Miao Xijiang, Waddell Peter J, Valafar Homayoun
Department of Computer Science and Engineering, University of South Carolina, 301 Main Street, Columbia, SC 29208, USA.
J Bioinform Comput Biol. 2008 Feb;6(1):163-81. doi: 10.1142/s0219720008003370.
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.
http://redcat.cse.sc.edu/index.php/
TALI/.
扭转角比对（TALI）是一种用于局部结构基序比对的新方法，它基于主链扭转角（φ，ψ），而非更为传统的原子距离矩阵。以扭转角序列的形式表示蛋白质结构能够轻松整合序列和结构信息，并采用序列比对中的成熟技术来提高性能和比对质量。我们表明，TALI能够匹配局部结构基序并识别全局结构相似性。还将TALI与其他结构比对方法（如DALI、CE和SSM）以及基于PSI-BLAST的序列比对进行了比较；在应用于具有挑战性的结构比对时，TALI与这些其他方法同样成功或更为成功。II类氨酰-tRNA合成酶进化树的推断显示了TALI在估计蛋白质结构进化以及识别同源结构间的结构差异方面的潜力。
http://redcat.cse.sc.edu/index.php/
TALI/
