authors.forename: Homayoun
authors.initials: H
authors.lastname: Valafar
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins