Structural Alignment - Representation of Structures

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 words representation of and/or structures:

    All great amusements are dangerous to the Christian life; but among all those which the world has invented there is none more to be feared than the theater. It is a representation of the passions so natural and so delicate that it excites them and gives birth to them in our hearts, and, above all, to that of love.
    Blaise Pascal (1623–1662)

    If there are people who feel that God wants them to change the structures of society, that is something between them and their God. We must serve him in whatever way we are called. I am called to help the individual; to love each poor person. Not to deal with institutions. I am in no position to judge.
    Mother Teresa (b. 1910)