3DCOMB is a software which can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments.
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Bioinformatics. 2011 Sep 15;27(18):2537-45. doi: 10.1093/bioinformatics/btr432.
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling.
Wang S, Peng J, Xu J.