Editing Structural alignment (section)

===Combinatorial extension===
The combinatorial extension (CE) method is similar to DALI in that it too breaks each structure in the query set into a series of fragments that it then attempts to reassemble into a complete alignment. A series of pairwise combinations of fragments called aligned fragment pairs, or AFPs, are used to define a similarity matrix through which an optimal path is generated to identify the final alignment. Only AFPs that meet given criteria for local similarity are included in the matrix as a means of reducing the necessary search space and thereby increasing efficiency.<ref name="shindyalov">{{cite journal
| pmid=9796821
| first = I.N.
| last = Shindyalov
|author2=Bourne P.E.
 | year = 1998
| journal = Protein Engineering
| volume=11
| title=Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
| issue = 9
| pages = 739–747
| doi=10.1093/protein/11.9.739
| doi-access = free
}}</ref> A number of similarity metrics are possible; the original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties such as secondary structure, solvent exposure, hydrogen-bonding patterns, and [[dihedral angle]]s.<ref name="shindyalov" />

An alignment path is calculated as the optimal path through the similarity matrix by linearly progressing through the sequences and extending the alignment with the next possible high-scoring AFP pair. The initial AFP pair that nucleates the alignment can occur at any point in the sequence matrix. Extensions then proceed with the next AFP that meets given distance criteria restricting the alignment to low gap sizes. The size of each AFP and the maximum gap size are required input parameters but are usually set to empirically determined values of 8 and 30 respectively.<ref name="shindyalov" /> Like DALI and SSAP, CE has been used to construct an all-to-all fold classification [http://cl.sdsc.edu/ database] {{Webarchive|url=https://web.archive.org/web/19981203071023/http://cl.sdsc.edu/ |date=1998-12-03 }} from the known protein structures in the PDB.

The [[Protein Data Bank|RCSB PDB]] has recently released an updated version of CE, Mammoth, and FATCAT as part of the [http://www.rcsb.org/pdb/workbench/workbench.do RCSB PDB Protein Comparison Tool]. It provides a new variation of CE that can detect [[Circular Permutation Proteins|circular permutations]] in protein structures.<ref name="prlic"/>