Focal initiation and subsequent spread along anatomically connected structures embody "structural template".
The alignment was used to build the 3D molecular model of HiGH61A, running MODELLER 9v4 (Eswar et al. 2007) and using the TtGH61E crystal-structure as structural template.
All fragments generated in this manner were threaded against the 13,391 representative structures in the structural template library and the threading score for each fragment was calculated.
In conclusion, the mapping of our results for 100 different family A GPCRs onto one structural template, the rhodopsin structure, might not be generally representative for these particular regions.
In all these packages, sequences are associated with a predicted structural template (RNA secondary structure).
We used as a structural template the X-ray structure of opsin (PDB code 3CAP [3CAP.
This program uses a combination of protein structure prediction techniques to produce potential models of secondary and tertiary structures for a given sequence, based on a structural template.
Thus, we examined the potential effect of the NA-N248D (Figure 5B) by utilizing the crystal structure of the H5N1 neuraminidase (PDB entry: 2HU4) as a structural template.
Alternatively, from the analysis of a number of structures sharing some property, it is possible to derive a structural template encoding the function-determining residues, and use that to screen the proteins of interest.
According to the score of BLAST search, the crystal structure of VIM-2, a Zn-β-lactamase from Pseudomonas aeruginosa [40], was selected as a structural template to perform homology modeling to develop the 3D structure of NDM-1.
Briefly, modeling of human REP-1 was based on the 2.2 Å crystal structure of rat Rep-1 protein (PDB file: 1vg0) as the structural template (Abola et al. 1987).
