The presented results show that predicted structures can be successfully used for virtual ligand screening, and by exploiting the ideas of LHM, diverse novel small molecule binders can be identified even when the closest template is distantly related to the protein target of interest.
Subsequently, we have shown that this approach can be used to identify functional sites in remote (e.g.10 20% sequence identity) homology models, even when the structural template used to build the model is itself un-annotated (Standley et al., 2008a).
Another important aspect of the ribosomal DNA is that it is a multi-copy segment such that it amplifies readily even when the initial amount of template DNA is moderate, as is often the case with environmental samples.
Unfortunately, none of the polymerases we studied showed significant activity with gNTP substrates and GNA templates, even when the primer and primer-binding region were composed of DNA.
On the other hand, we found that even when the predicted TM-distance is >0.5, a better template is usually present among the top 10 50 RF-ranked templates.
Again, the second verse loses its way slightly, Adams refusing to deviate from his set template for the song even when the original calls for it.
This increase was visible even when the target was only 1% relative to MYH7 template; the other 99% were complementary to the target RNA being analyzed.
Even when the current nucleotide in the flow should be incorporated by all template clones, clones might not, by chance, incorporate it (for example, if no dNTP molecule is found in the physical vicinity of the template).
Most people think of the cartoon smiley face, with its discrete eyes, nose and mouth, as the quintessential face template, but Dr. Sinha's computer can identify faces even when the pictures are of low resolution.
