By Des Higgins, Willie Taylor
This quantity covers functional vital themes within the research of protein sequences and constructions. It comprises evaluating amino acid sequences to buildings evaluating buildings to one another, looking out info on whole protein households in addition to looking with unmarried sequences, tips to use the net and the way to establish and use the SRS molecular biology database administration approach. ultimately, there are chapters on a number of series alignment and protein secondary constitution prediction. This e-book should be priceless to occasional clients of those ideas in addition to skilled pros or researchers.
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Additional info for Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (Practical Approach Series)
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.
32 COMPARISON OF PROTEIN THREE-DIMENSIONAL STRUCTURES (b) Those methods that sample the realm of possible solutions and, as a result, automatically find optimal alignments without specifying an initial starting alignment. Some of these procedures involve rigid-body comparisons and others generate a full alignment of the sequences on the basis of the structures. InFigure3, we show the extreme differences in results for the same proteins obtained with a multiple sequence alignment, a rigid-body structure comparison, and a procedure (7) that combines the comparison of properties and relationships to derive the structural matching.
E) Similarities/differences of two structures after superposing on an identical ligand or subset of residues or co-ordinate positions. 2 Comparisons In the comparison of identical proteins that have 3-D structures that differ to varying degrees, it is needed to compare the structures using a rigid-body approach one time only (Protocol 5). No iteration is necessarily required to achieve the best result, since one would typically supply all atom positions in the structure for comparison. Likewise, no pre-comparison is necessary to supply a seed set of residues for the comparison.
Bioinformatics: Sequence, Structure and Databanks: A Practical Approach (Practical Approach Series) by Des Higgins, Willie Taylor