Des Higgins, Willie Taylor's Bioinformatics: Sequence, Structure and Databanks: A PDF

By Des Higgins, Willie Taylor

This quantity covers sensible very important issues within the research of protein sequences and constructions. It contains evaluating amino acid sequences to buildings evaluating constructions to one another, looking out details on complete protein households in addition to looking with unmarried sequences, the right way to use the net and the way to establish and use the SRS molecular biology database administration method. ultimately, there are chapters on a number of series alignment and protein secondary constitution prediction. This e-book could be worthwhile to occasional clients of those innovations in addition to skilled pros or researchers.

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Extra resources for Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (Practical Approach Series)

Example text

In rigid-body superposition methods, a distance cut-off between equivalent atoms is frequently used. In methods were other structural features are considered, alt aligned positions might be considered to be topologically equivalent between two structures, or they may be assigned according to the degree of positional similarity of features used to make the comparison. 1 Definitions of structural equivalence: the alignment In determining a set of equivalent atom sets, distance criteria are often used.

Dynamic programming methods (6) 1 2 3 Construct a matrix with dimensions equivalent to the lengths of the structures to be compared. Each cell in the matrix corresponds to a residue in the first protein matching a residue in the second protein. The matrix accommodates all possible alignments. Cells are filled in with a score relating each two matched positions. These scores may be distances between Ca-atoms, for example, distance scores based on other 27 MARK S. JOHNSON AND JUKKA V. LEHTONEN 4 features of the protein (see Table t), or similarity scores derived from distances.

Homologous proteins are descended from a common ancestral protein, but have subsequently duplicated, evolved along separate paths, and thus changed over time. The independent evolution of related proteins with the same function, orihologous proteins, which are found in different species, and the paralogaus proteins, which have evolved different functions, all retain information on the original relationship. The amino acid sequences change over time reflecting the mutations, insertions and deletions that occur in their genes during evolution, and for many proteins the sequences themselves are so similar that common ancestry is apparent.

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