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As mentioned before, the templates are 'hardcoded' to the implementation patterns, meaning the structures of the template must be mapped to the programming language-specific structures.
Utilization of various additives without thorough analysis of secondary structures of the template as well as primers and subsequent PCR cycle conditions, generally leads to inadequate yields and/or truncated products.
The 2D structures of the template molecule and 61 derivatives were drawn using Chemsketch [ 40] which were then aligned with the most active molecule (reference molecule).
Primer sequences are listed in Additional file 2. In addition, to enhance primer efficiency, primer-binding sites were chosen such that secondary structures of the template were avoided.
To accomplish a natural looking auricle, the key structures of the template should always include the complete helix, the antihelix (anterior and posterior crus) with the triangular fossa, the tragus, and the antitragus [ 23].
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The deletion of one or two residues at the boundaries of the insertions/deletions was dependent on the structures of the templates.
However, such changes do not affect the secondary structure of AgAChE, because these regions do not adopt the helical conformation in the template structures (see secondary structures of the templates in Figure S1 of Supporting Information).
These scores indicate that the overall fold is correct; poor scores would have suggested that there were significant errors in the modeled structure of the prodomain, and in that case the model would not have resembled the structures of the templates on which it was based.
Sections of the sequence that show strong similarity may be used to construct a 3D model based upon the structures of the templates.
The alignment was corrected manually by adjusting the positions of insertions and deletions that were incompatible with the secondary-structure elements observed in the 3-dimensional (3D) structures of the templates.
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