Editing Structural alignment (section)

{{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]].

Structural alignments can compare two sequences or [[multiple sequence alignment|multiple sequences]]. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by [[X-ray crystallography]] or [[NMR spectroscopy]]. It is possible to perform a structural alignment on structures produced by [[protein structure prediction|structure prediction]] methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality.<ref name="casp11"/> Structural alignments are especially useful in analyzing data from [[structural genomics]] and [[proteomics]] efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based [[bioinformatics]] methods.<ref name="Malmstrom" /><ref name="robetta"/><ref name="skolnick"/>

The outputs of a structural alignment are a superposition of the atomic [[coordinates|coordinate sets]] and a minimal [[root mean square]] deviation ([[Root mean square deviation (bioinformatics)|RMSD]]) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple [[protein domain]]s within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.