Structural Alignment

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. 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.

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.

Read more about Structural AlignmentData Produced By Structural Alignment, Types of Comparisons, Representation of Structures, Methods, Recent Developments, RNA Structural Alignment, Software

Other articles related to "structural alignment, structural, alignment, alignments":

Structural Alignment - Software
... Choosing a software tool for structural alignment can be a challenge due to the large variety of available packages that differ significantly in methodology and reliability ... A more complete list of currently available and freely distributed structural alignment software can be found in structural alignment software ... Properties of some structural alignment servers and software packages are summarized and tested with examples at Structural Alignment Tools in Proteopedia.Org ...
Computational Immunology - Immunological Database
... IEDB-3D Structural data within the Immune Epitope Database ... The initial release of the database contained allele reports, alignment tools, submission tools as well as detailed descriptions of the source cells ... gene The IPD and HPA nomenclature committee hope to expand this to provide full sequence alignments when possible ...
Structural Alignment Software - Structural Comparison and Alignment
... Guda 2004 DaliLite Distance Matrix Alignment C-Map Pair No server L ... Holm 1993 TM-align TM-score based protein structure alignment Cα Pair nil server and download Y ... Skolnick 2005 VAST Vector Alignment Search Tool SSE Pair nil server S ...
Sequence Alignment - Structural Alignment - Combinatorial Extension
... The combinatorial extension method of structural alignment generates a pairwise structural alignment by using local geometry to align short fragments of the two proteins ... features such as residue neighbor hydrophobicity, local alignments called "aligned fragment pairs" are generated and used to build a similarity matrix representing all possible structural ... the other is then traced through the matrix by extending the growing alignment one fragment at a time ...

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