For structural alignment in cognitive science, see Analogy § Structural alignment.
Aligning molecular sequences using sequence and structural information
Structural alignment of thioredoxins 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 3TRX and 1XWC.
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures 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 evolutionary 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 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 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.[1] 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.[2][3][4]
The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (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 domains 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.
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and 25 Related for: Structural alignment information
Structuralalignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This...
functional or structural role. Very short or very similar sequences can be aligned by hand. However, most interesting problems require the alignment of lengthy...
alignment and multiple sequence alignment. See structuralalignment software for structuralalignment of proteins. *Sequence type: protein or nucleotide...
external landmarks Stone alignment, a linear arrangement of upright, parallel megalithic standing stones Structuralalignment, establishing similarities...
inferred (see homology). Usually this common ancestry is inferred from structuralalignment and mechanistic similarity, even if no sequence similarity is evident...
still is a challenge due to the high computational cost of structuralalignments. Structural signatures based on graph distance patterns among atom pairs...
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or...
is necessary because algorithms for both multiple sequence alignment and structuralalignment use heuristics which do not always perform perfectly. The...
structure prediction software Category:Molecular dynamics software Structuralalignment software Other Compression of genomic sequencing data Bioinformatics...
sequence conservation alone. The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures...
structure alignment program (SSAP) in chemistry, physics, and biology is a method that uses double dynamic programming to produce a structuralalignment based...
defined in IEEE 802.2 Sequential structure alignment program, double dynamic programming method in Structuralalignment Statements of Standard Accounting Practice...
Notredame C (2006). "The iRMSD: a local measure of sequence alignment accuracy using structural information" (PDF). Bioinformatics. 22 (14): e35–39. doi:10...
Duckett, Catherine N.; Kjer, Karl M.; Gillespie, Joseph J. (2009). "Structuralalignment of 18S and 28S rDNA sequences provides insights into phylogeny of...
Iyengar Yoga is a form of yoga as exercise with a focus on the structuralalignment of the physical body through the practice of asanas. It differs from...
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their...
voltage, or electrical pressure. Given the similarity in structure, or structuralalignment, between these domains, structure mapping theory would predict that...
area; Alignment Patterns and Assistant Alignment Patterns – is started from Version 4 and helps with the decoding of distorted code; Structural Information...
enzymatic activity necessary for a sequential set of reactions. Structuralalignment is an important tool for determining domains.[citation needed] Several...
certain degree. The combination of rigid and flexible chains induce structuralalignment and fluidity between liquid crystal moieties. In doing so, varying...
the "second brain" in the lower abdomen, improvement of health and structuralalignment. Chinese alchemy Dantian Huangdi Neijing Internal alchemy Jing Lee-style...
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