We present two algorithms that use spectral methods to align protein folds. One of the algorithms is suitable for database searches, the other for difficult alignments. We present computational results for 780 pairwise alignments used to classify 40 proteins as well as results for a separate set of 36 protein alignments used for comparison to four other alignment algorithms. We also provide a mathematically rigorous development of the intrinsic geometry underlying our spectral approach.
Shibberu, Yosi and Holder, Allen, "A Spectral Approach to Protein Structure Alignment" (2010). Mathematical Sciences Technical Reports (MSTR). 27.