Editing Structural alignment (section)

==Representation of structures==
Protein structures have to be represented in some coordinate-independent space to make them comparable. This is typically achieved by constructing a sequence-to-sequence matrix or series of matrices that encompass comparative metrics: rather than absolute distances relative to a fixed coordinate space. An intuitive representation is the [[distance matrix]], which is a two-dimensional [[matrix (mathematics)|matrix]] containing all pairwise distances between some subset of the atoms in each structure (such as the [[alpha carbon]]s). The matrix increases in dimensionality as the number of structures to be simultaneously aligned increases. Reducing the protein to a coarse metric such as [[secondary structure]] elements (SSEs) or structural fragments can also produce sensible alignments, despite the loss of information from discarding distances, as [[signal noise|noise]] is also discarded.<ref name="Mount">Mount DM. (2004). ''Bioinformatics: Sequence and Genome Analysis'' 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY {{ISBN|0879697121}}</ref> Choosing a representation to facilitate computation is critical to developing an efficient alignment mechanism.