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{{for|structural alignment in cognitive science|Analogy#Structural alignment}}
{{short description|Aligning molecular sequences using sequence and structural information}}
<div style="background: var(--background-color-transparent); color: inherit">[[Image:Alignment of thioredoxins2.png|thumb|300px|right|Structural alignment of [[thioredoxin]]s from humans and the fly [[Drosophila melanogaster]]. The proteins are shown as ribbons, with the human protein in red, and the fly protein in yellow. Generated from PDB [http://www.rcsb.org/pdb/explore.do?structureId=3TRX 3TRX] and [http://www.rcsb.org/pdb/explore.do?structureId=1XWC 1XWC].]]</div>
'''Structural alignment''' attempts to establish [[Sequence homology|homology]] between two or more [[polymer]] structures based on their shape and three-dimensional [[tertiary structure|conformation]]. This process is usually applied to [[protein]] [[tertiary structure]]s but can also be used for large [[RNA]] molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no ''a priori'' knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard [[sequence alignment]] techniques. Structural alignment can therefore be used to imply [[evolution]]ary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of [[convergent evolution]] by which multiple unrelated [[amino acid]] sequences converge on a common [[tertiary structure]].
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