DT of protein structure has also been used as a generic computational tool to analyze various aspects of protein structure such as secondary structure assignment [ 20], structural classification [ 21, 22], and analysis of small-world nature of protein contacts [ 23].
Secondary structure assignment was possible for the assigned residues as shown in Figure 5A where chemical shift indices for the Cα carbons in GIG47 and its homolog 1TOG [ 21] are displayed.
Also, PPII helices are not assigned by the widely used Secondary Structure Assignment Method (SSAM): DSSP [21].
The secondary structure assignment of the sequences was carried out using STRuctural Alignments of Proteins (STRAP) (Gille and Frommel 2001).
Two STRUCTURE assignment and ancestry analyses were performed, one with prior population information assigned and the second with putative hybrid population identity set as unknown to examine alternate parentage contributions.
Therefore, any information derived from each technique used has to be reported to provide a comprehensive and meaningful overview on the structure assignment, since each technique will provide additional information consolidating the structural assignment or illustrating exclusion of alternative structures.
CRFs can provide greater context-sensitivity (as in POS tagging and other types of sequence labeling); though they are not directly suited to structure assignment to text, they can be used to learn shallow parsers, which assign phrase types only to nonrecursive phrases (core NPs, PPs, VPs, etc).
Since structural superimposition studies showed mild deviation (figure 1), secondary structural analysis were performed using STRIDE 25 a software tool for secondary structure assignment from atomic resolution protein structures, that, however, did not show any significant change between the wild and the variant.
Two more features of NMR spectra are important aids to structure assignment.
For a polyatomic molecule, which is characterized by three moments of inertia, the microwave spectrum of a single molecular species provides insufficient information for making a complete structure assignment and calculating the magnitude of all bond angles and interatomic distances in the molecule.
We introduce a new method for protein secondary structure assignment based solely on Cα coordinates.
