Editing Sequence alignment (section)

===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 being analyzed and then assembles these fragments into a larger alignment.<ref name=shindyalov>{{cite journal | journal=Protein Eng | volume=11 | pages=739–47 | year=1998  |author1=Shindyalov IN |author2=Bourne PE. | title=Protein structure alignment by incremental combinatorial extension (CE) of the optimal path | pmid=9796821 | doi = 10.1093/protein/11.9.739 | issue=9 | doi-access=free }}</ref> Based on measures such as rigid-body [[Root mean square deviation (bioinformatics)|root mean square distance]], residue distances, local secondary structure, and surrounding environmental features such as residue neighbor [[hydrophobic]]ity, local alignments called "aligned fragment pairs" are generated and used to build a similarity matrix representing all possible structural alignments within predefined cutoff criteria. A path from one protein structure state to the other is then traced through the matrix by extending the growing alignment one fragment at a time. The optimal such path defines the combinatorial-extension alignment. A web-based server implementing the method and providing a database of pairwise alignments of structures in the Protein Data Bank is located at the [https://web.archive.org/web/19981203071023/http://cl.sdsc.edu/ Combinatorial Extension] website.