Different from many other tools, DeepAlign aligns two protein structures using evolutionary information and beta strand orientation in addition to geometric similarity. Therefore, DeepAlign favors the alignment of evolutionarily-related residues and also aligns beta sheets more correctly than the others. The DeepAlign alignments are also much more consistent with manual alignments than the others.
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Sci Rep. 2013;3:1448. doi: 10.1038/srep01448.
Protein structure alignment beyond spatial proximity.
Wang S, Ma J, Peng J, Xu J.