SANA is an algorithm for the alignment of two proteins. Specifically, core regions in two protein structures are first aligned by identifying connected components in a network of neighboring, geometrically compatible aligned fragment pairs (AFPs). The initial alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential alignments.
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Lin Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen.
SANA: an algorithm for sequential and non-sequential protein structure alignment.
Amino Acids. 2010 Jul;39(2):417-25. Epub 2010 Feb 2.