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 containing all pairwise distances between some subset of the atoms in each structure (such as the alpha carbons). 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 noise is also discarded. Choosing a representation to facilitate computation is critical to developing an efficient alignment mechanism.
Read more about this topic: Structural Alignment
Famous quotes containing the word structures:
“The philosopher believes that the value of his philosophy lies in its totality, in its structure: posterity discovers it in the stones with which he built and with which other structures are subsequently built that are frequently better—and so, in the fact that that structure can be demolished and yet still possess value as material.”
—Friedrich Nietzsche (1844–1900)