By Des Higgins, Willie Taylor
This quantity covers functional very important issues within the research of protein sequences and constructions. It contains evaluating amino acid sequences to constructions evaluating buildings to one another, looking info on whole protein households in addition to looking with unmarried sequences, how one can use the web and the way to establish and use the SRS molecular biology database administration procedure. eventually, there are chapters on a number of series alignment and protein secondary constitution prediction. This booklet may be useful to occasional clients of those strategies in addition to skilled pros or researchers.
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Extra info for Bioinformatics: Sequence, Structure and Databanks: A Practical Approach
The simplest type of comparison of 3-D structures involves the comparison of two (or more) sets of co-ordinates for the same protein. Self-comparisons are often used to reveal: (a) Similarities/differences between independent solutions of crystal structures. (b) Similarities/differences among sets of structures, generated using distance geometry, and consistent with distance information obtained in NMR spectroscopy. (c) Similarities/differences between structures obtained using X-ray diffraction and NMR spectroscopy.
Bowie, J. , and Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253,164. 11. Taylor, W. R. and Orengo, C. A. (1989). J. Mol. , 208, 1. 12. Jones, D. T. (1998). THREADER : Protein Sequence Threading by Double Dynamic Programming. In Computational methods in molecular biology (ed. S. Salzberg, D. Searls, and S. Kasif). Elsevier, Amsterdam. 13. Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force.
The alignment: determination of equivalent pairs Methods used to find the optimal match between entire structures or between parts of structures consisting of the best matching regions of the structures. e. g. all matched positions produced by dynamic programming methods). 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.
Bioinformatics: Sequence, Structure and Databanks: A Practical Approach by Des Higgins, Willie Taylor